From 0513aabb615ccc92ac8c9b0866c66afda5ac5137 Mon Sep 17 00:00:00 2001
From: Pavel Dimens <pdimens@live.com>
Date: Wed, 2 Feb 2022 15:28:39 -0500
Subject: [PATCH 01/46] update LM3 modules (needs testing)

---
 .../LepMap3/DataParser$PosteriorParser.class  | Bin 2525 -> 2529 bytes
 software/LepMap3/DataParser$VCFParser.class   | Bin 9452 -> 9451 bytes
 software/LepMap3/DataParser.class             | Bin 11979 -> 11984 bytes
 software/LepMap3/Error.class                  | Bin 23325 -> 24135 bytes
 software/LepMap3/Family2.class                | Bin 24561 -> 24812 bytes
 software/LepMap3/Filtering2.class             | Bin 15798 -> 15792 bytes
 software/LepMap3/GammaFunction.class          | Bin 2336 -> 2335 bytes
 software/LepMap3/IBD.class                    | Bin 16443 -> 16442 bytes
 software/LepMap3/Input.class                  | Bin 5202 -> 5201 bytes
 software/LepMap3/JoinSingles2All.class        | Bin 3476 -> 3511 bytes
 software/LepMap3/LMPlot.class                 | Bin 10558 -> 10593 bytes
 .../LepMap3/Misc$ArrayIndexComparator.class   | Bin 1800 -> 1800 bytes
 software/LepMap3/Misc$KthSmallest.class       | Bin 946 -> 946 bytes
 software/LepMap3/Misc.class                   | Bin 8962 -> 9630 bytes
 software/LepMap3/Order.class                  | Bin 17692 -> 18116 bytes
 .../LepMap3/OrderFinder$MergeRunner.class     | Bin 0 -> 2112 bytes
 .../LepMap3/OrderFinder$PhysicalFamily.class  | Bin 3047 -> 3437 bytes
 .../LepMap3/OrderFinder$PolishRunner.class    | Bin 0 -> 2035 bytes
 ...nder$SingleFamily$RecombinationScale.class | Bin 845 -> 845 bytes
 ...der$SingleFamily$RecombinationScale1.class | Bin 3848 -> 3852 bytes
 ...der$SingleFamily$RecombinationScale2.class | Bin 4280 -> 4284 bytes
 .../LepMap3/OrderFinder$SingleFamily.class    | Bin 21905 -> 23919 bytes
 software/LepMap3/OrderFinder.class            | Bin 31624 -> 39404 bytes
 software/LepMap3/OrderMarkers2.class          | Bin 6060 -> 6756 bytes
 software/LepMap3/ParameterParser.class        | Bin 7275 -> 7078 bytes
 software/LepMap3/ParentCall2.class            | Bin 25527 -> 25524 bytes
 software/LepMap3/Pileup2Likelihoods.class     | Bin 13976 -> 14053 bytes
 software/LepMap3/Pileup2Likelihoods2.class    | Bin 0 -> 15913 bytes
 software/LepMap3/QTL.class                    | Bin 10536 -> 10535 bytes
 .../LepMap3/Separate2$JoinSinglesThread.class | Bin 3329 -> 3329 bytes
 ...parate2$JoinSinglesThreadMaxDistance.class | Bin 3287 -> 3283 bytes
 .../Separate2$SeparateIdenticalThread.class   | Bin 3548 -> 3547 bytes
 .../LepMap3/Separate2$SeparateThread.class    | Bin 3289 -> 3416 bytes
 software/LepMap3/Separate2.class              | Bin 30521 -> 30747 bytes
 software/LepMap3/SeparateChromosomes2.class   | Bin 4422 -> 4506 bytes
 software/LepMap3/ShortPath.class              | Bin 10253 -> 10252 bytes
 software/LepMap3/UnionFind.class              | Bin 1705 -> 1705 bytes
 software/LepMap3/scripts/LICENSE              | 674 ++++++++++++++++++
 software/LepMap3/scripts/map2genotypes.awk    |   4 +-
 software/LepMap3/scripts/somePaternal.awk     |  26 +
 40 files changed, 702 insertions(+), 2 deletions(-)
 create mode 100644 software/LepMap3/OrderFinder$MergeRunner.class
 create mode 100644 software/LepMap3/OrderFinder$PolishRunner.class
 create mode 100644 software/LepMap3/Pileup2Likelihoods2.class
 create mode 100644 software/LepMap3/scripts/LICENSE
 create mode 100644 software/LepMap3/scripts/somePaternal.awk

diff --git a/software/LepMap3/DataParser$PosteriorParser.class b/software/LepMap3/DataParser$PosteriorParser.class
index af24204c70821bca596eb5b89da0389fe65467b8..4970103b0f5e9702decb3a09798fb36834420a2c 100644
GIT binary patch
delta 38
ucmcaB{7`tqYBol%$!pkDg@qVc7#Nrw8914o82Ff+8HAY}H$Pze%LD+xI|%gv

delta 34
qcmaDTd{=nGYBol<$!pkD`S}=_85o!x8914o82Ff+H$P$f%LD+V?Fg0t

diff --git a/software/LepMap3/DataParser$VCFParser.class b/software/LepMap3/DataParser$VCFParser.class
index a9c9a5b30a698767c61e1c2ddaca84a8f89284fa..d65d91a15a59d4a9de13aed4f5b31322d5c7aa21 100644
GIT binary patch
delta 29
lcmaFk`Py@Xs4U~=&0?~LS()E6=xn~Dbc>OZZ}JWm69BVV3km=L

delta 30
mcmaFu`NngDs4U}_&0?~LS(!gD=x)BFbc>ORn`!cP6%zow>kAA3

diff --git a/software/LepMap3/DataParser.class b/software/LepMap3/DataParser.class
index 0dfdb7735ac02d226f72c60b16c0fdf947d957f9..35d5dd62ed126b9db188adde8b32c74cfbccb212 100644
GIT binary patch
delta 735
zcmXAmSxD7U5XQgx&h>v?u5@w9de9a%O|cR;kX{6-EbXa8FcV2A(!?yY61hDI(L)cn
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kR0$&HkYUFzJ5Eb*s0Sh9n1LhMF^jZiVIFL5ZI26-|9yh4_y7O^

delta 747
zcmX9*TSyd85IuA5zFc?Bd>{mhCF`p~DeFTjXwhDv2tg?-A%^%-P?}nPw0#ux5eY33
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nYP7NoiT~iWqsWdriH@B{jJSdbVYF)sYoi%Ajdg*prIGR<Y8R{8

diff --git a/software/LepMap3/Error.class b/software/LepMap3/Error.class
index 4a3c416ab77accdc66fca926d8b37fa4b20c42ce..94ab6f18e195b5763b6c6c161533292b1d1cf961 100644
GIT binary patch
delta 2118
zcmaKt3vg3K6o&UtLmOxmX!E#4q*ocC6iAa4NM9+G6zId+jDkwBK%k+`kR~Nbfm)dk
zqkzcM9-%6N0!l#;glG%aBA|j+0jnqiK2Y&pQ5=SG7)RY*Ky;k(&fNXKbMEfRIp^-(
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delta 1631
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diff --git a/software/LepMap3/Family2.class b/software/LepMap3/Family2.class
index 9517aa3a80b0db1b262cf026b3288740cf505aac..f7a7dadef87bd7fae25c81e147deb9e12c208926 100644
GIT binary patch
delta 8836
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TY7XV8O6~R1M0{@qu?YGv>{lpL

diff --git a/software/LepMap3/Filtering2.class b/software/LepMap3/Filtering2.class
index aaa172b9874890be354fd42ae19629265394be2e..c2aabb4c3660fee0866c4c2a253c860c59996578 100644
GIT binary patch
delta 54
zcmdm1y`g%8v>s#eW*NO$W@b?a;mI|IZ<+rysBA7UYG!2Y-~7c`i-kFbL1eO`g)tK=
K>*ffHI934i01#pT

delta 60
zcmdl`y{&qKv>s#mW*NO$W@bqSk;yfNZ`uDaC^G+NVA`Bx)Xc~@aq|abEf(f92C>Pq
P7RD@0K(IN;B90XRR8$dR

diff --git a/software/LepMap3/GammaFunction.class b/software/LepMap3/GammaFunction.class
index dc5b8e1bd148bb30e0b2376eb665d86975144521..bd257e521dde3b573aa318d94fc33c80337fb19e 100644
GIT binary patch
delta 30
mcmZ1=G+$^#2rJ`(&7rKS%*?YGxF*+fL@@tnu$+98!yN#UlL>GD

delta 31
ncmbO)v_NP>2rJ{k&7rKS%*?YHxF^?gM6j6sXJDFqgToyFndS*{

diff --git a/software/LepMap3/IBD.class b/software/LepMap3/IBD.class
index c7cfb65d9f4e03ab6eea7781c9c611b68e494de5..f64f7963830832aa1a4ae8059dd70cfb7ceb49b5 100644
GIT binary patch
delta 30
mcmdnpz__b{al;vF#-*FjT1PW8doplO*0#4`<d~dle+>Y$%L<SH

delta 31
ncmdnhz_`1Cal;vF#$}t&T1PW8dol1#*0#4`Vr80~Vt)+)ymktb

diff --git a/software/LepMap3/Input.class b/software/LepMap3/Input.class
index 0c03486797cd81b2e25efdd761d0c9d2613b7838..198306c94ecc976ef51c6d1d415fe4635abb6d7a 100644
GIT binary patch
delta 32
ocmcblaZzK#PhQ63n}6{xU}RQf;G8^{Uy4PUok4E%9{y=80MI-NyZ`_I

delta 33
pcmcbpaY<vtPhQ3on}6{xU}RQj;F>&_Uy4<Mok5Oi^KSlWECAUK3cdgU

diff --git a/software/LepMap3/JoinSingles2All.class b/software/LepMap3/JoinSingles2All.class
index eea92b9d24c556e04c32f71cb5cc67c84dcee3b0..773553b94598e07906e5044f294504979696ee00 100644
GIT binary patch
delta 549
zcmZXQOKTHh6o#MkO=XgqOd3Z;n<65jRA@_^Ml0S{fg+|WN!7TDZ77iv3+Y1Qq8opJ
zGA_EQ2>k;VVJuZ^)p~2aR_hf7cY^;wtnnlkH{HGGyytnp^PQ`$w_2UWKeKZ{4_~I8
zCi|3=>Q48j5A^I$_c~O$9pesLgm|Sm)?c`gDOJV_<-uZvIl=1c?5fYq$GFb}!991r
zR6bEE504Zp!p62UnM^j@*IyV-9m?l}to^lV!Dcz=h*YCLaY%r<cJoGLz-(>z&-ybV
zBQs2e%(g^Z+;)G!zZ-aNM<V3jwC-mq0q@xt<lLq4(`JagnWTWL-4MT?#X}afikr(k
z;xWQDj`D=37>3M2p0TLvhlJ!<!V-~5o~zm*Nx8%eRkrMsi@f9&Q8^|#UMuU!Nm7jz
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z6bW~gW}Cf|uCWu#=7SbCN1(=cBL8d4Qm-oTJ4kw)hS#Rnx;7t0t<5!}IO`B~YI>w~
bMxD|;w%bf}ud=7{@Wd}{z1}BX&hYs!$0vH-

delta 479
zcmZXQK}%F|6vcn{J>~!Ay_uAU3w0<7F$z?i@!1HeD`5}~g2-T68I57e6eKQY;|Fjh
zuf@0!1V6zbOrm9(X*E`6Wwj}&m7hVh={mJ*b2;bUbI$+pe;j`lcgw%mHh^xv72O&$
zV0U$PIjjqAG7+SL-tNmm$|cX!C>uNzynFX2a@Qwvcc-!s1^?o$!NHM{^wqHk$t#)6
zP&jVB*K8X0!nBi*{KBIitc8`bGisS8uiYQ@SHqOo5pVZz`)ehpR#`6bq^JdKT%8{Y
z!f9`JHe(eSQ#+LKPa}BFrm{2E952{HXk>twY-4f9>S2dhiVmg74PIl5NP#zsYNc6b
zDJwG4Dl_czmWT|=HQuS$m7651DV}6$=Dj9IWs$Z?hS|fD13msl^WyM9Em2vbrD}=E
z57tSuPt59MQmb!iy*@3L)m<H*wC*zX-U)SvOA=H#k8Sv@#Ly2Fe&Q$(J7TTp{%vhr
p6?rinh(JSy2=1vQ7i&!XFM(su8VZRME>u$sM;QH@FZ!~@*FS&ZZJhuB

diff --git a/software/LepMap3/LMPlot.class b/software/LepMap3/LMPlot.class
index 0702bbfe06343ac2d90227462ea2d0881bc1f2eb..d91ed8ca295b7b958c64c60945de603050c12cea 100644
GIT binary patch
delta 46
zcmdlN^e|{cnl$73&FRuxIhlVlm`#>f4Pw-rT&x<z`k%p)L1=QLnhFyG<K{D}Ma%$+
C<__op

delta 42
ycmaDDv@d8wnlxk2=5*<;oXpo4EGEmV1~F+fO)gRmV*kTn#?H{;wE4Yi5i<ZsgbpA8

diff --git a/software/LepMap3/Misc$ArrayIndexComparator.class b/software/LepMap3/Misc$ArrayIndexComparator.class
index b651069bad3574f115b3c6b2d0178f8c70c49786..87a8c031fc3cdaa7adf2115ff57f54090ce61b89 100644
GIT binary patch
delta 63
zcmeC+>)_jPn}u^T0}I1e22O@;lb^8UbM650b}<Mu?4BIM+90?eD1Lx}kKqu5D3DfU
QI5PPyYb)c)$;E6_0aSt$GXMYp

delta 63
zcmeC+>)_jPn}u^e0}I1K22O@Wlb^8Ub1nh$mN5u3ET0_1+90?ZD87b)k6|5yD3DfU
Q*f9AmYb)c{$;E6_0XPy8LjV8(

diff --git a/software/LepMap3/Misc$KthSmallest.class b/software/LepMap3/Misc$KthSmallest.class
index 7779ff5a0701825fc2a71e1e6b8d8d38cd2fbd0b..300a279162f76297af93465d5d7c1d166c862205 100644
GIT binary patch
delta 114
zcmdnQzKMOq0!A)Ieg+msK?Y7np~<TlLs>-_co{_}voPKEm0)0Flw=TLlwuHPlwpu!
zlx9$8lx5Ijlw;5Z(pHS}433Nn3|@?i3=xb<42g`&3@MB%4Cz4id5r1|Rg4-8t&Exs
Q6B)G_W-@9|)?sb~0H#S0E&u=k

delta 114
zcmWN|Jq`g;007|`_Qzt8ST=D1iEsg(R-%+>B@&$j=;`HEI<-pnI*ua5R?~b_rB(WR
z*ycmTmyBO{x{V>%5H;SLh{Tw}gwhrhQ>JFj>SIxNX@`|v*5>T&vA55`0ms^(9CEhc
O;)t7L?v`QRy#4`eVi7k0

diff --git a/software/LepMap3/Misc.class b/software/LepMap3/Misc.class
index 0e6c4a0a0dcb59efd4de1b3b08ea91f88dd286a5..165162c16dd00390c6db21a01be5ced8ea0c83c8 100644
GIT binary patch
literal 9630
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diff --git a/software/LepMap3/Order.class b/software/LepMap3/Order.class
index d8bc83a28499b23448476abee5f6944402ecd267..f3a136b7564063592138682c4743b1079ccea089 100644
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literal 0
HcmV?d00001

diff --git a/software/LepMap3/OrderFinder$SingleFamily$RecombinationScale.class b/software/LepMap3/OrderFinder$SingleFamily$RecombinationScale.class
index 939ca88acda8ad4c7bffcc51081d348376ba2d1e..31f95a2f89249433af15da233a3d0ab4e94f399d 100644
GIT binary patch
delta 19
ZcmX@hc9w0!5hlj&$w!%Dfuu6C7647c2G0Nh

delta 19
ZcmX@hc9w0!5hg~@$w!%Dfuu6C763`221@_{

diff --git a/software/LepMap3/OrderFinder$SingleFamily$RecombinationScale1.class b/software/LepMap3/OrderFinder$SingleFamily$RecombinationScale1.class
index 7e200afcff5c3ceea1ff15f93d776598bad04ad7..45cbf52736031f19c5b4a298a1489f70f3572ca3 100644
GIT binary patch
delta 413
zcmWO2O-NK>0EOZA8_(4-Q&ezK3x$XVA_~M51x134u!I2-glunHDFPwUm5ad9i=n8P
zRF?Lmc-1UyMlD1u!G(#2e`PK-6-!Jq!M^o5a2`%=>iyK-u+L<<5ns?`xJgj~bJ5F=
ziuajJ?~2o6OqIJDT@W}!EGR^r>Pb`sDRMcfM$+_vvufgkn#oYeyB6a&*IR9+jXbq;
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S@pI_Jx=zBh3AwWg>Hh&?y?12*

delta 409
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Lqaj=PR+0G+Mmc3I

diff --git a/software/LepMap3/OrderFinder$SingleFamily$RecombinationScale2.class b/software/LepMap3/OrderFinder$SingleFamily$RecombinationScale2.class
index 36c807e947cee0a5ac70a07f665034393bd58a50..33c39374435779f8c7e079655c3a4109a1250884 100644
GIT binary patch
delta 507
zcmWNNVQ9>89L7K2J5RIDZP&ChjJq{vhuv+vZB}?88*Mf_8@5a{LsAHhHcaTo9JBc^
zZCJ7wqP?I_c%c;KjgmJCue?}!p`?^oYJM-DdY-4x^Sp|@jy#+7&8s!aycS#P`TbRv
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delta 503
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zh?EPhq^ZAfp%mq2tjYTni?K0gtma0||MIEN^XYjIyC1tf8n8OYvP`>MlnDkCt~S#U
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f)h?#An}16Aw|iZQx?GvMGiUN=12&L3TTuHST~%_C

diff --git a/software/LepMap3/OrderFinder$SingleFamily.class b/software/LepMap3/OrderFinder$SingleFamily.class
index 5344feaae35ca22dcd1091e29ae3c95330a92334..e79be2a7ce23cfb4b510315d2b8b72425ecdc506 100644
GIT binary patch
literal 23919
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diff --git a/software/LepMap3/OrderFinder.class b/software/LepMap3/OrderFinder.class
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diff --git a/software/LepMap3/OrderMarkers2.class b/software/LepMap3/OrderMarkers2.class
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delta 3315
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diff --git a/software/LepMap3/ParameterParser.class b/software/LepMap3/ParameterParser.class
index 8924c5c525ea2ccfb2dfa883e00d9b5b10365b4e..1f8dc92f8ff7b19ccb934480e3e775021a68b393 100644
GIT binary patch
delta 1868
zcmaJ>32YQq82;Yw?9S}$Y>#cX>}<DXdq8N*rjQ~?8wEAk6cLcB*rbWs(han3cVSsD
zB5@HB4<s0$h5$yu2n`;QBbgRTIkc#>DtMqAUVs-O3Wx_+*MDZ~7PK*$%)Iyg-~0am
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zygSek3W{iF$ZihI50uY~HHFG=i-bbK8L_5FSVl2+DCodWexI$xx=TSb*70X-7p*-C
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c#`WY*?|5}EnGeV~%Y5|1qTduN&<U*YZ>5peEdT%j

delta 1950
zcmZux3v5$W82<kD-rn~1uB_d<^|CSw+e9{(1tDNIh*1+3&=7DYWWGDr;7Hl#EGVcH
z6!1X|goEOEC{sg&j|d~)0aFAYpi{&bii$53MG-+klrgCPxrHt0lHSvEzW=-5|K0!m
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zZMu_E<7s%DqqP((xlDIPDQscXR7qVzSe4!z)LK!&d0a9<3dPRRY6`g~dkv~=a=T<N
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z^Lle$6l9NC7KJPt$ksE9LA{H?7RkjXyNl!%a5)SfMNL7aIfVBFd}SV|p?s0@%}zy<
HM#cXE=qt;c

diff --git a/software/LepMap3/ParentCall2.class b/software/LepMap3/ParentCall2.class
index 0bb8a36c10107f988b78b098e5f89dcc1019c613..cd7f580814ba3cc6bc0e88ceff1bf0b80ff223bb 100644
GIT binary patch
delta 77
zcmV-T0J8tL#{sm*0kFh10X(zCHH!-fumCpy0JQ)hlhH#;lTShkv#UW50Rn0Pv%Nyh
j0R~wA02cr(lhH#>lR!laldweyv+zU@0|6wn0Z6tRgMS;+

delta 76
zcmV-S0JHzJ#{sv;0kFh10Y9_FHH!-fvj92&0JQ)hlkr4KlTShkv#UW50Rv|N0<*kA
i%mD{g0{;LP04$U7L|BuqMF_L*L=OW3Ap*1hN46VcRU7;O

diff --git a/software/LepMap3/Pileup2Likelihoods.class b/software/LepMap3/Pileup2Likelihoods.class
index 144e44839e376e44734cb1cb0e20f74f88a0b06e..3dbf7ad50aa569f2d2b02c7c6cd14885b9087fb2 100644
GIT binary patch
delta 4315
zcmZu!33yaR60X1BId9(FG-N<90xA*`a^NU~yR3)@DtNH@Ab`6GBp}KWAtJEqh{S6b
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literal 0
HcmV?d00001

diff --git a/software/LepMap3/QTL.class b/software/LepMap3/QTL.class
index 6dd6e7fa77c58ccb6561576e51f2fd12affb968e..ea939a1c3db312c95129dbe14cacd9ec9dcf002a 100644
GIT binary patch
delta 29
lcmZ1xv^;3TMFGZbn=c8}Ffm&)a83>sR$`3WTq?X-6acDk3JU-L

delta 30
mcmZ1;v?6H3MFGa`n=c8}Ffm&(a7_*rR$>Zg+FT;MSrh=Wq6!TF

diff --git a/software/LepMap3/Separate2$JoinSinglesThread.class b/software/LepMap3/Separate2$JoinSinglesThread.class
index 93baa372e0b1c73957f95ce56a9af2dfe94cb0c4..20ff226848f1ef6a894a703d2b5f4d593adc2a1f 100644
GIT binary patch
delta 233
zcmWN`yDP*20KoC@_o7ZNiwrI@$RH&K{0Bx^luQ<b@&{O?+bjmoc?*X_BIoCQ9(kTu
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delta 233
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ISsVHJ1B}5y@c;k-

diff --git a/software/LepMap3/Separate2$JoinSinglesThreadMaxDistance.class b/software/LepMap3/Separate2$JoinSinglesThreadMaxDistance.class
index 4372a16761247c4c0612c852e89d591f8fb63326..15fab55388a933ecff9420baf82c26d052480bf1 100644
GIT binary patch
literal 3283
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B{_6k$

diff --git a/software/LepMap3/Separate2$SeparateIdenticalThread.class b/software/LepMap3/Separate2$SeparateIdenticalThread.class
index f3be6ae577680572f778f1b05b804d5da88f7d49..c491b2266f9599dfc92deb98282e066b7226b10a 100644
GIT binary patch
delta 341
zcmWN{&nv@m9LMq3`|~o5S%__ADHh|T#uVjXPJVNs{h%={`LUt-UC3`DzrM9)Qk07u
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delta 343
zcmWN{&nv@m9LMq3`|~o5Z6QBamSQnZ@?!@|+U7_3JsO7moGFB~n1(HxxlDe1iy}q2
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diff --git a/software/LepMap3/Separate2$SeparateThread.class b/software/LepMap3/Separate2$SeparateThread.class
index 283a9d51928167c02797bb59b6af9dfede34cba5..3f798c277569067cb839c58aea497da3aeecad73 100644
GIT binary patch
delta 1166
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delta 1003
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diff --git a/software/LepMap3/Separate2.class b/software/LepMap3/Separate2.class
index 1c9670ca7fcf3d746cfe5ee76f25eb62a7f87f6d..28e70f4577928c5772271cdb92df575d14831847 100644
GIT binary patch
literal 30747
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diff --git a/software/LepMap3/SeparateChromosomes2.class b/software/LepMap3/SeparateChromosomes2.class
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diff --git a/software/LepMap3/ShortPath.class b/software/LepMap3/ShortPath.class
index fccee924dbdd4a6df9d3dc614df14a98b5748db2..0bf46d3bbcfbb22e1224776fdd6a8ffaf58295d2 100644
GIT binary patch
delta 28
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diff --git a/software/LepMap3/UnionFind.class b/software/LepMap3/UnionFind.class
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GIT binary patch
delta 45
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diff --git a/software/LepMap3/scripts/LICENSE b/software/LepMap3/scripts/LICENSE
new file mode 100644
index 0000000..94a9ed0
--- /dev/null
+++ b/software/LepMap3/scripts/LICENSE
@@ -0,0 +1,674 @@
+                    GNU GENERAL PUBLIC LICENSE
+                       Version 3, 29 June 2007
+
+ Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
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+<http://www.gnu.org/licenses/>.
+
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+may consider it more useful to permit linking proprietary applications with
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+<http://www.gnu.org/philosophy/why-not-lgpl.html>.
diff --git a/software/LepMap3/scripts/map2genotypes.awk b/software/LepMap3/scripts/map2genotypes.awk
index 64cb5f3..a587300 100644
--- a/software/LepMap3/scripts/map2genotypes.awk
+++ b/software/LepMap3/scripts/map2genotypes.awk
@@ -1,7 +1,7 @@
 #converts phased data to "genotypes"
 #usage: 
-#java ... OrderMarkers2 ... outputPhasedData=1 > order_with_phase_software/LepMap3.txt
-#awk [-vchr=X] [-vfullData=1] -f map2genotypes.awk order_with_phase_software/LepMap3.txt
+#java ... OrderMarkers2 ... outputPhasedData=1 > order_with_phase_LM3.txt
+#awk [-vchr=X] [-vfullData=1] -f map2genotypes.awk order_with_phase_LM3.txt
 #output columns marker name, chr, male postion, female postion, genotypes coded as "1 1", "1 2", "2 2" and 0 as missing
 #providing fullData ouputs parents and pedigree...
 BEGIN{
diff --git a/software/LepMap3/scripts/somePaternal.awk b/software/LepMap3/scripts/somePaternal.awk
new file mode 100644
index 0000000..51234b1
--- /dev/null
+++ b/software/LepMap3/scripts/somePaternal.awk
@@ -0,0 +1,26 @@
+#flips informative markers based on a map
+#awk -f somePaternal map.txt data.call
+BEGIN{
+	FS="\t"
+	OFS="\t"
+}
+
+(NR==FNR && /^[^#]/) {
+	map[++markers] = $1
+}
+
+(NR!=FNR && FNR<=7){print}
+
+(NR!=FNR && FNR==2){for (i = 3; i<=NF; ++i) {if (!($i in d)) d[$i] = ++p; f[i]=d[$i]}}
+(NR!=FNR && FNR==4){for (i = 3; i<=NF; ++i) if ($i==0) pa[f[i], ++count[f[i]]]=i}
+
+(NR!=FNR && FNR>7){
+	for (j = 1; j <= p; ++j) {
+		if (map[FNR-7]>0) {
+			tmp = $(pa[j, 1])
+			$(pa[j, 1]) = $(pa[j, 2])
+			$(pa[j, 2]) = tmp
+		}
+ 	}
+	print
+}

From c5cdb225c2c8332b2876952b98b9c1ec6210f65a Mon Sep 17 00:00:00 2001
From: Pavel Dimens <pdimens@live.com>
Date: Wed, 2 Feb 2022 15:38:38 -0500
Subject: [PATCH 02/46] update LA modules (needs testing)

---
 software/LepAnchor/AltLinks.class             |  Bin 0 -> 19506 bytes
 software/LepAnchor/ChainPaf.class             |  Bin 0 -> 5741 bytes
 software/LepAnchor/CleanMap$CleanMarker.class |  Bin 1086 -> 1086 bytes
 software/LepAnchor/CleanMap.class             |  Bin 15036 -> 15324 bytes
 software/LepAnchor/ContigInterval.class       |  Bin 9363 -> 9362 bytes
 .../LepAnchor/CoverageAnalyser$Gaussian.class |  Bin 1248 -> 1248 bytes
 .../LepAnchor/CoverageAnalyser$Zeta.class     |  Bin 1330 -> 1330 bytes
 software/LepAnchor/CoverageAnalyser.class     |  Bin 9179 -> 10628 bytes
 software/LepAnchor/CoverageHMM.class          |  Bin 11631 -> 12308 bytes
 software/LepAnchor/FindContigErrors.class     |  Bin 12066 -> 12047 bytes
 software/LepAnchor/Input.class                |  Bin 5928 -> 5927 bytes
 software/LepAnchor/InputData.class            |  Bin 13948 -> 13938 bytes
 software/LepAnchor/Map2Bed.class              |  Bin 8487 -> 8486 bytes
 .../LepAnchor/Misc$ArrayIndexComparator.class |  Bin 1800 -> 1800 bytes
 .../Misc$ArrayIndexComparator2.class          |  Bin 1989 -> 1989 bytes
 software/LepAnchor/Misc.class                 |  Bin 3290 -> 4140 bytes
 software/LepAnchor/ParameterParser.class      |  Bin 7307 -> 7305 bytes
 .../PlaceAndOrientContigs$CalculateBest.class |  Bin 4010 -> 4062 bytes
 ...laceAndOrientContigs$LongComparator0.class |  Bin 851 -> 851 bytes
 ...laceAndOrientContigs$LongComparator1.class |  Bin 851 -> 851 bytes
 .../PlaceAndOrientContigs$PossibleError.class |  Bin 1844 -> 1844 bytes
 .../LepAnchor/PlaceAndOrientContigs.class     |  Bin 125735 -> 127057 bytes
 software/LepAnchor/Proximity.class            |  Bin 16701 -> 16693 bytes
 .../LICENSE => LepAnchor/scripts/COPYING}     |    0
 software/LepAnchor/scripts/chainpaf.awk       |  313 ++
 software/LepAnchor/scripts/cutBed.awk         |  152 +
 software/LepAnchor/scripts/cutBed_fixN.awk    |   23 +
 software/LepAnchor/scripts/hic.awk            |   33 +
 software/LepAnchor/scripts/ld.awk             |   22 +
 .../LepAnchor/scripts/lepanchor_wrapper.sh    |  268 +
 .../LepAnchor/scripts/lepanchor_wrapper2.sh   |  287 +
 .../LepAnchor/scripts/lepanchor_wrapper3.sh   |  292 +
 software/LepAnchor/scripts/longread.awk       |   72 +
 software/LepAnchor/scripts/makeagp2.awk       |    8 +-
 software/LepAnchor/scripts/makeagp_full2.awk  |    8 +-
 software/LepAnchor/scripts/normalise.awk      |   62 +
 software/LepAnchor/scripts/paf2chain.awk      |   52 +
 software/LepAnchor/scripts/plot_marey.R       |  108 +-
 software/LepAnchor/scripts/prox10x.awk        |   50 +
 .../LepAnchor/scripts/removeHaplotypes.awk    |    5 +-
 software/LepAnchor/scripts/sortpaf.awk        |    7 +
 software/LepAnchor/scripts/umi.awk            |   64 +
 software/LepAnchor/src/CleanMap.java          |  559 --
 software/LepAnchor/src/ContigInterval.java    |  382 --
 software/LepAnchor/src/CoverageAnalyser.java  |  420 --
 software/LepAnchor/src/CoverageHMM.java       |  571 --
 software/LepAnchor/src/FindContigErrors.java  |  557 --
 software/LepAnchor/src/Input.java             |  209 -
 software/LepAnchor/src/InputData.java         |  452 --
 .../LepAnchor/src/LiftoverHaplotypes.java     |   44 -
 software/LepAnchor/src/Map2Bed.java           |  334 --
 software/LepAnchor/src/Marker.java            |  139 -
 software/LepAnchor/src/Misc.java              |  224 -
 software/LepAnchor/src/ParameterParser.java   |  231 -
 .../LepAnchor/src/PlaceAndOrientContigs.java  | 4821 -----------------
 software/LepAnchor/src/Proximity.java         |  657 ---
 software/LepMap3/scripts/affx2post.awk        |   83 -
 software/LepMap3/scripts/allPaternal.awk      |   45 -
 software/LepMap3/scripts/genotypes2post.awk   |   81 -
 software/LepMap3/scripts/loc2genotypes.awk    |  102 -
 software/LepMap3/scripts/locsingle.awk        |    8 -
 software/LepMap3/scripts/map2genotypes.awk    |   66 -
 software/LepMap3/scripts/order2data.awk       |   65 -
 software/LepMap3/scripts/phasematch.awk       |  133 -
 software/LepMap3/scripts/pileup2posterior.awk |  156 -
 software/LepMap3/scripts/pileupParser2.awk    |   90 -
 software/LepMap3/scripts/somePaternal.awk     |   26 -
 67 files changed, 1765 insertions(+), 10516 deletions(-)
 create mode 100644 software/LepAnchor/AltLinks.class
 create mode 100644 software/LepAnchor/ChainPaf.class
 rename software/{LepMap3/scripts/LICENSE => LepAnchor/scripts/COPYING} (100%)
 create mode 100644 software/LepAnchor/scripts/chainpaf.awk
 create mode 100644 software/LepAnchor/scripts/cutBed.awk
 create mode 100644 software/LepAnchor/scripts/cutBed_fixN.awk
 create mode 100644 software/LepAnchor/scripts/hic.awk
 create mode 100644 software/LepAnchor/scripts/ld.awk
 create mode 100755 software/LepAnchor/scripts/lepanchor_wrapper.sh
 create mode 100755 software/LepAnchor/scripts/lepanchor_wrapper2.sh
 create mode 100755 software/LepAnchor/scripts/lepanchor_wrapper3.sh
 create mode 100644 software/LepAnchor/scripts/longread.awk
 create mode 100644 software/LepAnchor/scripts/normalise.awk
 create mode 100644 software/LepAnchor/scripts/paf2chain.awk
 create mode 100644 software/LepAnchor/scripts/prox10x.awk
 create mode 100644 software/LepAnchor/scripts/sortpaf.awk
 create mode 100644 software/LepAnchor/scripts/umi.awk
 delete mode 100644 software/LepAnchor/src/CleanMap.java
 delete mode 100644 software/LepAnchor/src/ContigInterval.java
 delete mode 100644 software/LepAnchor/src/CoverageAnalyser.java
 delete mode 100644 software/LepAnchor/src/CoverageHMM.java
 delete mode 100644 software/LepAnchor/src/FindContigErrors.java
 delete mode 100644 software/LepAnchor/src/Input.java
 delete mode 100644 software/LepAnchor/src/InputData.java
 delete mode 100644 software/LepAnchor/src/LiftoverHaplotypes.java
 delete mode 100644 software/LepAnchor/src/Map2Bed.java
 delete mode 100644 software/LepAnchor/src/Marker.java
 delete mode 100644 software/LepAnchor/src/Misc.java
 delete mode 100644 software/LepAnchor/src/ParameterParser.java
 delete mode 100644 software/LepAnchor/src/PlaceAndOrientContigs.java
 delete mode 100644 software/LepAnchor/src/Proximity.java
 delete mode 100644 software/LepMap3/scripts/affx2post.awk
 delete mode 100644 software/LepMap3/scripts/allPaternal.awk
 delete mode 100644 software/LepMap3/scripts/genotypes2post.awk
 delete mode 100644 software/LepMap3/scripts/loc2genotypes.awk
 delete mode 100644 software/LepMap3/scripts/locsingle.awk
 delete mode 100644 software/LepMap3/scripts/map2genotypes.awk
 delete mode 100644 software/LepMap3/scripts/order2data.awk
 delete mode 100644 software/LepMap3/scripts/phasematch.awk
 delete mode 100644 software/LepMap3/scripts/pileup2posterior.awk
 delete mode 100644 software/LepMap3/scripts/pileupParser2.awk
 delete mode 100644 software/LepMap3/scripts/somePaternal.awk

diff --git a/software/LepAnchor/AltLinks.class b/software/LepAnchor/AltLinks.class
new file mode 100644
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diff --git a/software/LepAnchor/ChainPaf.class b/software/LepAnchor/ChainPaf.class
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diff --git a/software/LepAnchor/ContigInterval.class b/software/LepAnchor/ContigInterval.class
index 321a47515141460af3b9e664967d2fb4ce6a086c..c83097262e75156f3709d9d6be9f9de1a8f3982d 100644
GIT binary patch
delta 27
jcmbR2ImvTFmMr6&$=R}xI5-(t{xHb0h;9y(vt<JSi=YUK

delta 28
kcmbQ_IoWeVmMr7j$=R}xIJp>D|1ik12r+FAm9u370Fv$qi~s-t

diff --git a/software/LepAnchor/CoverageAnalyser$Gaussian.class b/software/LepAnchor/CoverageAnalyser$Gaussian.class
index b96bf650ac8d01a6d3c42a3101a519a80f653dd2..6b4fa1373ec0f76c55847831215ee97db8b50885 100644
GIT binary patch
delta 75
zcmaFB`G9i+53^(@11CckgD^ujgFHhHgBC+BgFZtZgDFG)WL4$>#-hn(%r=bWlQ%O5
euvRnhFw{)uU`b$Y0J0h<=duJaCQjbRq67eaQW1p!

delta 75
zcmaFB`G9i+53^)E11CcQgD^uPgFHhLgBC+FgFZtFgDFGmWL4$>#*E2j%r=a<lQ%O5
euog1#FceMZU`b#t1G35|=duJahELwdq67eFo)Gx}

diff --git a/software/LepAnchor/CoverageAnalyser$Zeta.class b/software/LepAnchor/CoverageAnalyser$Zeta.class
index 66d386297b98d98456345447b1fefadeabafa115..927c8b6f539cdb5397d49bd273188b71e7b8603c 100644
GIT binary patch
delta 79
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hL^4ccr~uMU4AUp8vmEA}$-u!di-C(__T<kj_5k}&6N3N%

delta 79
zcmdnQwTWxPCuY+|22O^01`&p41}TOX23dwy24#je27QKh1~Y~Z24^7Om!XRxn4y~?
glA(v80!TM8^iEc1In3G5z`-zqfs0|{<j*Yj0O6$)*#H0l

diff --git a/software/LepAnchor/CoverageAnalyser.class b/software/LepAnchor/CoverageAnalyser.class
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GIT binary patch
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diff --git a/software/LepAnchor/CoverageHMM.class b/software/LepAnchor/CoverageHMM.class
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delta 5181
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zG_w_9;$;6)kkN}@b|ht?#j0c!?Ay@salyV-h$;+(<u|M0X_tSq-U)@Vj=gBERDJT>
zib~BVODigMpFC1g>F~*;6_rk(EUTz=`Q)*Ru$Wd;WNGrrN-CltO98i8NDiN@3d@>y
z+;`0$2#tHHgm0G&ZE83q>$(10;cAIaXsHc3{Q4Vk`5kXwvc#`(@ll^_w8cCWmd!S1
z*%g>)Y|LXmdG;dB7Qe;^p1i<856d>bmSnr-??@O-gP%RTk_wlS4nxU699<aT*hk61
z5Tz4_DY>{_>4LdRS1e^4vsNj@(@Fqal_In$-ElxE#@k8{98r4WsL~sMQLbWl(nnlM
zKk+L4B}o||X-bKGSmW%NOP3w8lLol>Bg-y%i3c~=;0+A31}cbQ6hun%TE2^PJFK3@
zTs~;Z8HjDDmS2%h#{o>1c0vw2=mKz@=RK1JOhl4#8u5GyG&B3j?h82U?pV!!Gsq$G
KvK2Y9=YIiI!CSuo

diff --git a/software/LepAnchor/FindContigErrors.class b/software/LepAnchor/FindContigErrors.class
index a6b87123265557ce22a4e50123694885236c746d..09aff0fa1a5c89c45864f3d8926e74a25a8a04c1 100644
GIT binary patch
delta 124
zcmZ1!*B`fmLy|FIGpFPkCW&SSzP}6x><p6Z42$^xFz^Feik!a~gf_pEPG(~~zd1;$
zkBQlVfo<|*6@5n8$;zs2jKZ5&sYbGh?qm@9%V5X?)F<$VK>(;v`9DL!WC<-<k^c-D
Z4D9R-jO+|GjEu}66$}iUy|u2h001I!9`67E

delta 150
zcmeB=TNJl}Ly|FYGpFPkCYcrn{=W<c><p6Z42$^xFz^Feik!a~_?iAQ2uwDV5!=ir
z<Hg2!e{-Nx9}{x`1N-DhD*A#_49x5djO+|GKurt`{~4Gj3#qm-if*2%8p$HMn?d9+
tgCPr0O5hKJ0MI<;{|vd4*|lWFfM%*PutRh*GBSgdFfcG}w$QrH0szcrA|3z$

diff --git a/software/LepAnchor/Input.class b/software/LepAnchor/Input.class
index e7ce976796b5dc10ac4c2a3d4b12566d0a6d7d2d..6b7f5458961aab5f730c7331cb10499fd9468133 100644
GIT binary patch
delta 53
zcmZ3Xw_I<-GXci_&Cdlg7!}nRIR7wkurq}HWng7z2xMo_7w2LB!@vy``NN<L<Zdn$
H+Rg$1s#OjO

delta 54
zcmZ3kw?c2jGXcg4o1Y70Fe<4taQ$K6U}p&X%fQOc5XjD;FV4gMhk+X?@`phI$Yt7G
IAhewY0JiuJ3;+NC

diff --git a/software/LepAnchor/InputData.class b/software/LepAnchor/InputData.class
index 8a21bd64133a088457cf85ad5dbb967b10644405..309b7b707f84c48ecbc51f389f5800eedb129e1f 100644
GIT binary patch
delta 188
zcmey9^C@S;97)FJ&2uGBF){C8;F_EzGoOY3Cxhf<epwC1)tfD3OE{U$7<4ADS2Gcj
z|HHt_n8VI!FT?bUf%6xG(Juzc%|F$yGBd_*KCi{a%pAnPKlzTX3JXw9ax$BqE$1Ev
zb_Nax2F7QT<&9i6PtcQOW)5Qzn7qbNmr-K!Z9{9uEt|!SdKtyl7})+YXs|P+vopBz
m|6$+-vMfMm>@ikltlRv^*oKMOk%4EjqL~H@7szq`X1V|sPc?r4

delta 185
zcmeyA^CxG+97)F3&2uGBF){CA;F+8yGoOuz=_i92(_~&*4aT*b&16eBnJpOfCa+a9
z5tCv1!@$az!_H_g!}N=R^B05BFQCfJU)8QMGsbT|t;NO69Ks+t`G&3v8yir87}F#@
zTgJVc?etQanZtn+%M5jyM42XEF|=mfx>>-emr+8Uf&DLo20KGKJA*6#9|m3^%L1fv
f@)l!N#)i$ejBS{hof-HhOPXo0u|wSDYNiVS@Z2*Z

diff --git a/software/LepAnchor/Map2Bed.class b/software/LepAnchor/Map2Bed.class
index 4f12cd1d7fec842ca7ee56e49066322d63538c0b..0bf99a7da778b20c816747443a0dbc6a2f36a719 100644
GIT binary patch
delta 29
lcmZ4Pw9IM48!<+U&2PmPvoTL$P?|hhHjt5P^D|jTW&o~l3T^-Z

delta 30
mcmZ4HwA^XK8!<-9&2PmPvoTL)P@X(lHjs&(Y4cNAM`i%G4hnDp

diff --git a/software/LepAnchor/Misc$ArrayIndexComparator.class b/software/LepAnchor/Misc$ArrayIndexComparator.class
index 3226bdcd2cbef4e573ba2491fe3094ad2c0be3af..339c34575133df78eeaa3ecfa393fa52901e29a2 100644
GIT binary patch
delta 63
zcmeC+>)_jPn}u^C0}I1s22O@4lb^8Ub4~;DW-tgd%$yv<+8{U=C_ayYk6{6WD3DfU
QSTy-9Yb)dO$;E6_0VFCBn*aa+

delta 63
zcmeC+>)_jPn}xHFfrViL11H18$xm4FIVS^oQyGLArcI7vZ4jIV6rat&$1s;c6i6#F
Q%%A+0wUu$n<YKm|03YTNcK`qY

diff --git a/software/LepAnchor/Misc$ArrayIndexComparator2.class b/software/LepAnchor/Misc$ArrayIndexComparator2.class
index 6b0b8b611c087b2291c149945bd806d067bd7a77..66a8bd3ab2f4c341a09ea17fa1551947b47457be 100644
GIT binary patch
delta 71
zcmX@gf0Tbi5-aa!1{Q{`44e$x82A{rPtIp;<=qJs+07upu!ljEVee!{wkd)Kf%1od
Y@<)IohZqzYj!j<1*2#E!vH|;40Ji`Wx&QzG

delta 71
zcmX@gf0Tbi5-aZp1{Q`*44e#`8Tc5sOwMO*<=qAp*})*du#-WQVb^3vwkd-9fb#o+
Y@&|z;`xz7&4o_aj*2#EcvH|;40I^gPkN^Mx

diff --git a/software/LepAnchor/Misc.class b/software/LepAnchor/Misc.class
index ada0e218237f0202e1e777d0934054c5aae160b8..040fbbdb251389bec5a6c14b64101ebe5b382ffb 100644
GIT binary patch
delta 1884
zcmZuyYiyHM7=BK_wqL)mt=n8%88Es0V3)QQgss5hLJ+2~0mapgZitkvZY5nix&o0+
ztFRCyYS0grix;j=5tW<WWQ6#`AI6v%OhiFr^oJL`BqshdhWUKGInb}oIq!MSIq!Mi
z_j%9vU8^`XQ~l(|g-ZbD<Kh{0P&kbP(H#*1sk&x`iW#V~p&B*XE>UH43pljP!lA0D
zh1Uib?$SOLcbezoZW;5mKg3jNJ{D+pL!Gfcx3t_kPemOT>T4Hq?G$auV9^d4&O4=K
zBqd;pMF&!?sYJhkk><H>sl|{s_JyNy0atZr%jWR5urC&l_xM^<$!NT%p{C75s`{gv
zCh|`KF%%4?U`PeSQZS4KLslX1ybaSZU4e!dW$Y6u)z3@k4}5eW73s6#CA`dJM3PAX
zXO2%a;R}!qc_$;`z6Kcw1n#(%>C&yySa&3;Vn3$n%_}y%iq{0p;r{+eyj#FqJt?|1
zn>I(fQVlgal)fqAyq^XO4hslHcXd>Eb?g=oh5Sr%nu7`s^qnVccmpF$dn%Eeq)OG<
zLnob?W|~#Jg|}s#6e!OIc5}!!oWeT-a=)I17^QMfj-|k)jhcp&Jp=UdKSFYQS7O_;
za4IaIwkEbFyCO}|80${aE}5o^_qD60Ix(h|m}A1C4Visnw|2@LN=xN1q8tz##xWx_
zidikS8O%NillycYSmhxyr#(Mf?ahw7<ERaZQFzAS^NgcTxBaxe++1&z>P=F;S@Fw?
zU-3H487%$~jgrrA^*Bwrfzju;EB+Ei8<Z<6ic3tsuwNNA3#Zv>Jc?4Uc1CutEY3>4
zeFr8!8o?Tu-7k-z)}<8PnS2p$Gzq6EyRnGt$K)`FOZI4`mg#A?t7HsIGH7adyUOyG
zOZJzz6n~k%^vJ{lw@WT8Q3}Rs-Vh@kY%}n(y%!cNM+urxhWk)~`+2ihpb9HF+l)nM
z;p}Q!YuE;`mcJlc(T;Qw-FOgNXr{0Z+Y!PJbl_=p;#sW6UOa@u*nner7$>n2qr^VL
zCVY-AT;a~Eh~PRN!EflnpXe1px0r&>;!ecG9K^+3B*bED5sgTSr3i@?NQqW#73+DD
zleCA^u<K%zXETQu(MG1tytx%(Iabj!pi20&%q297a`F!_?$x4{5d>huT4Bcnw9E(!
zl@SFYqg}|n_CY8l_!ol<!pZ=DM;k3W!~BK82AQkv_z6wxXqGW*@ReuGQ|TyD=`2#|
zC{pQw#4Lb`wf>DV88ar(t9`Fb6H~Pt%00>;Zo?2t@tC$u9aNs=XeURzw2#$Zu}7O{
zZ7|Pnbh9kAq%~gi1!cQJQeU#>zv4UeDy6$d>At3*-;mk2%=I<I@tvmFW{DQfZEI({
z%Qh#i;BlnMP9f(d44>R_qHt&2=8M*lqy|Dp2c8IoOb+Y}WJ@fIJ20G`+07aCCj6-^
zzUM#qGg<t(fAO(2_O6l|N8mk+7sj!lH}#;Wl6NVCL$|-4!4XfTabs?n!SM{<9F`1~
z9!7m+;_?|X&6RE~RN6l<2R~va#aM`+DdlzaQldWmiX`jm0Q=(<Pp_7&LO6kU@m`uk
z3ty9`v(?hat$N)Ukl@#7h)$%eq%I=4RUJ%KZdE5ST|PSuH;|-!{EHfbIxhpx;vD<g
aWO$xiGR*HN`w!UHvcEvab?nCtQ2zn?<)_vF

delta 1097
zcmZvbe@s(X6vw~k^|i0>(NYM!vTidVakZs|Cjxy_Pzg*$TNoRKN-;`BHVUOhTFr#S
zqO!65w|Gg6#+bN&_Rq3xS%PFFWPdD6_A6PY8~c$ZOZ>ycWPj{06BET#gqkILdAaAD
zch0@{^S$T3Pip?~Xx}~gauq-mKKNXlC2@mZ$?qgob|<qVJ0h9%+nt%osl;?5mzmzB
z!3)0wZqyMxzR3TTwE71$1ks?No}iB>&Lxbqxn#=d%%oDIBe`TIopr##E`prROy>xG
zU*vgJB$>^%Mnt>hk#{qLn3F0s4UK3nY}z7brJ4%UfmgAoFg-alO0f9+N5oZWS+}Qn
zZeK1l#i@eJsp-)#PFo_9xT*N$OH6#l?h*GC54|fMD=AXMxZR-3;<|k>FFl5g3V`}o
zP(64X+arOxCDg_?qwe5F6kLIKkZ!}bj6h%ojRn7n{mrVL;1WV1*%Go^LN?V@R8tM=
zwk7QS3i~aFSrX8#&jQ&novP_l&GL`&y>8QGF{@TmP<*IXRsCm1A@>nR+)7ZasxNwq
z3s{X&Q=PYxZY|`?0^(m)_Z73Uv3PC$Yqz2$OvSCZU5nRHRqu8!qkRd7V)ddydm&%%
zR<>ew%lV9Nfs9HXKShAY4%pF&QoP1ze-JO@5PUd{W*k8qj&e54UnA&3H+!$62fY}=
z8yG_$CJ;p${WyaG%prz(9K!+zaTRe~=c-$I9Oq4r;TxR5w>XI(F^r#(z~4B9dl<n3
zoW?^8lM8Q=jxpMXaoULqYQ!Y9AWeJFPwkkZqc}r-$U<k_c{mFVWVA3xcIsxhFbHls
zuz@I{jXaDQh6VW!s$k|`)_ai3n7S8MbdeKpvS&k>G*%IXf*w-v5_>9BKVn5ul(52o
zSXY#{n_$owdoEUcpXEeR&MJXAUiTSFyoeGnqQoKX-eehKmg8LFL&-XymQz7>@g*X8
z;{kMUl_Vs`KJ^`L$9a@tMszu5)e9WuIhqqcIL2r}v^ZOBq5T2Ah2oqu?f;qkcZVtO
z^3DE*d-y9nSVJ{_<F5YBtbg)huQB;w!dbeVdW2CL<8h(X+bH1zLrJ{&9NSt}bCKyU
V^C`@;eUGh|?E(tFCgFW(PXQx~-(LU#

diff --git a/software/LepAnchor/ParameterParser.class b/software/LepAnchor/ParameterParser.class
index 2dd946365ae444c653dae733c09a9abd464b738c..8250bae52716d521bad0ca5dccb31631969cd36f 100644
GIT binary patch
delta 80
zcmeCS?6ll)PJmHt@_B*3ViF82{}`m$8D!WQyx193{xB#3*<70+3(7Jx9^1?)YR1Ie
f&%iU;N<2$Ql7W?-fe|PT!a%hQ44b!$Uts|ND5Mch

delta 81
zcmeCQ?6%x+PJmH-@_B*3;*t!k{}`m$8D!WQyx193{xB$k*i4%r3Cc1v9^WKt#>6~<
ffp@Z{c$Tmj11mcNBTyQIfod5Tm^N<}zrq3lG~5wQ

diff --git a/software/LepAnchor/PlaceAndOrientContigs$CalculateBest.class b/software/LepAnchor/PlaceAndOrientContigs$CalculateBest.class
index c644c041924299bbb83e386164e07c3d5c3407a6..89601787de8ecc3b5c06aa4726b3cac724c912be 100644
GIT binary patch
delta 790
zcmZWnOHUJF6g}T`TFRxAnzq!Ikcm>Iv^Jn93lfzD5kp*{3mV)Q(tz=SiK!yKfFMQ^
zQIt<4<slT1@({FQYZXIWsnL}`09P)IOB0PT__$MCn7Ekl-h0lSd(U@f=CltQz5Vrk
z1wc6#6I5(A8JioAos7s*bBkljg8P^jFgJ$7O_7MVT%cOMHw2ef%_}0<iflRqE1iX%
z&cRJ>(C7kubP?rr347@>s;M2d)PXwcly7Ljcm+o4mWw$qc|NDic#W$bu6)Hx0ZcFg
zq9l!jRenPf#eR`Q$gn4lPyQzey+(bZF($v|Y&*2<Uq({{g9o1CDEDv{OyNirrZ~p*
z-V}~=2&B+bp*mGgt5S%>bh?v^>L`4Ej+^<}rISuop0+q0rT>DJe~G9?>u~s;Y7!-k
z1l1IJ;xKg^gkI@Oe>*q}y~<4E#l2B%)PWTG;;>e#ZhoU*Nn<bpA?(5<3L#;@K6bku
z8bH^fQZL(hgKfMC8}+f3x3Gh5V>k7qh9o*_=?)rb0Aad|W*S5bMbSz_=%Qg<r4jVf
zC=xV=RT{@fis3U&;0sOSD^1}$^$CThg`H-Ehh~LFbHYpW!bc0JVG%pmO~-!ZbES$c
z7{V|FY{HEZcvxy{1-dZGsVX#N;~vJKVw{^ju>6Ew6%_@hHMm3|;Q9e2`*0Q{@qn0o
zm)n;65LxsH0eXyjT9S2ESC&3WU|gQEy2>W7iRXlPiNZ0Lean24KpK+?2G(sNouo7@
z^h_qL+htK+zFf0zaJ|Urx9~9V9oF>=%t&wER`<*QIh&b(?^zkn^A?@Ru=+{`bD47<
N4>;<w1<J4h<qz)>u?7GD

delta 719
zcmYjNU2IEX7=FI?v^#ry+OFBwnQA&T?VM^t77{LKLQF&!TquHFnPg(v!a76~OBlxR
zZJKVg*^hPWCQ<Y#5|<>d#1%KYbjy{5Eap9@yYMC7_dZ{q=Y5|y&tfPaqECO{z6a2R
zX9bF?a+`X_Ii+D5PhaNM-y(him2?gsI*)4VL_KvOL>JLWm(WDr*hwkurXK90%Q!$+
z<YyXkT!Vwsvfb6}xX!3o8m`6$@dHjMfT%6uU_!SS5!FQz$sE4wuaNvG9ook2&-HgW
zb(H`6U*j~BjN%4bvvB4xXvz$<bBP%^yCcXTVW4ZmB)g^0QzL>h;)(Lx;;BzF8y!QH
z9xP%5<G5m=&#dOS<uIe<2Q-+)Kz|ngG8)K1YhlSlTM3y01RqtnAYsQIPN)-W0J;H%
zZgM7loXIWt=r&?>2V1Eh3A&42bPtDUAdTa6AFcENZ6wh_gXp0lT%||or3`YE#TOdJ
zHyXhrjp92G`bpzL(1cKFQfM?Ks%To&&<vW{ST84sz3}r-5k3rK1OgpMVHB%j7aCMN
z#uzU;&WcqCxR&5kHV2$bs1>^Y2i29wDj-#EdLozIsq`!=XpT3Z$6;EqO#HBMYjVZJ
zMCNE=4OC!@>5Na{B&*!4vta^jExq09b8~|0_-=`nFj-)t92uD;6`;|J|4iJFzdT_v
zBLm(@UC|;mo(?!x+y!#-h&LkM$h5ak%*u>6yuQuSnLFArXT5pMb0zK+*n|bx{s9Aj
Bm>2*6

diff --git a/software/LepAnchor/PlaceAndOrientContigs$LongComparator0.class b/software/LepAnchor/PlaceAndOrientContigs$LongComparator0.class
index 3b69197586dc12c28fb9af9cb1a67f3049bca00d..13be9af082d95ca3a733b8128376d1eb6fc7ded9 100644
GIT binary patch
delta 19
acmcc2cA0HMFB7Bt<US@xM(@cNn3@4c7Y5P*

delta 19
acmcc2cA0HMFB7A~<US@xMwiJKn3@4brv}6T

diff --git a/software/LepAnchor/PlaceAndOrientContigs$LongComparator1.class b/software/LepAnchor/PlaceAndOrientContigs$LongComparator1.class
index 3281509be7464b3ec2bc75e595abb2b6b6a3e2a4..b6925bfa4f250fd58f5676a4b823788dfce8c973 100644
GIT binary patch
delta 19
acmcc2cA0HMFB7Bx<US@x#^A{pn3@4cmj>bh

delta 19
acmcc2cA0HMFB7B3<US@xMxV(Sn3@4cCkE62

diff --git a/software/LepAnchor/PlaceAndOrientContigs$PossibleError.class b/software/LepAnchor/PlaceAndOrientContigs$PossibleError.class
index 7afb90332c5dc0e5eee80407114114493b6c1c6f..c48918a5717225185b6b829075d64f700ee9763b 100644
GIT binary patch
delta 125
zcmdnOw}o$m42$4u22P$e417Fm8AN#2F-Y;OpRCJLBe?-6x)CV42`IW5D7u9~foCg&
z8qc=Lhgk9$w@)@?4HewQz{9f}sAdmPelLRz&%VjiSpygk0_8*}|7BHYJOXA}v8gj2
UpPa;2%(!y$H8x`)$;GY(02rMjnE(I)

delta 125
zcmdnOw}o$m42$3r22P%(417Gx7({rMGf45Qn5@fEBe@bNx(X<|8YsF3D7uzGfoC0q
z8qfO4hgk9$H%vBU4HewXz{9fzsAelrej9@f&-TgFSpyh%0p&y||7BHY+zVz|v8gj2
Un4H8`%(!UsH8x`)$;GY(0PbBO_y7O^

diff --git a/software/LepAnchor/PlaceAndOrientContigs.class b/software/LepAnchor/PlaceAndOrientContigs.class
index cde0f6ea6f2b5411ae5fa7ca91de9d251f9a02f9..8551faf62b690194caaf501452dedebc4d8d6a66 100644
GIT binary patch
literal 127057
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diff --git a/software/LepAnchor/Proximity.class b/software/LepAnchor/Proximity.class
index 01baebf302678f8f50bcf499a3cf63c51744978a..d7b246037cca27fca814772bb275536a4159f905 100644
GIT binary patch
delta 160
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delta 163
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diff --git a/software/LepMap3/scripts/LICENSE b/software/LepAnchor/scripts/COPYING
similarity index 100%
rename from software/LepMap3/scripts/LICENSE
rename to software/LepAnchor/scripts/COPYING
diff --git a/software/LepAnchor/scripts/chainpaf.awk b/software/LepAnchor/scripts/chainpaf.awk
new file mode 100644
index 0000000..144820c
--- /dev/null
+++ b/software/LepAnchor/scripts/chainpaf.awk
@@ -0,0 +1,313 @@
+#chains paf files
+#assumes paf is sorted on first column (query string) as in output of minimap2
+#awk -f chainpaf.awk aln20DP.paf 
+BEGIN{
+#not implemented yet
+#	if (maxDistance == "")
+#		maxDistance=2000
+
+	if (gapPenalty == "")
+		gapPenalty=-1
+	if (gapOpen == "")
+		gapOpen=-12
+	OFS="\t"
+	FS="\t"
+}
+{
+	if (prev == "" || $1 == prev)
+		data[++lines] = $0
+	else {
+		tmp = $0
+		processData()
+		lines=1
+		data[lines] = tmp
+		$0 = tmp
+	}
+	prev = $1
+}
+END{
+	processData()
+}
+function gapScore(end, start) {
+	if (start >= end) {
+		#print "error"
+		#exit
+		return 0
+	}
+	return gapOpen + gapPenalty  * (end - start)
+}
+
+function max(a, b) {
+	if (a >= b)
+		return a
+	return b
+}
+function min(a, b) {
+	if (a < b)
+		return a
+	return b
+}
+
+
+function processData(i,j,k,n,gl1,gl2,gp1,gp2,start1,start2,end1,end2,bj,starts,cstarts,startsi,other,cother,best,prev,deleted,ret,mydata,s,cigar,score,trim)
+{
+	for (i = 1; i <= lines; ++i) {
+		$0=data[i]
+		starts[i] = $3
+		startsi[$3, ++cstarts[$3]]=i
+	}
+	n = asort(starts)
+
+	#sort data based on query start
+	#and separate by target
+	for (i = 1; i <= lines; ++i) {
+		start = starts[i]
+		$0 = data[startsi[start, cstarts[start]]]
+		s = 0
+		for (j = 13; j <= NF; ++j) {
+			if ($j ~ /^AS:i:/) {
+				s = substr($j, 6)+0
+				break
+			}
+		}
+		if (s <= 0) #do not store chains with score <= 0
+			continue
+		--cstarts[start]
+		other[$6,$5]
+		mydata[$6,$5,++cother[$6,$5]] = $0
+	}
+
+	for (o in other) {
+		if (cother[o] == 1)
+			print mydata[o,1]
+		else { # find max score non-overlapping chain...
+		first = 1
+		while (cother[o] > 1) {
+			for (j = 1; j <= cother[o]; ++j) {
+				$0 = mydata[o,j]
+				if (first)
+					print
+				for (i = 13; i <= NF; ++i) {
+					if ($i ~ /^AS:i:/)
+						score[j] = substr($i, 6)+0
+					if ($i ~ /^cg:Z:/)
+						cigar[j] = substr($i, 6)
+				}
+				best[j] = score[j]
+				prev[j] = j
+				trim[j] = 0 #trim cigar if needed
+			}
+			first = 0
+
+			for (j = 1; j < cother[o]; ++j) {
+				$0 = mydata[o,j]
+				end1 = $4
+				if ($5 == "+") {
+					end2 = $9
+					for (k = j + 1; k <= cother[o]; ++k) {
+						$0 = mydata[o,k]
+						#($5 == "+"), both alignments are in the same orientation
+						start1 = $3
+						start2 = $8
+						#if (start1 >= end1 && start2 >= end2) { #non-overlapping, increasing
+						ov = max(end1 - start1, end2 - start2) #overlap
+						if (ov <= 0 || ov <= maxTrim1(cigar[k])) {
+							if (ov <= 0) {
+								gp1 = gapScore(start1, end1)
+								gp2 = gapScore(start2, end2)
+							}
+							else {
+								gp1 = gapScore(start1 + ov, end1)
+								gp2 = gapScore(start2 + ov, end2) - score[k] * ov /  min($9 - $8, $4 - $3)
+							}
+							if (best[j] + gp1 <= 0)
+								break
+							nb = best[j] + score[k] + gp1 + gp2
+							if (nb > best[k]) {
+								best[k] = nb
+								prev[k] = j
+								trim[k] = ov
+							}
+						}
+					}
+				} else { #"-" orientation
+					end2 = $8
+					for (k = j + 1; k <= cother[o]; ++k) {
+						$0 = mydata[o,k]
+						#($5 == "-"), both alignments are in the same orientation
+						start1 = $3
+						start2 = $9
+						#if (start1 >= end1 && start2 <= end2) { #non-overlapping, increasing (decreasing orientation -)
+                                              ov = max(end1 - start1, start2 - end2) #overlap
+						if (ov <= 0 || ov <= maxTrim1(cigar[k])) {
+							if (ov <= 0) {
+								gp1 = gapScore(start1, end1)
+								gp2 = gapScore(end2, start2)
+							}
+							else {
+                                                      	gp1 = gapScore(start1 + ov, end1)
+                                                      	gp2 = gapScore(end2, start2 - ov) - score[k] * ov /  min($9 - $8, $4 - $3)
+							}
+							if (best[j] + gp1 <= 0)
+								break
+							nb = best[j] + score[k] + gp1 + gp2
+							if (nb > best[k]) {
+								best[k] = nb
+								prev[k] = j
+                                                            	trim[k] = ov
+							}
+						}
+					}
+				}
+			}
+			while (1) {
+				bj = 1
+				for (j = 2; j <= cother[o]; ++j) {
+					if ((best[j] > best[bj] && !(j in deleted)) || (bj in deleted))
+						bj = j
+				}
+				n = 1
+				ret[1] = bj;
+				while (prev[bj] != bj) {
+					bj = prev[bj] 
+					ret[++n] = bj
+				}
+				s = 0
+				for (i = 1; i <= n; ++i)
+					if (ret[i] in deleted) {
+						s = 1
+						break
+					}
+				if (s)
+					break
+					
+				for (i = 1; i <= n; ++i)
+					deleted[ret[i]]
+					
+				if (n == 1)
+					continue
+
+				$0 = mydata[o,ret[n]]
+				start1 = $3
+				if ($5 == "+") {
+					start2 = $8
+				} else {
+					end2 =  $9
+				}
+
+				$0 = mydata[o,ret[1]]
+				end1 = $4
+				if ($5 == "+") {
+					end2 = $9
+				} else {
+					start2 =  $8
+				}
+				s = $1 "\t" $2 "\t" start1 "\t" end1 "\t" $5 "\t" $6 "\t" $7 "\t" start2 "\t" end2 "\t0\t0\t0\tAS:i:" int(best[ret[1]]) "\t"  "CH:i:" n "\tcg:Z:"
+
+
+				$0 = mydata[o,ret[n]]
+				end1 = $4
+				if ($5 == "+")
+					end2 = $9
+				else
+					end2 = $8
+
+				#construct combined cigar
+				c = cigar[ret[n]]
+
+				for (i = n - 1; i >= 1; --i) {
+					j = ret[i]
+					$0 = mydata[o,j]
+
+					gl1 = $3 - end1
+					end1 = $4
+					if ($5 == "+") {
+						gl2 = $8 - end2
+						end2 = $9
+					}
+					else {
+						gl2 = end2 - $9
+						end2 = $8
+					}
+					if (trim[j] > 0) {
+						gl1 += trim[j]
+						gl2 += trim[j]
+					}
+
+					if (gl1 < 0 || gl2 < 0)  {
+						print "\nerror:negative gap" gl1 gl2
+						exit
+					}
+					if (gl1 > 0)
+						c = c gl1 "I"
+					if (gl2 > 0)
+						c = c gl2 "D"
+					if (trim[j] > 0)
+						c = c "" trim1(cigar[j], trim[j])
+					else	
+						c = c "" cigar[j]
+
+				}
+				if (n > 1)
+					print s c
+			} #while (1)
+				
+			k = 1
+			for (j = 1; j <= cother[o]; ++j) {
+				mydata[o, k] = mydata[o, j]
+				if (!(j in deleted))
+					++k;
+			}
+			cother[o] = k - 1
+			delete(deleted)
+		}
+		}
+	}
+}
+#how much you can trim cigar aligment from the first (match)
+function maxTrim1(cigar)
+{
+	return cigar+0
+}
+#and remove overlap from first match
+function trim1(cigar,ov){
+	return (cigar - ov) substr(cigar, index(cigar, "M"))
+}
+
+#how much you can trim cigar aligment from the last (match)
+function maxTrim2(cigar ,i)
+{
+	i = length(cigar) - 1
+	while (substr(cigar, i, 1) ~ /[0-9]/)
+		--i
+	
+	return substr(cigar, i + 1) + 0
+}
+#function trim1(cigar, ov    ,s1,s2,le,op){
+#	s1 = ov
+#	s2 = ov
+#	while (1) {
+#		le = (cigar + 0)
+#		op = substr(cigar, length(le) + 1, 1)
+#		if (op == "M") {
+#			if (s1 - le <= 0 && s2 - le <= 0) {
+#				if (s1 <= 0 && s2 <= 0) 
+#					return cigar
+#				return (cigar - max(s1, s2)) substr(cigar, length(le) + 1)
+#			}
+#			s1 -= le
+#			s2 -= le
+#		} else if (op == "I") {
+#			s1 -= le
+#		}
+#		else if (op == "D") {
+#			s2 -= le
+#		}
+#		else {
+#			print "error parsing cigar string"
+#			exit
+#		}
+#		cigar = substr(cigar, length(le) + 2)
+#	}
+#}
+
diff --git a/software/LepAnchor/scripts/cutBed.awk b/software/LepAnchor/scripts/cutBed.awk
new file mode 100644
index 0000000..0ab51a0
--- /dev/null
+++ b/software/LepAnchor/scripts/cutBed.awk
@@ -0,0 +1,152 @@
+#cuts bed based on extra cut sites
+#usage: awk -f cutBed.awk map.bed cut_sites.txt >cut.bed
+#       awk -f cutBed_fixN.awk contigs.length cut.bed >cut_fix.bed
+#map.bed is from Map2Bed
+#cut_sites is contig, start [,stop]
+#both input files with non-overlapping intervals and sorted by start
+BEGIN{
+#        FS="\t"
+        OFS="\t"
+}
+#store bed
+(NR==FNR  && /^[^#]/){
+	end[$1] = substr($3, index($3, "-") + 1) + 0
+	if (!($1 in c))
+		start[$1] = $2 + 0
+	++c[$1]
+	bed[$1,c[$1]]=$0
+	beds[$1,c[$1]] = substr($2, index($2, "-") + 1) + 0
+	bede[$1,c[$1]] = $3 + 0
+	bedc[$1,c[$1]] = $5
+	contigs[$1]
+	if ($5 > maxChr)
+		maxChr = $5
+}
+#store cutsites
+(NR!=FNR){
+	if (NF < 2)
+		next
+	#gap can be in ($3-$2+2) positions, start-1...end are the possible positions
+	if (NF >= 3)
+		$2 = $2 - 1
+	else
+		$3 = $2
+	
+	#remove cut if it intersects several contig boundaries
+	#trim if only one...
+	trim = 0
+	for (i = 1; i <= c[$1]; ++i) {
+		if ($2 < beds[$1,i] && $3 >= beds[$1,i]) {
+			if (trim > 0) {
+				print "cutBed: " $0 " removed" >"/dev/stderr"
+				next
+			}
+			trim = i
+		}
+		if ($2 <= bede[$1,i] && $3 > bede[$1,i]) {
+			if (trim > 0) {
+				print "cutBed: " $0 " removed" >"/dev/stderr"
+				next
+			}
+			trim = i	
+		}
+	}
+	if (trim > 0)
+		for (i = 1; i <= c[$1]; ++i) {
+			if ($2 < beds[$1,i] && $3 >= beds[$1,i]) {
+				printf "cutBed: " $0 " trimmed => " >"/dev/stderr"
+				$3 = beds[$1,i] - 1
+				print $0 >"/dev/stderr"
+				
+			}
+			if ($2 <= bede[$1,i] && $3 > bede[$1,i]) {
+				printf "cutBed: " $0 " trimmed => " >"/dev/stderr"
+				$2 = bede[$1,i] + 1
+				print $0 >"/dev/stderr"
+			}
+		}
+	cut1[$1,++d[$1]] = $2
+	cut2[$1,  d[$1]] = $3
+}
+END{
+	for (contig in contigs) {
+		if (d[contig] + 0 == 0) { #no cuts
+			for (i = 1; i <= c[contig]; ++i)
+				print bed[contig, i]
+		} else { #at least one cut for contig
+			j = 1
+			i = 1
+			st = start[contig]
+
+			#before bed i, split zero chr
+			printed = 0
+			while (j <= d[contig] && cut2[contig, j] < beds[contig, i]) {
+				c1 = cut1[contig, j]
+				c2 = cut2[contig, j]
+				for (chr = 1; chr <= maxChr; ++chr) ## put to all chromosomes
+					print contig, st, c1"-"c2, "?", chr
+				st = (c1+1)"-"(c2+1)
+				++j
+				printed = 1
+			}
+			if (printed == 0)
+				st = st "-" beds[contig, i]
+
+			while (i <= c[contig]) {
+				#split bed i, chr in bedc				
+				#printed = 0
+				while (j <= d[contig] && cut1[contig, j] >= beds[contig, i] && cut2[contig, j] <= bede[contig, i]) {
+					c1 = cut1[contig, j]
+					c2 = cut2[contig, j]
+					print contig, st, c1"-"c2, "?", bedc[contig, i]
+					st = (c1+1)"-"(c2+1)
+					++j
+					#printed = 1
+				}
+				
+				#after bed i, chr in bedc for first
+				printed = 0
+				while (j <= d[contig] && cut1[contig, j] > bede[contig, i] && (i == c[contig] || cut2[contig, j] < beds[contig, i + 1])) {
+					c1 = cut1[contig, j]
+					c2 = cut2[contig, j]
+					if (printed == 0) {
+						print contig, st, c1"-"c2, "?", bedc[contig, i]
+						printed = 1
+					} else
+						for (chr = 1; chr <= maxChr; ++chr) ## put to all chromosomes
+							print contig, st, c1"-"c2, "?", chr
+					st = (c1+1)"-"(c2+1)
+					++j
+				}
+				if (printed == 0) {
+					if (i == c[contig])
+						e2 = end[contig]"*"
+					else
+						e2 = beds[contig, i + 1] - 1
+					e1 = bede[contig, i]
+					print contig, st, e1"-"e2, "?", bedc[contig, i]
+					st = (e1+1)"-"(e2+1)
+				} else if (i == c[contig]) {
+					for (chr = 1; chr <= maxChr; ++chr) ## put to all chromosomes
+						print contig, st, end[contig]"*", "?", chr
+	
+				}
+
+				++i
+			}
+		}
+	}
+	for (contig in d) 
+		if (!(contig in contigs)){
+			st = 1
+			for (j = 1; j <= d[contig]; ++j) {
+				c1 = cut1[contig, j]
+				c2 = cut2[contig, j]
+				for (chr = 1; chr <= maxChr; ++chr) ## put to all chromosomes
+					print contig, st, c1"-"c2,"?",chr
+				st = (c1+1)"-"(c2+1)
+			}
+			for (chr = 1; chr <= maxChr; ++chr) ## put to all chromosomes
+				print contig, st, "N*","?",chr
+		}	
+}
diff --git a/software/LepAnchor/scripts/cutBed_fixN.awk b/software/LepAnchor/scripts/cutBed_fixN.awk
new file mode 100644
index 0000000..a484163
--- /dev/null
+++ b/software/LepAnchor/scripts/cutBed_fixN.awk
@@ -0,0 +1,23 @@
+#awk -f cutBed_fixN.awk contigs.length cut.bed
+BEGIN{
+#	FS="\t"
+	OFS="\t"
+}
+(NR==FNR){
+	l[$1]=$2
+}
+(NR!=FNR){
+	if ($3 == "N*") {
+		if ($1 in l)
+			$3 = l[$1]"*"
+		else {
+			print "error: length for contig " $1 " not found!"
+			exit
+		}
+	}
+	d[++line] = $0
+}
+END{
+	for (i = 1; i <= line; ++i)
+		print d[i]
+}
diff --git a/software/LepAnchor/scripts/hic.awk b/software/LepAnchor/scripts/hic.awk
new file mode 100644
index 0000000..48bbf0a
--- /dev/null
+++ b/software/LepAnchor/scripts/hic.awk
@@ -0,0 +1,33 @@
+#samtools view hic.bam|awk -f hic.awk
+#or samtools view -h hic.bam|samblaster/samblaster -r|awk -f hic.awk
+#hic.bam: bwa mem -t16 -5SPM REF R1.fq.gz R2.fq.gz|samtools view -b - >hic.bam
+#process hic data for Lep-Anchor
+BEGIN{
+	#mapping quality limit
+	if (qLimit == "")
+		qLimit=20
+	FS="\t"
+}
+(NF>=7 && $5>=qLimit){
+	if ($1 == prevR) {
+		for (i = 1; i <= n; ++i) { #print both ways
+			print $3"\t"$4"\t"c[i]"\t"p[i]"\t?\t"min(q[i], $5)
+			print c[i]"\t"p[i]"\t"$3"\t"$4"\t?\t"min(q[i], $5)
+		}
+		++n
+	} else
+		n = 1
+	c[n]=$3
+	p[n]=$4
+	q[n]=$5
+	prevR = $1
+
+}
+function min(a,b){
+	if (a <= b)
+		return a
+	else
+		return b
+}
+END{
+}
diff --git a/software/LepAnchor/scripts/ld.awk b/software/LepAnchor/scripts/ld.awk
new file mode 100644
index 0000000..113eabc
--- /dev/null
+++ b/software/LepAnchor/scripts/ld.awk
@@ -0,0 +1,22 @@
+#zcat sorted_ld.gz|awk -f perm|awk -f maxmatch3
+#awk -vOFS="\t" '(!(($1"\t"$2"\t"$3) in d) && !(($3"\t"$4"\t"$1) in d) ){d[$1"\t"$2"\t"$3];d[$3"\t"$4"\t"$1]; print;t=$1;$1=$3;$3=t;t=$2;$2=$4;$4=t;print}'
+BEGIN{
+	if (window == "")
+		window = 10000
+}
+function round(p)
+{
+	return 1 + window * int((p-1)/window)
+}
+{
+	r1 = round($2)
+	r2 = round($4)
+	i1 = $1"\t"$2"\t"$3"\t"r2"\t"r1
+	i2 = $3"\t"$4"\t"$1"\t"r1"\t"r2
+	if (d[i1] == "" && d[i2] == "") {
+		++d[i1]
+		++d[i2]
+		print $1"\t"r1"\t"$3"\t"r2"\t"$5"\t"$6"\t"$2"\t"$4
+		print $3"\t"r2"\t"$1"\t"r1"\t"$5"\t"$6"\t"$4"\t"$2
+	}
+}
diff --git a/software/LepAnchor/scripts/lepanchor_wrapper.sh b/software/LepAnchor/scripts/lepanchor_wrapper.sh
new file mode 100755
index 0000000..67c4b37
--- /dev/null
+++ b/software/LepAnchor/scripts/lepanchor_wrapper.sh
@@ -0,0 +1,268 @@
+#!/bin/bash
+##########################################################
+#
+#  Lep-Anchor wrapper
+#
+#  usage: lepanchor_wrapper.sh -f ref.fasta -n num_chr -e extra_cut_site_file -c chain_file -p paf_file -r prox_file -m map_file1 -m map_file2, ... 
+#
+#  output: LA_REF.fa.gz anchored reference genome
+#          LA_REF.agp   agp file describing the genome
+#          marey*.png   Marey maps for visual verification
+#          chr*.agp     agp files for each chromosome
+#          scaffolds_chr*.agp agp files for each chromosome in scaffolds (each block of linked contigs as a scaffold)
+#
+#
+#  Pasi Rastas, (c) 2020, pasi.rastas@gmail.com
+#
+##########################################################
+
+#if [ "$#" -ne 3 ]; then
+#    echo "At least three input parameters must be provided"
+#    exit 1
+#fi
+
+
+#parse parameters
+
+function print_usage()
+{
+echo "##########################################################"
+echo "#"
+echo "#  Lep-Anchor wrapper"
+echo "#"
+echo "#  usage: lepanchor_wrapper.sh -t threads -f ref.fasta -n num_chr -e extra_cut_site_file -c chain_file -r prox_file -p paf_file -m map_file1 -m map_file2, ... "
+echo "#"
+echo "#  download Lep-Anchor by"
+echo "#  wget https://sourceforge.net/projects/lep-anchor/files/binary%2Bcode.zip/download -O la.zip;unzip la.zip"
+echo "#"
+echo "#  Pasi Rastas, (c) 2020, pasi.rastas@gmail.com"
+echo "#"
+echo "##########################################################"
+}
+
+while getopts ":e:n:c:p:m:f:t:r:" OPTION; do
+	case ${OPTION} in
+	t)
+	THREADS=$OPTARG;;
+	n)
+	CHR=$OPTARG;;
+	c)
+	CHAIN=$OPTARG;;
+	p)
+	PAF=$OPTARG;;
+        e)
+	CUT=$OPTARG;;
+	r)
+	PROX=$OPTARG;;
+	m)
+	MAP="$MAP $OPTARG";;
+	f)
+	REF=$OPTARG;;
+	*)
+        echo "Incorrect options provided"
+        exit 1;;
+    esac
+done
+
+if [[ $MAP =~ ^$ ]];then
+	print_usage
+	echo "Please provide at least one map"
+	exit 1
+fi
+
+if [[ $REF =~ ^$ ]];then
+    if [[ ! -e "contigs.length" ]];then
+	print_usage
+	echo "Please provide either reference fasta or contigs.length file"
+	exit 1
+    fi
+fi
+
+if [[ $CHR =~ ^[0-9]+$ ]];then
+	echo "Number of chromosomes = $CHR"
+else
+	print_usage
+	echo "Please provide parameter n (number of chromosomes)"
+	exit 1
+fi
+
+if [[ $CHAIN =~ ^$ ]];then
+	echo "No chain provided"
+	CHAIN="/dev/null"
+fi
+
+if [[ $PROX =~ ^$ ]];then
+        echo "No proximity data provided"
+        PROX="/dev/null"
+fi
+
+
+if [[ $PAF =~ ^$ ]];then
+	echo "No paf provided" 
+	PAF="/dev/null"
+fi
+
+#number of threads
+if [[ $THREADS =~ ^$ ]];then
+	THREADS=8
+fi
+
+#get Lep-Anchor
+#wget https://sourceforge.net/projects/lep-anchor/files/binary%2Bcode.zip/download -O la.zip
+#unzip la.zip
+
+#where Lep-Anchor binaries are located
+LABIN=bin/
+
+#java runtime located here
+JAVA=java
+
+#parallel 
+if ! command -v "parallel"
+then
+	echo "command parallel not found, using only one thread"
+	PARALLEL=bash
+else
+	PARALLEL="parallel --jobs $THREADS"
+fi
+
+if [[ ! $REF =~ ^$ ]];then
+	echo "calculating contigs.length file..."
+	echo "gunzip -fc $REF|awk -f contigLength.awk >contigs.length"|bash
+fi
+
+
+echo "finding full haplotypes..."
+echo "gunzip -fc $CHAIN|awk -f findFullHaplotypes.awk >fullHaplotypes50.txt"|bash
+wc -l fullHaplotypes50.txt
+
+
+echo "running liftoverHaplotypes for all input maps..."
+for i in $MAP
+do
+echo "gunzip -fc $CHAIN|$JAVA -cp $LABIN LiftoverHaplotypes map=$i haplotypes=fullHaplotypes50.txt chain=- >$i.liftover"
+done|$PARALLEL
+
+#store lift overed maps to $MAPL
+for i in $MAP
+do
+	MAPL="$MAPL $i.liftover"
+done
+
+
+#make input for CleanMap
+for i in $MAP
+do
+cat $i.liftover
+done|sort -V -k 1,1 -k 2,2n >map_all_sorted.liftover
+
+
+#CleanMap
+echo "running CleanMap..."
+$JAVA -cp $LABIN CleanMap map=map_all_sorted.liftover >map_all.clean
+
+#Map2Bed
+echo "running Map2Bed..."
+$JAVA -cp $LABIN Map2Bed map=map_all.clean contigLength=contigs.length >map.bed
+
+if [[ ! $CUT =~ ^$ ]];then
+echo "adding extra cuts to map.bed..."
+awk '{print $1"\t"$2"\t"$3}' $CUT|sort -V -k 1,1 -k 2,2n|awk -f cutBed.awk map.bed - >map.bed.tmp
+awk -f cutBed_fixN.awk contigs.length map.bed.tmp >map.bed
+fi
+
+
+#find contigs not put into chromosomes
+cut -f 1 contigs.length|grep -v -w -F -f <(cut -f 2 fullHaplotypes50.txt; cut -f 1 map.bed) >not_used.txt
+
+grep -w -F -f not_used.txt contigs.length|awk -vn=$CHR '{s=$1"\t1\t"$2"\t?\t"; for (i=1;i<=n;++i) print s i}' >chr0.bed
+cat map.bed chr0.bed >map_extra.bed
+
+
+#PlaceAndOrientContigs
+echo "running PlaceAndOrientContigs (first iteration)..."
+for i in $(seq $CHR)
+do
+echo "gunzip -fc $CHAIN|$JAVA -cp $LABIN PlaceAndOrientContigs bed=map_extra.bed chromosome=$i map=$MAPL chain=- paf=$PAF proximity=$PROX keepEmptyIntervals=1 >chr$i.la 2>chr$i.la.err"
+done|$PARALLEL
+
+
+#propagate
+echo "running propagate..."
+
+awk -f propagate.awk chr*.la >tmp1.la
+awk -f propagate.awk tmp1.la >tmp2.la
+i=2
+
+while ! cmp -s "tmp$i.la" "tmp$(( $i-1 )).la" ;do
+	awk -f propagate.awk tmp$i.la >tmp$[$i+1].la
+	i=$[$i+1]
+done
+
+#create prop*.la
+awk '/^[^#]/{++d[$1 "\t" $7+0 "\t" $8+0]; data[++line]=$0}END{for (i = 1; i <= line; ++i) {$0=data[i];if (d[$1 "\t" $7+0 "\t" $8+0] == 1) fn="prop"$5".la"; else if ($5==1) fn="prop0.la"; else fn=""; if (fn != "") print $0>fn}}' tmp$i.la
+
+#use propagate2 to include possible bridge contigs as well...
+#awk -f propagate2.awk tmp$i.la|awk '(/^[^#]/ && NF>=8){++d[$1 "\t" $7+0 "\t" $8+0]; data[++line]=$0}END{for (i = 1; i <= line; ++i) {$0=data[i];if (d[$1 "\t" $7+0 "\t" $8+0] == 1) fn="prop"$5".la"; else if ($5==1) fn="prop0.la"; else fn=""; if (fn != "") print $0>fn}}'
+
+#create a new bed by combining prop[1-9]*.la and map.bed
+awk '(NR==FNR){print;c[$1]}(NR!=FNR && !($1 in c)){print $1 "\t" $7+0 "\t" $8+0"\t?\t"$5}' map.bed prop[1-9]*.la >map_prop.bed
+
+#PlaceAndOrientContigs
+echo "running PlaceAndOrientContigs (second iteration)..."
+for i in $(seq $CHR)
+do
+echo "gunzip -fc $CHAIN|$JAVA -cp $LABIN PlaceAndOrientContigs bed=map_prop.bed chromosome=$i map=$MAPL chain=- paf=$PAF proximity=$PROX keepEmptyIntervals=1 >ichr$i.la 2>ichr$i.la.err"
+done|$PARALLEL
+
+#pruning contig blocks without map support
+for i in $(seq $CHR)
+do
+        awk -f prune.awk ichr$i.la >ichr${i}_pruned.la
+done 2>pruned.la
+
+#remove overlap(s)
+awk -f removeOverlaps.awk map_prop.bed ichr*_pruned.la >iall.la
+
+#construct agp files
+for i in $(seq $CHR)
+do
+awk -vn=$i '($5==n)' iall.la|awk -vprefix="LG" -vlg=$i -f makeagp_full2.awk - >chr$i.agp
+awk -vn=$i '($5==n)' iall.la|awk -vprefix="LG" -vlg=$i -f makeagp2.awk - >scaffolds_chr$i.agp
+done
+
+#find contigs not used
+cut -f 1 contigs.length|grep -v -w -F -f <(cut -f 2 fullHaplotypes50.txt;awk '($5!="U"){print $6}' chr*.agp) >not_used_final.txt
+
+grep -F -w -f not_used_final.txt contigs.length|awk '{print $1,1,$2,1,"W",$1,1,$2,"+"}' >not_used.agp
+
+cat chr*.agp not_used.agp >REF_LA.agp
+#one could use scaffolds_chr*.agp as well instead of chr*.agp
+cat scaffolds_chr*.agp not_used.agp >REF_LA_scaffolds.agp
+
+#make final fasta
+if [[ ! $REF =~ ^$ ]];then
+	echo "constructing final fasta (REF_LA.fa.gz)..."
+	echo "gunzip -fc $REF|awk -f makefasta.awk - REF_LA.agp|gzip >REF_LA.fa.gz"|bash
+
+	echo "constructing final fasta (REF_LA_scaffolds.fa.gz)..."
+	echo "gunzip -fc $REF|awk -f makefasta.awk - REF_LA_scaffolds.agp|gzip >REF_LA_scaffolds.fa.gz"|bash
+fi
+
+#construct Marey map
+echo "constructing Marey maps... (marey*.png)"
+j=1
+for m in $MAP
+do
+	for c in $(seq $CHR)
+	do
+#	awk -vn=$c '($3==n)' $m.liftover|awk -f liftover.awk chr$c.agp -|awk -vm=$j '(/LG/ && NF>=4){if (NF==4) $5=$4;print $1"\t"$2"\t"$3"\t"m"\t"$4"\t"$5}'
+	awk -vn=$c '($3==n)' $m.liftover|awk -f liftover.awk chr$c.agp -|awk -vm=$j '(/LG/ && NF>=4){if (NF==4) {print $1"\t"$2"\t"$3"\t"m"\t"$4"\t"$4} else for (i=4;i<NF;i+=2) print $1"\t"$2"\t"$3"\t"m"\t"$(i)"\t"$(i+1)}'
+	done
+	j=$[$j + 1]
+done|gzip >marey.data.gz
+
+Rscript plot_marey.R
+
+#TODO: lepanchor_wrapper_step2.sh
+
diff --git a/software/LepAnchor/scripts/lepanchor_wrapper2.sh b/software/LepAnchor/scripts/lepanchor_wrapper2.sh
new file mode 100755
index 0000000..a5f7991
--- /dev/null
+++ b/software/LepAnchor/scripts/lepanchor_wrapper2.sh
@@ -0,0 +1,287 @@
+#!/bin/bash
+##########################################################
+#
+#  Lep-Anchor wrapper, version 2
+#
+#  usage: lepanchor_wrapper2.sh -f ref.fasta -e extra_cut_site_file -n num_chr -c chain_file -p paf_file -r prox_file -m map_file1 -m map_file2, ... 
+#
+#  output: REF_LA.fa.gz anchored reference genome
+#          REF_LA.agp   agp file describing the genome
+#          REF_LA_scaffolds.fa.gz anchored reference genome in scaffolds
+#          REF_LA_scaffolds.agp anchored reference genome in scaffolds agp file
+#          marey*.png   Marey maps for visual verification
+#
+#          chr*.agp     agp files for each chromosome
+#          scaffolds_chr*.agp agp files for each chromosome in scaffolds (each block of linked contigs as a scaffold)
+#
+#
+#  Pasi Rastas, (c) 2021, pasi.rastas@gmail.com
+#
+##########################################################
+
+#if [ "$#" -ne 3 ]; then
+#    echo "At least three input parameters must be provided"
+#    exit 1
+#fi
+
+
+#parse parameters
+
+function print_usage()
+{
+echo "##########################################################"
+echo "#"
+echo "#  Lep-Anchor wrapper2"
+echo "#"
+echo "#  usage: lepanchor_wrapper2.sh -T thread_per_run -t threads -f ref.fasta -n num_chr -e extra_cut_site_file -c chain_file -r prox_file -p paf_file -m map_file1 -m map_file2, ... "
+echo "#"
+echo "#  download Lep-Anchor by"
+echo "#  wget https://sourceforge.net/projects/lep-anchor/files/binary%2Bcode.zip/download -O la.zip;unzip la.zip"
+echo "#"
+echo "#  Pasi Rastas, (c) 2021, pasi.rastas@gmail.com"
+echo "#"
+echo "##########################################################"
+}
+
+while getopts ":e:n:c:p:m:f:t:r:T:" OPTION; do
+	case ${OPTION} in
+	T)
+	THREADS2=$OPTARG;;
+	t)
+	THREADS=$OPTARG;;
+	n)
+	CHR=$OPTARG;;
+	c)
+	CHAIN=$OPTARG;;
+	p)
+	PAF=$OPTARG;;
+        e)
+	CUT=$OPTARG;;
+	r)
+	PROX=$OPTARG;;
+	m)
+	MAP="$MAP $OPTARG";;
+	f)
+	REF=$OPTARG;;
+	*)
+        echo "Incorrect options provided"
+        exit 1;;
+    esac
+done
+
+if [[ $MAP =~ ^$ ]];then
+	print_usage
+	echo "Please provide at least one map"
+	exit 1
+fi
+
+if [[ $REF =~ ^$ ]];then
+    if [[ ! -e "contigs.length" ]];then
+	print_usage
+	echo "Please provide either reference fasta or contigs.length file"
+	exit 1
+    fi
+fi
+
+if [[ $CHR =~ ^[0-9]+$ ]];then
+	echo "Number of chromosomes = $CHR"
+else
+	print_usage
+	echo "Please provide parameter n (number of chromosomes)"
+	exit 1
+fi
+
+if [[ $CHAIN =~ ^$ ]];then
+	echo "No chain provided"
+	CHAIN="/dev/null"
+fi
+
+if [[ $PROX =~ ^$ ]];then
+        echo "No proximity data provided"
+        PROX="/dev/null"
+fi
+
+
+if [[ $PAF =~ ^$ ]];then
+	echo "No paf provided" 
+	PAF="/dev/null"
+fi
+
+#number of threads
+if [[ $THREADS =~ ^$ ]];then
+	THREADS=8
+fi
+
+if [[ $THREADS2 =~ ^$ ]];then
+	THREADS2=1
+fi
+
+#get Lep-Anchor
+#wget https://sourceforge.net/projects/lep-anchor/files/binary%2Bcode.zip/download -O la.zip
+#unzip la.zip
+
+#where Lep-Anchor binaries are located
+LABIN=bin/
+
+#java runtime located here
+JAVA=java
+
+#parallel 
+if ! command -v "parallel"
+then
+	echo "command parallel not found, using only one thread"
+	PARALLEL=bash
+else
+	PARALLEL="parallel --jobs $THREADS"
+fi
+
+if [[ ! $REF =~ ^$ ]];then
+	echo "calculating contigs.length file..."
+	echo "gunzip -fc $REF|awk -f contigLength.awk >contigs.length"|bash
+fi
+
+
+echo "finding full haplotypes..."
+echo "gunzip -fc $CHAIN|awk -f findFullHaplotypes.awk >fullHaplotypes50.txt"|bash
+wc -l fullHaplotypes50.txt
+
+
+echo "running liftoverHaplotypes for all input maps..."
+for i in $MAP
+do
+echo "gunzip -fc $CHAIN|$JAVA -cp $LABIN LiftoverHaplotypes map=$i haplotypes=fullHaplotypes50.txt chain=- >$i.liftover"
+done|$PARALLEL
+
+#store lift overed maps to $MAPL
+for i in $MAP
+do
+	MAPL="$MAPL $i.liftover"
+done
+
+#make input for CleanMap
+for i in $MAPL
+do
+cat $i
+done|sort -V -k 1,1 -k 2,2n >map_all_sorted.liftover
+
+
+#CleanMap
+echo "running CleanMap..."
+$JAVA -cp $LABIN CleanMap map=map_all_sorted.liftover >map_all.clean
+
+#Map2Bed
+echo "running Map2Bed..."
+$JAVA -cp $LABIN Map2Bed map=map_all.clean contigLength=contigs.length >map.bed
+
+if [[ ! $CUT =~ ^$ ]];then
+echo "adding extra cuts to map.bed..."
+awk '{print $1"\t"$2"\t"$3}' $CUT|sort -V -k 1,1 -k 2,2n|awk -f cutBed.awk map.bed - >map.bed.tmp
+awk -f cutBed_fixN.awk contigs.length map.bed.tmp >map.bed
+fi
+
+
+#find contigs not put into chromosomes
+cut -f 1 contigs.length|grep -v -w -F -f <(cut -f 2 fullHaplotypes50.txt; cut -f 1 map.bed) >not_used.txt
+#cut -f 1 contigs.length|grep -v -w -F -f <(cut -f 1 map.bed) >not_used.txt
+
+
+grep -w -F -f not_used.txt contigs.length|awk -vn=$CHR '{s=$1"\t1\t"$2"\t?\t"; for (i=1;i<=n;++i) print s i}' >chr0.bed
+cat map.bed chr0.bed >map_extra.bed
+
+#PlaceAndOrientContigs
+echo "running PlaceAndOrientContigs (first iteration)..."
+for i in $(seq $CHR)
+do
+echo "gunzip -fc $CHAIN|$JAVA -cp $LABIN PlaceAndOrientContigs numThreads=$THREADS2 bed=map_extra.bed chromosome=$i map=$MAPL chain=- paf=$PAF proximity=$PROX keepEmptyIntervals=0 >chr$i.la 2>chr$i.la.err"
+done|$PARALLEL
+
+#propagate4
+echo "running propagate4..."
+awk -f propagate4.awk pass=1 chr*[0-9].la pass=2 chr*[0-9].la.err|awk -f pickbed.awk - map_extra.bed >map_extra_prop.bed
+
+#PlaceAndOrientContigs
+echo "running PlaceAndOrientContigs (second iteration)..."
+for i in $(seq $CHR)
+do
+echo "gunzip -fc $CHAIN|$JAVA -cp $LABIN PlaceAndOrientContigs numThreads=$THREADS2 $(awk -f pickorientation.awk chr$i.la) bed=map_extra_prop.bed chromosome=$i map=$MAPL chain=- paf=$PAF proximity=$PROX keepEmptyIntervals=1 >ichr$i.la 2>ichr$i.la.err"
+done|$PARALLEL
+
+#propagate
+echo "running propagate..."
+
+awk -f propagate.awk ichr*.la >tmp1.la
+awk -f propagate.awk tmp1.la >tmp2.la
+i=2
+
+while ! cmp -s "tmp$i.la" "tmp$(( $i-1 )).la" ;do
+	awk -f propagate.awk tmp$i.la >tmp$[$i+1].la
+	i=$[$i+1]
+done
+
+#create prop*.la, take only contig put to uniquely to a chromosome
+#use propagate2 to include possible bridge contigs as well...
+awk -f propagate2.awk tmp$i.la|awk '(/^[^#]/ && NF>=8){++d[$1"\t"($7+0)"\t"($8+0)]; data[++line]=$0}END{for (i=1; i<=line; ++i) {$0=data[i];if (d[$1"\t"($7+0)"\t"($8+0)] == 1) {fn="prop"$5".la";print $0>fn}}}'
+
+#create a new bed by combining prop[1-9]*.la and map_extra_prop.bed
+awk '{print $1"\t"($7+0)"\t"($8+0)"\t?\t"$5}' prop[1-9]*.la|awk -f pickbed.awk - map_extra_prop.bed >map_extra_prop2.bed
+
+#third iteration could be just improveOrder
+
+#PlaceAndOrientContigs
+echo "running PlaceAndOrientContigs (third iteration)..."
+for i in $(seq $CHR)
+do
+echo "gunzip -fc $CHAIN|$JAVA -cp $LABIN PlaceAndOrientContigs numThreads=$THREADS2 $(awk -f pickorientation.awk chr$i.la) bed=map_extra_prop2.bed chromosome=$i map=$MAPL chain=- paf=$PAF proximity=$PROX keepEmptyIntervals=1 evaluateAnchoring=prop$i.la improveAnchoring=1 numRuns=1 >iichr$i.la 2>iichr$i.la.err"
+done|$PARALLEL
+
+#pruning contig blocks without map support
+for i in $(seq $CHR)
+do
+        awk -f prune.awk iichr$i.la >iichr${i}_pruned.la
+done 2>pruned.la
+
+#remove overlap(s)
+awk -f removeOverlaps.awk map_extra_prop2.bed iichr*_pruned.la >iiall.la
+
+#construct agp files
+for i in $(seq $CHR)
+do
+awk -vn=$i '($5==n)' iiall.la|awk -vprefix="LG" -vlg=$i -f makeagp_full2.awk - >chr$i.agp
+awk -vn=$i '($5==n)' iiall.la|awk -vprefix="LG" -vlg=$i -f makeagp2.awk - >scaffolds_chr$i.agp
+done
+
+#find contigs not used
+cut -f 1 contigs.length|grep -v -w -F -f <(cut -f 2 fullHaplotypes50.txt;awk '($5!="U"){print $6}' chr*.agp) >not_used_final.txt
+
+grep -F -w -f not_used_final.txt contigs.length|awk '{print $1,1,$2,1,"W",$1,1,$2,"+"}' >not_used.agp
+
+cat chr*.agp not_used.agp >REF_LA.agp
+#one could use scaffolds_chr*.agp as well instead of chr*.agp
+cat scaffolds_chr*.agp not_used.agp >REF_LA_scaffolds.agp
+
+#make final fasta
+if [[ ! $REF =~ ^$ ]];then
+	echo "constructing final fasta (REF_LA.fa.gz)..."
+	echo "gunzip -fc $REF|awk -f makefasta.awk - REF_LA.agp|gzip >REF_LA.fa.gz"|bash
+
+	echo "constructing final fasta (REF_LA_scaffolds.fa.gz)..."
+	echo "gunzip -fc $REF|awk -f makefasta.awk - REF_LA_scaffolds.agp|gzip >REF_LA_scaffolds.fa.gz"|bash
+fi
+
+#construct Marey map
+echo "constructing Marey maps... (marey*.png)"
+j=1
+for m in $MAP
+do
+	for c in $(seq $CHR)
+	do
+#	awk -vn=$c '($3==n)' $m.liftover|awk -f liftover.awk chr$c.agp -|awk -vm=$j '(/LG/ && NF>=4){if (NF==4) $5=$4;print $1"\t"$2"\t"$3"\t"m"\t"$4"\t"$5}'
+	awk -vn=$c '($3==n)' $m.liftover|awk -f liftover.awk chr$c.agp -|awk -vm=$j '(/LG/ && NF>=4){if (NF==4) {print $1"\t"$2"\t"$3"\t"m"\t"$4"\t"$4} else for (i=4;i<NF;i+=2) print $1"\t"$2"\t"$3"\t"m"\t"$(i)"\t"$(i+1)}'
+	done
+	j=$[$j + 1]
+done|gzip >marey.data.gz
+
+Rscript plot_marey.R
+
+#TODO: lepanchor_wrapper_step2.sh
+
diff --git a/software/LepAnchor/scripts/lepanchor_wrapper3.sh b/software/LepAnchor/scripts/lepanchor_wrapper3.sh
new file mode 100755
index 0000000..3df50a4
--- /dev/null
+++ b/software/LepAnchor/scripts/lepanchor_wrapper3.sh
@@ -0,0 +1,292 @@
+#!/bin/bash
+##########################################################
+#
+#  Lep-Anchor wrapper, version 3 (allopolyploid version)
+#
+#  usage: lepanchor_wrapper3.sh -f ref.fasta -e extra_cut_site_file -n num_chr -c chain_file -p paf_file -r prox_file -m map_file1 -m map_file2, ... 
+#
+#  output: REF_LA.fa.gz anchored reference genome
+#          REF_LA.agp   agp file describing the genome
+#          REF_LA_scaffolds.fa.gz anchored reference genome in scaffolds
+#          REF_LA_scaffolds.agp anchored reference genome in scaffolds agp file
+#          marey*.png   Marey maps for visual verification
+#
+#          chr*.agp     agp files for each chromosome
+#          scaffolds_chr*.agp agp files for each chromosome in scaffolds (each block of linked contigs as a scaffold)
+#
+#
+#  Pasi Rastas, (c) 2021, pasi.rastas@gmail.com
+#
+##########################################################
+
+#if [ "$#" -ne 3 ]; then
+#    echo "At least three input parameters must be provided"
+#    exit 1
+#fi
+
+
+#parse parameters
+
+function print_usage()
+{
+echo "##########################################################"
+echo "#"
+echo "#  Lep-Anchor wrapper3 (allopolyploid)"
+echo "#"
+echo "#  usage: lepanchor_wrapper3.sh -T thread_per_run -t threads -f ref.fasta -e extra_cut_site_file -n num_chr -c chain_file -r prox_file -p paf_file -m map_file1 -m map_file2, ... "
+echo "#"
+echo "#  download Lep-Anchor by"
+echo "#  wget https://sourceforge.net/projects/lep-anchor/files/binary%2Bcode.zip/download -O la.zip;unzip la.zip"
+echo "#"
+echo "#  Pasi Rastas, (c) 2021, pasi.rastas@gmail.com"
+echo "#"
+echo "##########################################################"
+}
+
+while getopts ":e:n:c:p:m:f:t:r:T:" OPTION; do
+	case ${OPTION} in
+	T)
+	THREADS2=$OPTARG;;
+	t)
+	THREADS=$OPTARG;;
+	n)
+	CHR=$OPTARG;;
+	c)
+	CHAIN=$OPTARG;;
+	p)
+	PAF=$OPTARG;;
+        e)
+	CUT=$OPTARG;;
+	r)
+	PROX=$OPTARG;;
+	m)
+	MAP="$MAP $OPTARG";;
+	f)
+	REF=$OPTARG;;
+	*)
+        echo "Incorrect options provided"
+        exit 1;;
+    esac
+done
+
+if [[ $MAP =~ ^$ ]];then
+	print_usage
+	echo "Please provide at least one map"
+	exit 1
+fi
+
+if [[ $REF =~ ^$ ]];then
+    if [[ ! -e "contigs.length" ]];then
+	print_usage
+	echo "Please provide either reference fasta or contigs.length file"
+	exit 1
+    fi
+fi
+
+if [[ $CHR =~ ^[0-9]+$ ]];then
+	echo "Number of chromosomes = $CHR"
+else
+	print_usage
+	echo "Please provide parameter n (number of chromosomes)"
+	exit 1
+fi
+
+if [[ $CHAIN =~ ^$ ]];then
+	echo "No chain provided"
+	CHAIN="/dev/null"
+fi
+
+if [[ $PROX =~ ^$ ]];then
+        echo "No proximity data provided"
+        PROX="/dev/null"
+fi
+
+
+if [[ $PAF =~ ^$ ]];then
+	echo "No paf provided" 
+	PAF="/dev/null"
+fi
+
+#number of threads
+if [[ $THREADS =~ ^$ ]];then
+	THREADS=8
+fi
+
+if [[ $THREADS2 =~ ^$ ]];then
+	THREADS2=1
+fi
+
+#get Lep-Anchor
+#wget https://sourceforge.net/projects/lep-anchor/files/binary%2Bcode.zip/download -O la.zip
+#unzip la.zip
+
+#where Lep-Anchor binaries are located
+LABIN=bin/
+
+#java runtime located here
+JAVA=java
+
+#parallel 
+if ! command -v "parallel"
+then
+	echo "command parallel not found, using only one thread"
+	PARALLEL=bash
+else
+	PARALLEL="parallel --tmpdir . --jobs $THREADS"
+fi
+
+if [[ ! $REF =~ ^$ ]];then
+	echo "calculating contigs.length file..."
+	echo "gunzip -fc $REF|awk -f contigLength.awk >contigs.length"|bash
+fi
+
+#make input for CleanMap
+for i in $MAP
+do
+cat $i
+done|sort -V -k 1,1 -k 2,2n >map_all_sorted
+
+
+#CleanMap
+echo "running CleanMap..."
+$JAVA -cp $LABIN CleanMap map=map_all_sorted >map_all.clean
+
+#Map2Bed
+echo "running Map2Bed..."
+$JAVA -cp $LABIN Map2Bed map=map_all.clean contigLength=contigs.length >map.bed
+
+
+if [[ ! $CUT =~ ^$ ]];then
+echo "adding extra cuts to map.bed..."
+awk '{print $1"\t"$2"\t"$3}' $CUT|sort -V -k 1,1 -k 2,2n|awk -f cutBed.awk map.bed - >map.bed.tmp
+awk -f cutBed_fixN.awk contigs.length map.bed.tmp >map.bed
+fi
+
+#find contigs not put into chromosomes
+cut -f 1 contigs.length|grep -v -w -F -f <(cut -f 1 map.bed) >not_used.txt
+
+grep -w -F -f not_used.txt contigs.length|awk -vn=$CHR '{s=$1"\t1\t"$2"\t?\t"; for (i=1;i<=n;++i) print s i}' >chr0.bed
+cat map.bed chr0.bed >map_extra.bed
+
+#PlaceAndOrientContigs
+echo "running PlaceAndOrientContigs (first iteration)..."
+for i in $(seq $CHR)
+do
+echo "gunzip -fc $CHAIN|$JAVA -cp $LABIN PlaceAndOrientContigs numThreads=$THREADS2 bed=map_extra.bed chromosome=$i map=$MAP chain=- paf=$PAF proximity=$PROX keepEmptyIntervals=0 >chr$i.la 2>chr$i.la.err"
+done|$PARALLEL
+
+#propagate4
+echo "running propagate4..."
+awk -f propagate4.awk pass=1 chr*[0-9].la pass=2 chr*[0-9].la.err|awk -f pickbed.awk - map_extra.bed >map_extra_prop.bed
+
+#PlaceAndOrientContigs
+echo "running PlaceAndOrientContigs (second iteration)..."
+for i in $(seq $CHR)
+do
+echo "gunzip -fc $CHAIN|$JAVA -cp $LABIN PlaceAndOrientContigs numThreads=$THREADS2 $(awk -f pickorientation.awk chr$i.la) bed=map_extra_prop.bed chromosome=$i map=$MAP chain=- paf=$PAF proximity=$PROX keepEmptyIntervals=1 >ichr$i.la 2>ichr$i.la.err"
+done|$PARALLEL
+
+#propagate
+echo "running propagate..."
+
+awk -f propagate.awk ichr*.la >tmp1.la
+awk -f propagate.awk tmp1.la >tmp2.la
+i=2
+
+while ! cmp -s "tmp$i.la" "tmp$(( $i-1 )).la" ;do
+	awk -f propagate.awk tmp$i.la >tmp$[$i+1].la
+	i=$[$i+1]
+done
+
+#create prop*.la, take only contig put to uniquely to a chromosome
+#use propagate2 to include possible bridge contigs as well...
+awk -f propagate2.awk tmp$i.la|awk '(/^[^#]/ && NF>=8){++d[$1"\t"($7+0)"\t"($8+0)]; data[++line]=$0}END{for (i=1; i<=line; ++i) {$0=data[i];if (d[$1"\t"($7+0)"\t"($8+0)] == 1) {fn="prop"$5".la";print $0>fn}}}'
+
+#create a new bed by combining prop[1-9]*.la and map_extra_prop.bed
+awk '{print $1"\t"($7+0)"\t"($8+0)"\t?\t"$5}' prop[1-9]*.la|awk -f pickbed.awk - map_extra_prop.bed >map_extra_prop2.bed
+
+#third iteration could be just improveOrder
+
+#PlaceAndOrientContigs
+echo "running PlaceAndOrientContigs (third iteration)..."
+for i in $(seq $CHR)
+do
+echo "gunzip -fc $CHAIN|$JAVA -cp $LABIN PlaceAndOrientContigs numThreads=$THREADS2 $(awk -f pickorientation.awk chr$i.la) bed=map_extra_prop2.bed chromosome=$i map=$MAP chain=- paf=$PAF proximity=$PROX keepEmptyIntervals=1 evaluateAnchoring=prop$i.la improveAnchoring=1 numRuns=1 >iichr$i.la 2>iichr$i.la.err"
+done|$PARALLEL
+
+echo "finding full haplotypes..."
+awk '($NF=="haplotype")' iichr*.err|sort -n -r|awk -vlimit=2000 '($NF=="haplotype" && ($1>=($4-$3+1-limit)/limit) && (!(($5 SUBSEP $6 SUBSEP $7) in h))){h[$2,$3,$4]; print}' >fullHaplotypes50.txt
+wc -l fullHaplotypes50.txt
+
+echo "running liftoverHaplotypes for all input maps..."
+for i in $MAP
+do
+echo "gunzip -fc $CHAIN|$JAVA -cp $LABIN LiftoverHaplotypes map=$i haplotypes=fullHaplotypes50.txt chain=- >$i.liftover"
+done|$PARALLEL
+
+#store lift overed maps to $MAPL
+for i in $MAP
+do
+        MAPL="$MAPL $i.liftover"
+done
+
+awk -f removeHaplotypes.awk map_extra_prop2.bed fullHaplotypes50.txt > map_extra_prop2_nh.bed
+
+#PlaceAndOrientContigs
+echo "running PlaceAndOrientContigs (fourth iteration)..."
+for i in $(seq $CHR)
+do
+echo "gunzip -fc $CHAIN|$JAVA -cp $LABIN PlaceAndOrientContigs numThreads=$THREADS2 $(awk -f pickorientation.awk chr$i.la) bed=map_extra_prop2_nh.bed chromosome=$i map=$MAPL chain=- paf=$PAF proximity=$PROX keepEmptyIntervals=1 evaluateAnchoring=iichr$i.la improveAnchoring=1 numRuns=1 >iiichr$i.la 2>iiichr$i.la.err"
+done|$PARALLEL
+
+
+#pruning contig blocks without map support
+for i in $(seq $CHR)
+do
+        awk -f prune.awk iiichr$i.la >iiichr${i}_pruned.la
+done 2>pruned.la
+
+#remove overlap(s)
+awk -f removeOverlaps.awk map_extra_prop2.bed iiichr*_pruned.la >iiall.la
+
+#construct agp files
+for i in $(seq $CHR)
+do
+awk -vn=$i '($5==n)' iiall.la|awk -vprefix="LG" -vlg=$i -f makeagp_full2.awk - >chr$i.agp
+awk -vn=$i '($5==n)' iiall.la|awk -vprefix="LG" -vlg=$i -f makeagp2.awk - >scaffolds_chr$i.agp
+done
+
+#find contigs not used
+cut -f 1 contigs.length|grep -v -w -F -f <(cut -f 2 fullHaplotypes50.txt;cut -f 1 iiall.la) >not_used_final.txt
+
+grep -F -w -f not_used_final.txt contigs.length|awk '{print $1,1,$2,1,"W",$1,1,$2,"+"}' >not_used.agp
+
+cat chr*.agp not_used.agp >REF_LA.agp
+#one could use scaffolds_chr*.agp as well instead of chr*.agp
+cat scaffolds_chr*.agp not_used.agp >REF_LA_scaffolds.agp
+
+#make final fasta
+if [[ ! $REF =~ ^$ ]];then
+	echo "constructing final fasta (REF_LA.fa.gz)..."
+	echo "gunzip -fc $REF|awk -f makefasta.awk - REF_LA.agp|gzip >REF_LA.fa.gz"|bash
+
+	echo "constructing final fasta (REF_LA_scaffolds.fa.gz)..."
+	echo "gunzip -fc $REF|awk -f makefasta.awk - REF_LA_scaffolds.agp|gzip >REF_LA_scaffolds.fa.gz"|bash
+fi
+
+#construct Marey map
+echo "constructing Marey maps... (marey*.png)"
+j=1
+for m in $MAPL
+do
+	for c in $(seq $CHR)
+	do
+	awk -vn=$c '($3==n)' $m|awk -f liftover.awk REF_LA.agp -|awk -vm=$j '(/LG/ && NF>=4){if (NF==4) {print $1"\t"$2"\t"$3"\t"m"\t"$4"\t"$4} else for (i=4;i<NF;i+=2) print $1"\t"$2"\t"$3"\t"m"\t"$(i)"\t"$(i+1)}'
+	done
+	j=$[$j + 1]
+done|gzip >marey.data.gz
+
+Rscript plot_marey.R
+
+#TODO: lepanchor_wrapper_step2.sh
+
diff --git a/software/LepAnchor/scripts/longread.awk b/software/LepAnchor/scripts/longread.awk
new file mode 100644
index 0000000..8a97b97
--- /dev/null
+++ b/software/LepAnchor/scripts/longread.awk
@@ -0,0 +1,72 @@
+#awk -f longread.awk aln.paf
+#aln.paf: minimap2
+#process long read alignment data for Lep-Anchor
+BEGIN{
+	#mapping quality limit
+	if (qLimit == "")
+		qLimit=1
+	FS="\t"
+	rev["+"] = "-"
+	rev["-"] = "+"
+}
+(NF>=12 && $12>=qLimit){
+	if ($1 == prevR) {
+		for (i = 1; i <= n; ++i) { 
+			processOnePair($6,$8,$9,$3,$4,$5,c[i],start[i],end[i],rstart[i],rend[i],o[i],min(q[i], $12))
+		}
+		++n
+	} else
+		n = 1
+	#print within contig part
+	print $6"\t"$8"\t"$6"\t"$9"\t++\t"$12
+	print $6"\t"$9"\t"$6"\t"$8"\t--\t"$12
+	o[n]=$5 #orientation 
+	c[n]=$6 #contig
+
+	start[n]=$8 #start
+	end[n]=$9 #end
+
+	rstart[n]=$3 #read start
+	rend[n]=$4 #read end
+	
+	q[n]=$12 #quality
+	
+	prevR = $1
+
+}
+function min(a,b){
+	if (a <= b)
+		return a
+	else
+		return b
+}
+function processOnePair(c1, start1, end1, rstart1, rend1, o1, c2, start2, end2, rstart2, rend2, o2, quality   ,lp1,lp2,overlap)
+{
+	if (rstart1 > rstart2) {
+		processOnePair(c2, start2, end2, rstart2, rend2, o2, c1, start1, end1, rstart1, rend1, o1, quality)
+		return;
+	}
+	#now rstart1 <= rstart2
+#	print "process"	
+	overlap = 0 
+	if (rend1 > rstart2)
+		overlap = rend1 - rstart2
+	overlap = int(overlap * 0.5)
+	
+	if (o1 == "+")
+		lp1 = end1 + 1 - overlap
+	else
+		lp1 = start1 + overlap
+
+	if (o2 == "+")
+		lp2 = start2 + overlap
+	else
+		lp2 = end2 + 1 - overlap
+		
+	#print both ways
+	print c1"\t"lp1"\t"c2"\t"lp2"\t"o1 o2"\t"quality
+	print c2"\t"lp2"\t"c1"\t"lp1"\t"rev[o2] rev[o1]"\t"quality
+#	print "end"	
+}
+END{
+}
diff --git a/software/LepAnchor/scripts/makeagp2.awk b/software/LepAnchor/scripts/makeagp2.awk
index 6b460f1..668df04 100644
--- a/software/LepAnchor/scripts/makeagp2.awk
+++ b/software/LepAnchor/scripts/makeagp2.awk
@@ -26,12 +26,16 @@ BEGIN{
 			pos = 0
 			n = ""
 		} else if (gapLength > 0 && ($9=="null" || ($10!="null" && substr($10, 1, 5) != "chain"))) { #do not add gap for partial haplotypes
-			print prefix lg "." suffix "\t" pos + 1 "\t" pos + gapLength "\t" ++n "\tU\t" gapLength "\tcontig\tno\tna"
-			pos += gapLength
+			if ($9 != $1 || prevO != $4 || ((($4 ~ /+/) || $4=="?") && $2 != prevE + 1) || (($4 ~ /-/) && $3 != prevS - 1)) { #do not add gap if we have cut the same contig...
+				print prefix lg "." suffix "\t" pos + 1 "\t" pos + gapLength "\t" ++n "\tU\t" gapLength "\tcontig\tno\tna"
+				pos += gapLength
+			}
 		}
 	}
 	print prefix lg "." suffix "\t" pos + 1 "\t" pos + ($3-$2+1)  "\t" ++n "\tW\t" $1 "\t" $2 "\t" $3 "\t" map[$4]
 	pos += ($3-$2+1)
 	prevO = $4
+	prevS = $2
+	prevE = $3
 }
 
diff --git a/software/LepAnchor/scripts/makeagp_full2.awk b/software/LepAnchor/scripts/makeagp_full2.awk
index 25e39de..3a8ddea 100644
--- a/software/LepAnchor/scripts/makeagp_full2.awk
+++ b/software/LepAnchor/scripts/makeagp_full2.awk
@@ -19,12 +19,16 @@ BEGIN{
 (/^[^#]/ && /^[^$]/ && $3-$2>=0){
 	if (n != "") {
 		if (gapLength > 0 && ($9=="null" || ($10!="null" && substr($10, 1, 5) != "chain"))) { #do not add gap for partial haplotypes
-			print prefix lg "\t" pos + 1 "\t" pos + gapLength "\t" ++n "\tU\t" gapLength "\tcontig\tno\tna"
-			pos += gapLength
+			if ($9 != $1 || prevO != $4 || ((($4 ~ /+/) || $4=="?") && $2 != prevE + 1) || (($4 ~ /-/) && $3 != prevS - 1)) { #do not add gap if we have cut the same contig...
+				print prefix lg "\t" pos + 1 "\t" pos + gapLength "\t" ++n "\tU\t" gapLength "\tcontig\tno\tna"
+				pos += gapLength
+			}
 		}
 	}
 	print prefix lg "\t" pos + 1 "\t" pos + ($3-$2+1)  "\t" ++n "\tW\t" $1 "\t" $2 "\t" $3 "\t" map[$4]
 	pos += ($3-$2+1)
 	prevO = $4
+	prevS = $2
+	prevE = $3
 }
 
diff --git a/software/LepAnchor/scripts/normalise.awk b/software/LepAnchor/scripts/normalise.awk
new file mode 100644
index 0000000..3192958
--- /dev/null
+++ b/software/LepAnchor/scripts/normalise.awk
@@ -0,0 +1,62 @@
+#normalise proximity data based on within bin proximity
+#awk -f normalise prox.data prox.data
+BEGIN{
+	OFS="\t"
+}
+(NR==FNR && $1==$3 && $2==$4){ #same position
+	sum2[$1,$2]+=$5
+}
+(NR!=FNR) {
+	if (!first) {
+		for (i in sum2) {
+			s = sum2[i]
+			if (max == "" || max <= s)
+				max = s
+			if (min == "" || min >= s)
+				min = s
+			sum  += s
+			sumS += s**2
+			++n
+		}
+
+		avg = sum / n
+		iavg = 100.0 / avg
+		sd = sqrt((sumS + n * avg**2 - 2 * avg * sum)/(n - 1))
+		print avg "\tsd=\t" sd "\tmin=\t" min "\tmax=\t" max  "\tn=" n > "/dev/stderr"
+		first = 1
+	}
+	s1 = sum2[$1,$2] + 0
+	s2 = sum2[$3,$4] + 0
+	$5 *= normalise(s1, s2)
+	print
+}
+function maxf(s1, s2)
+{
+	if (s1 >= s2)
+		return s1
+	return s2
+}
+function minf(s1, s2)
+{
+        if (s1 < s2)
+                return s1
+        return s2
+
+}
+#maxf
+function normalise(s1, s2)
+{
+	if (s1 <= 0.5 * avg && s2 <= 0.5 * avg)
+		return 2 * iavg
+	else
+		return 100.0 / maxf(s1, s2)
+}
+#minf
+function normalise2(s1, s2)
+{
+	if (s1 <= avg || s2 <= avg)
+		return iavg
+	else
+		return 100.0 / minf(s1, s2)
+}
+
diff --git a/software/LepAnchor/scripts/paf2chain.awk b/software/LepAnchor/scripts/paf2chain.awk
new file mode 100644
index 0000000..66f6ee6
--- /dev/null
+++ b/software/LepAnchor/scripts/paf2chain.awk
@@ -0,0 +1,52 @@
+#makes a chain file from minimap2 (-c) paf
+#minimap2 --no-long-join -c -PD -g 20000 -r 1000,40000 -k15 -w8 -A3 -B6 -O12 -E1 -s200 -z600 -N50 --min-occ-floor=100 -t 20 ref.fa ref.fa >ref-self.paf
+#awk -f chainpaf.awk ref-self.paf|awk -f sortpaf.awk| sort -T . -n -r -k 1,1 | cut -f 2- > ref-self_sorted.paf
+#awk -f paf2chain.awk rf-self_sorted.paf | gzip > paf.chain.gz
+BEGIN{
+	OFS="\t"
+	if (scale == "")
+		scale = 33
+}
+($1!=$6){
+	score = -1
+	cigar = ""
+	for (i=13; i<=NF; ++i) {
+		if ($i ~ /^AS:i:/)
+			score = substr($i, 6)+0
+		if ($i ~ /^cg:Z:/)
+			cigar = substr($i, 6)
+	}
+	if ($5 == "+")
+		print "chain\t" scale * score, $1, $2, "+", $3, $4, $6, $7, "+" ,$8, $9, NR
+	else
+		print "chain\t" scale * score, $1, $2, "+", $3, $4, $6, $7, "-" ,$7-$9, $7-$8, NR
+
+	c = cigar
+
+	d = 0
+	i = 0
+	prev = ""
+	do {
+		n = c+0
+		o = substr(c, length(n)+1, 1)
+		c = substr(c, length(n)+2)
+#		print n " " o
+		if (o == "M") {
+			if (prev != "")
+				print prev, i, d 
+			prev = n
+			i = 0
+			d = 0
+		} else if (o == "I") {
+			i+=n
+		} else if (o == "D") {
+			d+=n
+		} else {
+			print "error: cannot parse cigar operation " n " " o
+			exit
+		}
+	} while (c != "")
+	print prev
+#	print cigar
+#"\t" cigar
+}
diff --git a/software/LepAnchor/scripts/plot_marey.R b/software/LepAnchor/scripts/plot_marey.R
index 8bf6538..3cd3ced 100644
--- a/software/LepAnchor/scripts/plot_marey.R
+++ b/software/LepAnchor/scripts/plot_marey.R
@@ -1,57 +1,55 @@
-#! /usr/bin/env Rscript
-# Written by Pasi Rastas (2021)
-# modified by Pavel Dimens for Lep-Wrap (2021)
-
 library(scales)
 
-args <- commandArgs(trailingOnly = TRUE)
-
-# args[1] = path/to/marey.data.gz
-# args[2] = directory/of/chrom AGP files
-
-map <- read.table(gzfile(args[1]))
-
-basedir <- dirname(args[1])
-
-NN <- unique(map$V3)
-MM <- unique(map$V4)
-
-cl <- rainbow(length(MM))
-
-for (lg in NN) {
-    #print(lg)
-    png(paste0(basedir, "/LG.", lg ,".mareymap", ".png"), width = 1024, height = 1024)
-    ymax <- 0
-    for (m in MM) {
-        map_tmp <- map[map$V3 == lg & map$V4 == m, ]
-        ymax <- max(ymax, max(map_tmp$V5))
-    }
-
-    index <- 1
-    for (m in MM) {
-        map_tmp <- map[map$V3 == lg & map$V4 == m, ]
-        if (glm(map_tmp$V2 ~ map_tmp$V5)$coefficients[2] < 0) {
-            map_tmp$V5 <- max(map_tmp$V5) - map_tmp$V5
-            map_tmp$V6 <- max(map_tmp$V6) - map_tmp$V6
-        }
-        if (index == 1) {
-            plot(map_tmp$V2, map_tmp$V5, xlab = "Position (Mb)", ylab = "Recombination Distance (cM)", xaxt = "n", main = paste0("LG", lg), col = alpha(cl[index], 0.3), pch = 20, cex = 1.0, ylim = c(0, ymax))
-            points(map_tmp$V2, map_tmp$V6, col = alpha(cl[index], 0.3), pch = 20, cex = 1.0)
-            arrows(map_tmp$V2, map_tmp$V5, map_tmp$V2, map_tmp$V6, length = 0.0, col = alpha(cl[index], 0.5), lwd = 1.5)
-        }
-        else {
-            points(map_tmp$V2, map_tmp$V5, col = alpha(cl[index], 0.3), pch = 20, cex = 1.0)
-            points(map_tmp$V2, map_tmp$V6, col = alpha(cl[index], 0.3), pch = 20, cex = 1.0)
-            arrows(map_tmp$V2, map_tmp$V5, map_tmp$V2, map_tmp$V6, length = 0.0, col = alpha(cl[index], 0.5), lwd = 1.5)
-        }
-        index <- index + 1
-    }
-
-    agp <- read.table(paste0(normalizePath(args[2]), "/chr.", lg, ".agp"))
-    agp <- agp[agp$V1 == paste0("LG", lg) & agp$V5 == "W", c(1:3)]
-
-    segments(agp$V2, 2 * c(1:2), agp$V3, 2 * c(1:2), col = c("red", "blue"), lwd = 2, lend = 1)
-    axis(1, seq(0, 500000000, 5000000), seq(0, 500, 5))
-    segments(agp$V2, 0, agp$V2, ymax, lwd = 0.5, col = rgb(0.5, 0.5, 0.5, 0.2))
-    dev.off()
-}
\ No newline at end of file
+map=read.table(gzfile("marey.data.gz")) 
+
+NN=unique(map$V3)
+MM=unique(map$V4)
+
+cl=rainbow(length(MM))
+
+
+for(lg in NN) {
+	print(lg)
+	png(paste0("marey", lg, ".png"),width=1024,height=1024)
+	ymax = 0
+	xmax = 0
+	for (m in MM) {
+		map_tmp = map[map$V1==paste0("LG",lg) & map$V3==lg & map$V4==m,]
+		if (nrow(map_tmp) > 0) {
+			ymax = max(ymax, max(map_tmp$V5))
+			xmax = max(xmax, max(map_tmp$V2))
+		}
+	}
+
+	index = 1
+	for (m in MM) {
+		map_tmp = map[map$V1==paste0("LG",lg) & map$V3==lg & map$V4==m,]
+		if (nrow(map_tmp) > 0) {
+			orientation=glm(map_tmp$V2 ~ map_tmp$V5)$coefficients[2] 
+			if (!is.na(orientation) && orientation < 0) {
+				map_tmp$V5 = max(map_tmp$V6) - map_tmp$V5
+				map_tmp$V6 = max(map_tmp$V6) - map_tmp$V6
+			}
+		}
+		if (index == 1) {
+			plot(map_tmp$V2, map_tmp$V5, xlab="Position (Mb)",ylab="Recombination Distance",xaxt="n", main=paste0("LG", lg), col=alpha(cl[index],0.3), pch=20, cex=1.0, ylim=c(0,ymax), xlim=c(0,xmax))
+			points(map_tmp$V2, map_tmp$V6, col=alpha(cl[index],0.3), pch=20, cex=1.0)
+        		arrows(map_tmp$V2, map_tmp$V5, map_tmp$V2, map_tmp$V6, length=0.0, col=alpha(cl[index],0.5),lwd=1.5)
+		}
+		else {
+			points(map_tmp$V2, map_tmp$V5, col=alpha(cl[index],0.3), pch=20, cex=1.0)
+			points(map_tmp$V2, map_tmp$V6, col=alpha(cl[index],0.3), pch=20, cex=1.0)
+        		arrows(map_tmp$V2, map_tmp$V5, map_tmp$V2, map_tmp$V6, length=0.0, col=alpha(cl[index],0.5),lwd=1.5)
+		}
+		index = index + 1
+	}
+
+	agp <- read.table(paste0("chr", lg, ".agp"))
+	agp=agp[agp$V1==paste0("LG",lg) & agp$V5=="W",c(1:3)]
+
+	segments(agp$V2,2*c(1:2),agp$V3,2*c(1:2),col=c("red","blue"),lwd=2,lend=1)
+	axis(1,seq(0,500000000,5000000),seq(0,500,5))
+	segments(agp$V2,0,agp$V2,ymax,lwd=0.5,col=rgb(0.5,0.5,0.5,0.2))
+	dev.off()
+}
+
diff --git a/software/LepAnchor/scripts/prox10x.awk b/software/LepAnchor/scripts/prox10x.awk
new file mode 100644
index 0000000..e39c363
--- /dev/null
+++ b/software/LepAnchor/scripts/prox10x.awk
@@ -0,0 +1,50 @@
+#samtools view -f 0x40 -q 20 5148.bam|awk -f umi.awk|awk -vbin=10000 -f prox10x.awk
+#low memory version
+BEGIN{
+	if (bin == "")
+		bin = 10000
+	ibin = 1.0 / bin
+	if (minD == "")
+		minD = 2
+
+}
+function toBin(p) {
+	return 1 + bin * int((p - 1) * ibin)
+}
+{
+	p = toBin($2)
+	i = $1 "\t" p "\t" $3
+	if (!(i in used)) {
+		snpUmi[$3,++numUmi[$3]] = $1"\t"p
+		used[i]
+	}
+	if (!($1 in contigs)) {
+		print "processing contig " $1 > "/dev/stderr"
+		contigs[$1]=$2
+	}
+	else if ($2 > contigs[$1])
+		contigs[$1]=$2
+
+}
+END{
+	for (u in numUmi)
+		for (i = 1; i <= numUmi[u]; ++i)
+			umi[snpUmi[u,i], ++count[snpUmi[u,i]]] = u
+
+	for (c in contigs) {
+		for (p = 1; p <= contigs[c]; p+=bin) {
+			delete dist
+			s1 = c "\t" p
+			for (i = 1; i <= count[s1]; ++i) {
+				u = umi[s1, i]
+				for (j = 1; j <= numUmi[u]; ++j) {
+					s2 = snpUmi[u,j]
+                                	++dist[s1"\t"s2]
+				}
+			}
+		        for (d in dist)
+				if (dist[d] >= minD)
+                			print d "\t" dist[d]
+		}
+	}
+}
diff --git a/software/LepAnchor/scripts/removeHaplotypes.awk b/software/LepAnchor/scripts/removeHaplotypes.awk
index a3d6510..7867095 100644
--- a/software/LepAnchor/scripts/removeHaplotypes.awk
+++ b/software/LepAnchor/scripts/removeHaplotypes.awk
@@ -7,7 +7,7 @@
 #chr*.err are the output from Lep-Anchor error stream, e.g. java PlaceAndOrientContigs ... chromosome=X ... 2>chrX.err
 #haplotypes are put to maxChr+1
 BEGIN{
-	FS="\t"
+#	FS="\t"
 	OFS="\t"
 }
 
@@ -74,9 +74,10 @@ BEGIN{
 			bed[contig, jmax + 1] = $0
 		}
 	}
+	++numHaplotypes
 }
 END{
-	if (jmax != "")
+	if (jmax != "" || numHaplotypes == 0)
 		for (i in contigs) {
 			for (j = 1; j <= c[i]; ++j)
 				print bed[i, j]
diff --git a/software/LepAnchor/scripts/sortpaf.awk b/software/LepAnchor/scripts/sortpaf.awk
new file mode 100644
index 0000000..ee2c38a
--- /dev/null
+++ b/software/LepAnchor/scripts/sortpaf.awk
@@ -0,0 +1,7 @@
+{
+	for (j = 13; j <= NF; ++j)
+		if ($j ~ /^AS:i:/) {
+			print (substr($j, 6)+0) "\t" $0
+			break
+		}
+}
diff --git a/software/LepAnchor/scripts/umi.awk b/software/LepAnchor/scripts/umi.awk
new file mode 100644
index 0000000..45d0b15
--- /dev/null
+++ b/software/LepAnchor/scripts/umi.awk
@@ -0,0 +1,64 @@
+#samtools view -f 0x40 10x.bam|awk -f umi.awk
+#10x.bam: bwa mem -t 16 REF R1.fq.gz R2.fq.gz|samtools view -b -|samtools sort - -@4 -T tmp1 -o 10x.bam
+#get 10x barcodes from bam aligning raw reads (without cutting barcode off)
+#process 10x data for Lep-Anchor
+BEGIN{
+	#store possible cigar codes for soft clipping of barcode (16bp + 7bp), 16..24 should work
+	for (i = 16; i<=24; ++i)
+		s[i "S"]
+}
+function reverseComplement(s ,i,n,map,ret,nc) {
+        n = length(s)
+        map["A"]="T"
+        map["C"]="G"
+        map["G"]="C"
+        map["T"]="A"
+        map["Y"]="R"
+        map["R"]="Y"
+        map["S"]="S"
+        map["W"]="W"
+        map["K"]="M"
+        map["M"]="K"
+        map["B"]="V"
+        map["V"]="B"
+        map["D"]="H"
+        map["H"]="D"
+        map["N"]="N"
+
+        map["a"]="t"
+        map["c"]="g"
+        map["g"]="c"
+        map["t"]="a"
+        map["y"]="r"
+        map["r"]="y"
+        map["s"]="s"
+        map["w"]="w"
+        map["k"]="m"
+        map["m"]="k"
+        map["b"]="v"
+        map["v"]="b"
+        map["d"]="h"
+        map["h"]="d"
+        map["n"]="n"
+
+        ret = ""
+        for (i = n; i >= 1; --i) {
+                nc = map[substr(s, i, 1)]
+                if (nc == "") {
+                        print "Error, letter " substr(s, i, 1) " in fasta"
+                        exit
+                }
+                ret = ret nc
+        }
+        return ret
+}
+
+
+(and($2, 0x40)!=0){
+	if (and($2, 0x10)==0) { #+ orientation
+		if (substr($6,1,3) in s)
+			print $3"\t"$4"\t"substr($10,1,16) "\t+"
+	}
+	else if (substr($6,length($6)-2) in s) #-orientation
+		print $3"\t"$4"\t"reverseComplement(substr($10,length($10)-15)) "\t-"
+}
diff --git a/software/LepAnchor/src/CleanMap.java b/software/LepAnchor/src/CleanMap.java
deleted file mode 100644
index 887c28f..0000000
--- a/software/LepAnchor/src/CleanMap.java
+++ /dev/null
@@ -1,559 +0,0 @@
-/**
-    This file is part of Lep-Anchor.
-
-    Lep-Anchor is free software: you can redistribute it and/or modify
-    it under the terms of the GNU General Public License as published by
-    the Free Software Foundation, either version 3 of the License, or
-    (at your option) any later version.
-
-    Lep-Anchor is distributed in the hope that it will be useful,
-    but WITHOUT ANY WARRANTY; without even the implied warranty of
-    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-    GNU General Public License for more details.
-
-    You should have received a copy of the GNU General Public License
-    along with Lep-Anchor.  If not, see <http://www.gnu.org/licenses/>.
-
-	Copyright (C) 2019 Pasi Rastas, pasi.rastas@gmail.com, University of Helsinki
-	
-*/
-//User interface and implementation of ScaffoldHMM  
-import java.io.BufferedReader;
-import java.io.FileReader;
-import java.text.DecimalFormat;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.HashMap;
-
-public class CleanMap {
-
-	int markerDistance = 50;
-	int chimericDistance = 1000;
-	int numChromosomes;
-	
-	int numMarkerTypes = 1; // how many different marker types, used for having different error parameters for repeats or different maps... 
-	
-	double P_CHIMERA = 0.01;
-	//double P_ERROR = 0.01;//new double[]{0.01};
-	double P_ERROR[] = new double[]{0.01};
-	
-	int MAX_ITERATIONS = 20;
-	
-	public void setMarkerDistance(int value)
-	{
-		markerDistance = value;
-	}
-
-	public void setChimericDistance(int value)
-	{
-		chimericDistance = value;
-	}
-
-	public void setInitialValues(double p_c, double p_e)
-	{
-		for (int type = 0; type < numMarkerTypes; ++type)
-			P_ERROR[type] = p_e;
-		//P_ERROR = p_e;
-		P_CHIMERA = p_c;
-	}
-	private class CleanMarker {
-		public CleanMarker(long position, int chr, int density, int type){
-			this.position = position;
-			this.chr = chr;
-			this.density = density;
-			this.type = type;
-		}
-		
-		public long getPosition()
-		{
-			return position;
-		}
-		public int getChr()
-		{
-			return chr;
-		}
-		public int getDensity()
-		{
-			return density;
-		}
-		public int getType()
-		{
-			return type;
-		}
-		public void setDensity(int value)
-		{
-			density = value;
-		}
-		public void setType(int value)
-		{
-			type = value;
-		}
-		
-		long position;
-		int chr;
-		int density;
-		int type;
-	}
-	
-	
-	public void cleanMap(String mapFile, int annotation)
-	{
-		
-		HashMap<String, ArrayList<CleanMarker>> scaffoldMap = new HashMap<String, ArrayList<CleanMarker>>();
-		
-		HashMap<Integer,Integer> numAnnotations = new HashMap<Integer,Integer>(); 
-
-		numChromosomes = 0;
-		
-		int noAnnotation = 0;
-		
-		try {
-			BufferedReader br = new BufferedReader(new FileReader(mapFile));
-			
-			ArrayList<String> line = Input.loadTableRow(br, " \t");
-			while (line != null) {
-				if (!line.get(0).equals("CHR") && !line.get(0).equals("CHROM")) { 
-					String scaffold = line.get(0);
-					long position = InputData.myParseLong(line.get(1));
-					
-					int chr = Integer.parseInt(line.get(2));
-					if (chr > 0) {
-						if (!scaffoldMap.containsKey(scaffold))
-							scaffoldMap.put(scaffold, new ArrayList<CleanMarker>());
-						ArrayList<CleanMarker> list = scaffoldMap.get(scaffold);
-
-						//load possible annotation...
-						int annot = 0;
-						if (annotation > 0 && line.size() >= annotation) {
-							annot = Integer.parseInt(line.get(annotation - 1));
-							if (annot >= 0) { // no negative annotations... 
-								if (!numAnnotations.containsKey(annot))
-									numAnnotations.put(annot, 0);
-								numAnnotations.put(annot, numAnnotations.get(annot) + 1);
-							} else
-								++noAnnotation;
-						} else
-							++noAnnotation;
-						
-						list.add(new CleanMarker(position, chr - 1, 1, annot));
-						// code chr as 0..(c-1), negative missing
-						// density = 1, for calculating marker density...
-						numChromosomes = Math.max(numChromosomes, chr);
-					}
-				}
-				line = Input.loadTableRow(br, " \t");
-			}
-		} catch (Exception e) {
-			e.printStackTrace();
-			System.exit(-1);
-		}
-		
-		
-		int numScaffolds = scaffoldMap.keySet().size();
-//		double markerDensityScales[][] = new double[numScaffolds][]; 
-		ArrayList<ArrayList<CleanMarker>> positionsAndChrs = new ArrayList<ArrayList<CleanMarker>>();
-		ArrayList<String> scaffolds = new ArrayList<String>();
-		for (String scaffold : scaffoldMap.keySet())
-			scaffolds.add(scaffold);
-
-		int totalPads = 0;
-		for (String scaffold : scaffolds) {
-			ArrayList<CleanMarker> positionsAndChr = scaffoldMap.get(scaffold); 
-			positionsAndChrs.add(positionsAndChr);
-			int numM = positionsAndChr.size();
-//			markerDensityScales[si] = new double[numM];
-			for (int i = 1; i < numM; ++i) {
-				if (positionsAndChr.get(i - 1).getPosition() > positionsAndChr.get(i).getPosition()) {
-					System.err.println("physical positions must be increasing...");
-					System.exit(0);
-				}
-			}
-			int j = 0;
-			int k = 1;
-			for (int i = 0; i < numM; ++i) {
-				while (positionsAndChr.get(i).getPosition() - positionsAndChr.get(j).getPosition() > markerDistance)
-					++j;
-				while (k < numM && positionsAndChr.get(k).getPosition() - positionsAndChr.get(i).getPosition() <= markerDistance)
-					++k;
-				positionsAndChr.get(i).setDensity(k - j);
-				//markerDensityScales[si][i] = 1.0 / (k - j);
-			}
-
-			ArrayList<CleanMarker> positionsAndChr_padded = new ArrayList<CleanMarker>();
-			
-			for (int i = 0; i < numM; ++i) {
-				if (i > 0) {
-					long prevP = positionsAndChr.get(i - 1).getPosition();
-					long pos = positionsAndChr.get(i).getPosition();
-							
-					long numPads = (pos - prevP) / chimericDistance;
-					if (numPads >= 2)
-						totalPads += numPads - 1;
-					for (j = 1; j < numPads; ++j) {
-						double p = ((double) j) / numPads;
-						// chr missing
-						// density is 1
-						positionsAndChr_padded.add(new CleanMarker((long)(pos + p * (prevP - pos)), -1, 1, 0));
-					}
-				}
-				positionsAndChr_padded.add(positionsAndChr.get(i));
-			}
-			positionsAndChr.clear();
-			positionsAndChr.addAll(positionsAndChr_padded);
-			
-		}
-		System.err.println("Number of scaffolds = " + numScaffolds);
-		System.err.println("Number of chromosomes = " + numChromosomes);
-		
-		System.err.println("Number of padding markers = " + totalPads);
-		
-		System.err.println("Number of markers without annotation = " + noAnnotation);
-		if (numAnnotations.size() > 0) {
-			for (int key : numAnnotations.keySet()) {
-				numMarkerTypes = Math.max(numMarkerTypes, key + 1);
-				System.err.println("Number of markers with annotation " + key + " = " + numAnnotations.get(key));
-			}
-		}
-		
-		DecimalFormat df = new DecimalFormat("#0.000"); 
-		
-		for (int iterations = 0; iterations <= MAX_ITERATIONS; ++iterations) {
-			initParameters();
-			
-			double QE[][] = new double[numMarkerTypes][2];
-//			double QE[] = new double[2];
-			double QT[] = new double[2];
-			double logL = 0.0;
-			double l = 1.0;
-			for (int scaffold=0; scaffold < numScaffolds; ++scaffold) {
-				ArrayList<CleanMarker> positionsAndChr = positionsAndChrs.get(scaffold);
-//				double markerDensityScale[] = markerDensityScales[scaffold];
-				int numM = positionsAndChr.size();
-				double forward[][] = new double[numM + 1][numChromosomes];
-
-				for (int j = 0; j < numChromosomes; ++j)
-					forward[0][j] = 1.0 / numChromosomes;
-				
-				long prevPos = 0;
-				double scale[] = new double[numM + 1];
-				scale[0] = 1.0;
-
-				for (int i = 0; i < numM; ++i) {
-					CleanMarker m = positionsAndChr.get(i);
-					long pos = m.getPosition();
-					int chr = m.getChr();
-					int density = m.getDensity();
-					int type = m.getType();
-
-					double p1 = 1.0;
-					if (i > 0)
-						p1 = transition((int)(pos - prevPos));
-
-					double p2 = (1.0 - p1) / numChromosomes;
-					
-					double sum = 0.0;
-					for (int j = 0; j < numChromosomes; ++j)
-						sum += forward[i][j];
-					double sump2 = p2 * sum;
-					
-					for (int j = 0; j < numChromosomes; ++j)
-						forward[i + 1][j] = (sump2 + p1 * forward[i][j]) * emission(chr, j, density, type);
-
-					sum = 0;
-					for (int j = 0; j < numChromosomes; ++j)
-						sum += forward[i + 1][j];
-					double isum = 1.0 / sum;
-					
-					for (int j = 0; j < numChromosomes; ++j)
-						forward[i + 1][j] *= isum;
-					scale[i + 1] = isum;
-					
-					l *= sum;
-					if (l < 1e-100) {
-						logL += Math.log10(l); 
-						l = 1.0;
-					}
-
-					prevPos = pos;
-				}
-
-				//backward
-				double backward[][] = new double[numM + 1][numChromosomes];
-				for (int j = 0; j < numChromosomes; ++j)
-					backward[numM][j] = 1.0;
-
-				for (int i = numM - 1; i >= 0; --i) {
-					CleanMarker m = positionsAndChr.get(i);
-					long pos = m.getPosition();
-					int chr = m.getChr();
-					int density = m.getDensity();
-					int type = m.getType();
-					double p1 = 1.0;
-					if (i > 0) {
-							prevPos = positionsAndChr.get(i - 1).getPosition();
-							p1 = transition(pos - prevPos);
-					}
-					double p2 = (1.0 - p1) / numChromosomes;
-
-					double sum = 0.0;
-					for (int j = 0; j < numChromosomes; ++j)
-						sum += backward[i + 1][j];
-					
-					double sump2 = sum * p2;
-					
-					for (int j = 0; j < numChromosomes; ++j)
-						backward[i][j] = (sump2 + p1 * backward[i + 1][j]) * scale[i + 1] * emission(chr, j, density, type);
-				}
-				//for (int j = 0; j < numChromosomes; ++j) {
-				//	System.err.println(backward[0][j]);
-				//}
-
-				//QE
-				for (int i = 0; i < numM; ++i) {
-					CleanMarker m = positionsAndChr.get(i);
-					int chr = m.getChr();
-					int density = m.getDensity();
-					int type = m.type;
-					for (int j = 0; j < numChromosomes; ++j) {
-						if (chr < 0) {
-							//QE[0] += ?
-							//QE[1] += ?
-						} else {
-							if (chr == j)
-								QE[type][0] += backward[i + 1][j] * forward[i + 1][j] / density;
-							else
-								QE[type][1] += backward[i + 1][j] * forward[i + 1][j] / density;
-						}
-					}
-				}
-
-				//QT
-				for (int i = 0; i < numM; ++i) {
-					CleanMarker m = positionsAndChr.get(i);
-					long pos = m.getPosition();
-					if (i > 0) {
-						int chr = m.getChr();
-						int density = m.getDensity();
-						int type = m.getType();
-
-						double sum  = 0.0;
-						for (int j = 0; j < numChromosomes; ++j)
-							sum += backward[i + 1][j];
-
-						double p1 = transition(pos - prevPos);
-						double p2 = (1.0 - p1) / numChromosomes;
-						//if (ts != 1.0)
-						//	System.err.println(ts);
-						for (int j = 0; j < numChromosomes; ++j) {
-								
-							double se = scale[i + 1] * emission(chr, j, density, type);
-							QT[0] += p1 * forward[i][j] * backward[i + 1][j] * se;
-							QT[1] += p2 * forward[i][j] * sum * se; 
-						}
-						
-					}
-					prevPos = pos;
-				}
-				
-				if (iterations == MAX_ITERATIONS) {
-					// Viterbi
-					double viterbi[][] = new double[numM + 1][numChromosomes];
-					int path[][] = new int[numM + 1][numChromosomes];
-
-					for (int j = 0; j < numChromosomes; ++j)
-						viterbi[0][j] = 1.0 / numChromosomes;
-					
-					prevPos = 0;
-
-					for (int i = 0; i < numM; ++i) {
-						CleanMarker m = positionsAndChr.get(i);
-						long pos = m.getPosition();
-						int chr = m.getChr();
-						int density = m.getDensity();
-						int type = m.getType();
-
-						double p1 = 1.0;
-						if (i > 0)
-							p1 = transition((int)(pos - prevPos));
-
-						double p2 = (1.0 - p1) / numChromosomes;
-						
-						int maxj = 0;
-						for (int j = 1; j < numChromosomes; ++j)
-							if (viterbi[i][j] > viterbi[i][maxj])
-								maxj = j;
-
-						double sump2 = p2 * viterbi[i][maxj];
-						
-						for (int j = 0; j < numChromosomes; ++j) {
-							double sump1 = p1 * viterbi[i][j]; 
-							if (sump2 > sump1) {
-								viterbi[i + 1][j] = sump2 * emission(chr, j, density, type);
-								path[i + 1][j] = maxj;
-							}
-							else {
-								viterbi[i + 1][j] = sump1 * emission(chr, j, density, type);
-								path[i + 1][j] = j;
-							}
-						}
-
-						double max = 0.0;
-						for (int j = 0; j < numChromosomes; ++j)
-							max = Math.max(max, viterbi[i + 1][j]);
-						
-						double imax = 1.0 / max;
-						for (int j = 0; j < numChromosomes; ++j)
-							viterbi[i + 1][j] *= imax;
-
-						prevPos = pos;
-					}
-					//backtrack path
-					int finalPath[] = new int[numM];
-
-					int maxj = 0;
-					for (int j = 1; j < numChromosomes; ++j)
-						if (viterbi[numM][j] > viterbi[numM][maxj])
-							maxj = j;
-					
-					for (int i = numM; i >= 1; --i) {
-						finalPath[i - 1] = maxj;
-						maxj = path[i][maxj];
-					}
-					
-					StringBuilder sb = new StringBuilder();
-					for (int i = 0; i < numM; ++i) {
-						/*int maxJ = 0;
-						for (int j = 1; j < numChromosomes; ++j) {
-							if (backward[i + 1][j] * forward[i + 1][j] > backward[i + 1][maxJ] * forward[i + 1][maxJ])
-								maxJ = j;
-						}*/
-						int maxJ = finalPath[i]; // Viterbi path
-						double max2 = Double.NEGATIVE_INFINITY;
-						for (int j = 0; j < numChromosomes; ++j) {
-							if (j != maxJ) {
-								max2 = Math.max(max2, backward[i + 1][j] * forward[i + 1][j]);
-							}
-						}
-						max2 = Math.log10(backward[i + 1][maxJ] * forward[i + 1][maxJ] / max2);
-						CleanMarker m = positionsAndChr.get(i);
-						long pos = m.getPosition();
-						int chr = m.getChr();
-						if (chr >= 0) {// do not print padding markers
-							sb.append(scaffolds.get(scaffold));
-							sb.append('\t');
-							sb.append(pos);
-							sb.append('\t');
-							sb.append((maxJ + 1));
-							sb.append('\t');
-							sb.append((chr + 1));
-							sb.append('\t');
-							sb.append(df.format(max2));
-							sb.append('\n');
-							if (sb.length() >= 10000) {
-								System.out.print(sb.toString());
-								sb.setLength(0);
-							}
-							//System.out.println(scaffolds.get(scaffold) + "\t" + pos + "\t" + (maxJ + 1) + "\t" + (chr + 1) + "\t" + max2);
-						}
-					}
-					if (sb.length() > 0)
-						System.out.print(sb.toString());
-				}
-				//System.err.println(scaffolds.get(scaffold) + "\t" + logScale + "\t" + QE[0] + "\t" + QE[1]);
-			}
-			logL = logL + Math.log10(l);
-			System.err.println("logL = " + logL);
-			for (int type = 0; type < numMarkerTypes; ++type)
-				System.err.print(P_ERROR[type] + "\t");
-			System.err.println(P_CHIMERA);
-			for (int type = 0; type < numMarkerTypes; ++type)
-				P_ERROR[type] = QE[type][1] / (QE[type][0] + QE[type][1]);
-			P_CHIMERA = QT[1] / (QT[0] + QT[1]);
-		}
-	}	
-
-	private double transition(long distance)
-	{
-		return (1 - P_CHIMERA);
-	}
-
-	private double emissionTable1[][] = null; 
-	private double emissionTable2[][] = null; 
-	
-	private void initParameters()
-	{
-		if (P_ERROR.length == 1 && numMarkerTypes > 1) {
-			double oldValue = P_ERROR[0];
-			P_ERROR = new double[numMarkerTypes];
-			Arrays.fill(P_ERROR, oldValue);
-		}
-		if (emissionTable1 == null) {
-			emissionTable1 = new double[numMarkerTypes][1000];
-			emissionTable2 = new double[numMarkerTypes][1000];
-		}
-		
-		for (int type = 0; type < numMarkerTypes; ++type) {
-			double e = P_ERROR[type] / (double) (numChromosomes - 1); // P_ERROR/0 does not matter!
-			for (int i = 0; i < emissionTable1[type].length; ++i) {
-				emissionTable1[type][i] = Math.pow(e, 1.0 / i);
-				emissionTable2[type][i] = Math.pow(1.0 - P_ERROR[type], 1.0 / i);
-			}
-		}
-		
-	}
-	
-	private double emission(int chr, int state, int density, int type){
-		if (chr < 0)
-			return 1;
-
-		assert(density >= 1);
-		
-		if (density < emissionTable1[type].length) {
-			if (chr != state)
-				return emissionTable1[type][density];
-			else
-				return emissionTable2[type][density];
-			
-		}
-		return	Math.pow(emission(chr, state, 1, type), 1.0 / density); 
-	}
-
-	private static void usage()
-	{
-		System.err.println("Usage: java CleanMap map=contig_pos_map.txt [options]");
-        System.err.println("       map=file               a map file containing columns contig, position and chromosome");
-        System.err.println("       markerDistance=NUM     Minimum effective distance of markers [50]");
-        System.err.println("       chimericDistance=NUM   The default distance of markers for transition (change of chromosome) [1000]");
-        System.err.println("       initialValues=NUM NUM  Initial values for theta and epsilon [0.01 0.01]");
-
-        System.err.println("       markerAnnotation=NUM   Load marker annotation from input map column NUM");
-	}
-	
-	
-	public static void main(String args[])
-	{
-		ParameterParser pp = new ParameterParser();
-
-		String extraParameters = "";
-	    for (int i = 0; i < args.length; ++i) {
-	            extraParameters +=  " " + args[i];
-	    }
-	    
-		if (args.length == 0 || !pp.init(extraParameters)) {
-			usage();
-            System.exit(0);
-		}
-		pp.warning(new String[]{"map", "markerDistance", "chimericDistance", "initValues", "markerAnnotation"});
-		
-		
-		System.out.println("#java CleanMap" + extraParameters);
-			
-		CleanMap cm = new CleanMap();
-		cm.setChimericDistance(Integer.parseInt(pp.getValueAsString("chimericDistance", "1000")));
-		cm.setMarkerDistance(Integer.parseInt(pp.getValueAsString("markerDistance", "50")));
-		cm.setInitialValues(Double.parseDouble(pp.getValueAsString("initialValues",1,"0.01")), Double.parseDouble(pp.getValueAsString("initialValues", 2,"0.01")));
-		
-		cm.cleanMap(pp.getValueAsString("map", null), Integer.parseInt(pp.getValueAsString("markerAnnotation", "-1")));
-	}
-
-}
diff --git a/software/LepAnchor/src/ContigInterval.java b/software/LepAnchor/src/ContigInterval.java
deleted file mode 100644
index 2a84d45..0000000
--- a/software/LepAnchor/src/ContigInterval.java
+++ /dev/null
@@ -1,382 +0,0 @@
-/**
-    This file is part of Lep-Anchor.
-
-    Lep-Anchor is free software: you can redistribute it and/or modify
-    it under the terms of the GNU General Public License as published by
-    the Free Software Foundation, either version 3 of the License, or
-    (at your option) any later version.
-
-    Lep-Anchor is distributed in the hope that it will be useful,
-    but WITHOUT ANY WARRANTY; without even the implied warranty of
-    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-    GNU General Public License for more details.
-
-    You should have received a copy of the GNU General Public License
-    along with Lep-Anchor.  If not, see <http://www.gnu.org/licenses/>.
-
-	Copyright (C) 2019 Pasi Rastas, pasi.rastas@gmail.com, University of Helsinki
-	
-*/
-import java.util.*;
-
-public class ContigInterval implements Comparable<ContigInterval>{
-	private String name;
-	private long start;
-	private long end;
-	
-	private long startI[];
-	private long endI[];
-	
-	private int chr;
-	
-	private int currentOrientation = 0;
-	private int rank = 0;
-	
-	public ArrayList<ArrayList<Marker>> markers = new ArrayList<ArrayList<Marker>>();
-	
-	public void setRank(int rank) {
-		this.rank = rank;
-	}
-	
-	public String getContig()
-	{
-		return name;
-	}
-
-	public int getChromosome()
-	{
-		return chr;
-	}
-	public void setChromosome(int value)
-	{
-		chr = value;
-	}
-
-	public long getMinStart() {
-		if (startI != null)
-			return startI[0];
-		return start;
-	}
-	public long getMaxStart() {
-		if (startI != null)
-			return startI[1];
-		return start;
-	}
-
-	public long getMaxEnd() {
-		if (endI != null)
-			return endI[1];
-		return end;
-	}
-	public long getMinEnd() {
-		if (endI != null)
-			return endI[0];
-		return end;
-	}
-	
-	public long getStart() {
-		return start;
-	}
-	
-	public long[] getStartI()
-	{
-		long[] ret = new long[2];
-		ret[0] = getMinStart();
-		ret[1] = getMaxStart();
-		return ret;
-	}
-
-	public long[] getEndI()
-	{
-		if (endI == null)
-			return new long[]{end, end};
-
-		long[] ret = new long[endI.length];
-		ret[0] = getMinEnd();
-		ret[1] = getMaxEnd();
-		return ret;
-	}
-
-
-	public void setStart(long value) {
-		start = value;
-	}
-
-	public long getEnd() {
-		return end;
-	}
-
-	public void setEnd(long value) {
-		end = value;
-	}
-
-	public int getRank(){
-		return rank;
-	}
-	public void setOrientation(int o) {
-		this.currentOrientation = o;
-	}
-	public int getOrientation(){
-		return currentOrientation;
-	}
-	public void flipOrientation()
-	{
-		if (currentOrientation == 0)
-			currentOrientation = -1;
-		else 
-			currentOrientation = -currentOrientation;
-	}
-	//copy ContigInterval
-	public ContigInterval(ContigInterval c) {
-		this.name = c.name;
-		this.start = c.start;
-		this.end = c.end;
-
-		//TODO: consider Arrays.copyOf
-		this.startI = c.startI;
-		this.endI = c.endI;
-		
-		this.chr = c.chr;
-		this.currentOrientation = c.currentOrientation;
-		this.rank = c.rank;
-
-		this.markers = new ArrayList<ArrayList<Marker>>();
-		for (ArrayList<Marker> mm: c.markers) {
-			ArrayList<Marker> mm_new = new ArrayList<Marker>(); 
-			this.markers.add(mm_new);
-			for (Marker m : mm)
-				mm_new.add(new Marker(m, this));
-		}
-	}
-	
-	public ContigInterval(String name, long start, long end)
-	{
-		this.name = name;
-		this.start = start;
-		this.end = end;
-	}
-
-	public ContigInterval(String name, long start[], long end[])
-	{
-		this.name = name;
-		if (start[0] == 1)
-			this.start = 1;
-		else
-			this.start = (start[0] + start[1]) / 2;
-		
-		if (end.length > 2)
-			this.end = end[1];
-		else
-			this.end = (end[0] + end[1]) / 2;
-		startI = start;
-		endI = end;
-	}
-	
-	public boolean inside(long p)
-	{
-        if (p >= start && p <= end)
-            return true;
-        return false;
-	}
-    @Override
-    public int hashCode() {
-        return name.hashCode() + Long.hashCode(start);
-    }
-    @Override
-    public boolean equals(Object o) {
-        if (this == o) 
-        	return true;
-        if (o == null) 
-        	return false;
-        if (this.getClass() != o.getClass()) 
-        	return false;
-        
-        ContigInterval cio = (ContigInterval) o;
-        return (name.equals(cio.name) && start == cio.start);
-    }
-	@Override
-	public int compareTo(ContigInterval o) {
-		int strcmp = name.compareTo(o.name);
-		if (strcmp != 0)
-			return strcmp; 
-		
-		if (start < o.start)
-			return -1;
-		if (start > o.start)
-			return 1;
-		return 0;
-	}
-	@Override
-	public String toString()
-	{
-		return name + "\t" + start + "\t" + end;
-	}
-	public void addMap()
-	{
-		markers.add(new ArrayList<Marker>());
-	}
-	public void addMarker(Marker m, int map)
-	{
-		while (markers.size() <= map)
-			addMap();
-		markers.get(map).add(m);
-		
-		if (chr > 0 && chr != m.getChromosome()) {
-			System.err.println(this);
-			System.err.println("Error: Multiple chromosomes in one interval in bed");
-			System.exit(-1);
-		}
-		chr = m.getChromosome();
-		m.ci = this;
-	}
-	public int getNumMarkers()
-	{
-		int ret = 0;
-		for (ArrayList<Marker> m : markers)
-			ret += m.size();
-		return ret;
-	}
-	
-	public ArrayList<Marker> getMarkers(int map) {
-		if (markers.size() > map) {
-			if (currentOrientation >= 0) {			
-				ArrayList<Marker> ret = new ArrayList<Marker>();
-				ret.addAll(markers.get(map));
-				return ret;
-			}
-			else {
-				ArrayList<Marker> ret = new ArrayList<Marker>();
-				ret.addAll(markers.get(map));
-				Collections.reverse(ret);
-				return ret;
-			}
-		} else
-			return new ArrayList<Marker>();
-	}
-	public ArrayList<Marker> getMarkersReverse(int map) {
-		return getMarkers(map, (currentOrientation >= 0) ? -1 : 0);
-	}
-
-	
-	public ArrayList<Marker> getMarkers(int map, int orientation) {
-		if (markers.size() > map) {
-			if (orientation == 0) {		
-				ArrayList<Marker> ret = new ArrayList<Marker>();
-				ret.addAll(markers.get(map));
-				return ret;
-			}
-			else {
-				ArrayList<Marker> ret = new ArrayList<Marker>();
-				ret.addAll(markers.get(map));
-				Collections.reverse(ret);
-				return ret;
-			}
-		} else
-			return new ArrayList<Marker>();
-	}
-
-	public Marker getMarker(int map, int index) {
-		return markers.get(map).get(index);
-	}
-
-	//calculate gap length for
-	//  ci in orientation -> c2 with alignment [astart to aend]
-	public long calculateGapLength(int orientation, long astart, long aend){
-		long l = 0;
-		if (orientation == 0) { // + orientation
-			if (astart > getEnd())
-				l = astart - getEnd() - 1;
-			else if (aend < getEnd())
-				l = getEnd() - aend;
-		} else { // - orientation
-			if (aend < getStart())
-				l = getStart() - aend - 1;
-			else if (astart > getStart())
-				l = astart - getStart();
-		}
-		return l;
-	}
-
-	//ci is the haplotype, calculate how much of it does not align...
-	public long calculateGapLengthHaplotype(long astart, long aend){
-
-		long g1 = Math.max(0,  astart - getStart()); // getStart()
-		long g2 = Math.max(0,  getEnd() - aend); // getEnd()
-		
-		return g1 + g2; 
-	}
-	
-	//split ContigInterval (this) to start..position and position+1,...end 
-	public ContigInterval[] splitContigInterval(long position[])
-	{
-		if (position[0] < start || position[1] >= end) // no need to split
-			return new ContigInterval[]{this};
-
-		long pos = (position[0] + position[1]) / 2;
-		
-		ContigInterval c1 = new ContigInterval(name, new long[]{getMinStart(), getMaxStart()}, position);
-		ContigInterval c2 = new ContigInterval(name, new long[]{position[0] + 1, position[1] + 1}, new long[]{getMinEnd(), getMaxEnd()});
-		int numMaps = markers.size();
-		
-		for (int map = 0; map < numMaps; ++map) {
-			ArrayList<Marker> list = markers.get(map);
-			for (Marker m : list) {
-				if (m.getPosition() > pos) {
-					Marker mNew = new Marker(m);
-					mNew.ci = c2;
-					c2.addMarker(mNew, map);
-				} else {
-					Marker mNew = new Marker(m);
-					mNew.ci = c1;
-					c1.addMarker(mNew, map);
-				}
-			}
-		}
-		if (c1.getNumMarkers() == 0 || c2.getNumMarkers() == 0)
-			return new ContigInterval[]{this};
-		
-		return new ContigInterval[]{c1, c2};
-	}
-	public ContigInterval[] splitContigInterval(long position1[], long position2[], long position3[])
-	{
-		if (position1[0] > position2[0]) {
-			long tmp[] = position1;
-			position1 = position2;
-			position2 = tmp;
-		}
-		if (position1[0] > position3[0]) {
-			long tmp[] = position1;
-			position1 = position3;
-			position3 = tmp;
-		}
-		ContigInterval sp1[] = splitContigInterval(position2, position3);
-		ContigInterval sp2[] = sp1[0].splitContigInterval(position1);
-		ArrayList<ContigInterval> list = new ArrayList<ContigInterval>();
-		for (int i = 0; i < sp2.length; ++i)
-			list.add(sp2[i]);
-		for (int i = 1; i < sp1.length; ++i)
-			list.add(sp1[i]);
-		ContigInterval s[] = new ContigInterval[list.size()]; 
-		return list.toArray(s);
-			
-	}
-
-	public ContigInterval[] splitContigInterval(long position1[], long position2[])
-	{
-		if (position1[0] > position2[0]) {
-			long tmp[] = position1;
-			position1 = position2;
-			position2 = tmp;
-		}
-		ContigInterval sp1[] = splitContigInterval(position1);
-		if (sp1.length == 2) {
-			ContigInterval sp2[] = sp1[1].splitContigInterval(position2);
-			if (sp2.length == 2)
-				return new ContigInterval[]{sp1[0], sp2[0], sp2[1]};
-			else
-				return sp1;
-		} else
-			return splitContigInterval(position2);
-	}
-	
-}
diff --git a/software/LepAnchor/src/CoverageAnalyser.java b/software/LepAnchor/src/CoverageAnalyser.java
deleted file mode 100644
index 40368a0..0000000
--- a/software/LepAnchor/src/CoverageAnalyser.java
+++ /dev/null
@@ -1,420 +0,0 @@
-import java.io.BufferedReader;
-import java.io.FileReader;
-import java.io.InputStreamReader;
-import java.util.ArrayList;
-import java.util.HashMap;
-
-public class CoverageAnalyser {
-
-	// private HashMap<String, ArrayList<Long>> posDepth = new HashMap<String,
-	// ArrayList<Long>>();
-	private int column = 2;
-	private int numCategories = 2;
-	
-	private double normalDepth = 100.0;
-	
-	private int maxDepth = 1000;
-	private double zetaK = 1.5;
-	
-	private int MAX_ITERATIONS = 100;
-
-	private long[] count = null;
-
-	private double[] freq = new double[3];
-
-	boolean findNormal = false;
-
-	// private ArrayList<Double> variance = new ArrayList<Double>();
-
-	/*
-	 * public void loadDepth(String fn) { try { BufferedReader br = null; if
-	 * (fn.equals("-")) br = new BufferedReader(new
-	 * InputStreamReader(System.in)); else br = new BufferedReader(new
-	 * FileReader(fn));
-	 * 
-	 * do { ArrayList<String> row = Input.loadTableRow(br, "[\t ]"); if (row ==
-	 * null) break; if (row.size() <= column) {
-	 * System.err.println("Warning: skipping " + row); continue; }
-	 * 
-	 * String contig = row.get(0); ArrayList<Long> list = posDepth.get(contig);
-	 * if (list == null) { list = new ArrayList<Long>(); posDepth.put(contig,
-	 * list); } //only store last position with same depth... int lsize =
-	 * list.size(); long cov = 0; if (lsize == 0) { cov =
-	 * Long.parseLong(row.get(1)) list.add(cov); // genomic position
-	 * list.add(Long.parseLong(row.get(column))); // depth } else { long lastcov
-	 * = list.get(lsize - 1); long cov = Long.parseLong(row.get(column)); if
-	 * (lastcov == cov) { list.set(lsize - 2, Long.parseLong(row.get(1))); //
-	 * update position } else { list.add(Long.parseLong(row.get(1))); // genomic
-	 * position list.add(cov); // depth } } } while (true); br.close(); } catch
-	 * (Exception e) { e.printStackTrace(); System.err.println("Error in file "
-	 * + fn); System.exit(-1); } }
-	 */
-
-	public void loadDepth(String fn) {
-		count = new long[maxDepth + 2];
-		try {
-			BufferedReader br = null;
-			if (fn.equals("-"))
-				br = new BufferedReader(new InputStreamReader(System.in));
-			else
-				br = new BufferedReader(new FileReader(fn));
-
-			do {
-				ArrayList<String> row = Input.loadTableRow(br, "[\t ]");
-				if (row == null)
-					break;
-				if (row.size() <= column) {
-					System.err.println("Warning: skipping " + row);
-					continue;
-				}
-				int depth = Integer.parseInt(row.get(column));
-				if (depth > maxDepth)
-					depth = maxDepth + 1;
-				++count[depth];
-			} while (true);
-			br.close();
-		} catch (Exception e) {
-			e.printStackTrace();
-			System.err.println("Error in file " + fn);
-			System.exit(-1);
-		}
-	}
-
-	public static final double isqrtPI = 1.0 / Math.sqrt(Math.PI);
-	public static final double isqrt2 = 1.0 / Math.sqrt(2.0);
-
-	private class Gaussian {
-		private double mean;
-		private double stdev;
-		private double istdev;
-		private double istdev2sp;
-		private double logIstdev2sp;
-
-		// Misc.i2sqrtPI = 1.0 / Math.sqrt(2.0 * Math.PI);
-
-		public Gaussian(double mean, double stdev) {
-			istdev = isqrt2 / stdev;
-			istdev2sp = istdev * isqrtPI;
-			logIstdev2sp = Math.log(istdev2sp);
-			this.mean = mean;
-			this.stdev = stdev;
-		}
-		public double getMean()
-		{
-			return mean;
-		}
-
-		public double getStdev()
-		{
-			return stdev;
-		}
-
-		public double density(double x) {
-			double tmp = (x - mean) * istdev;
-			return istdev2sp * Math.exp(-tmp * tmp);
-		}
-
-		public double logDensity(double x) {
-			double tmp = (x - mean) * istdev;
-			return logIstdev2sp - tmp * tmp;
-		}
-	}
-	
-	//distribution zeta - 1  
-	private class Zeta {
-		//double k;
-		int max;
-		ArrayList<Double> d = new ArrayList<Double>();
-		//ArrayList<Double> ld = new ArrayList<Double>();
-		public Zeta(double k, int max) {
-			//this.k = k;
-			this.max = max;
-			double sum = 0.0;
-			for (int i = 0; i <= max; ++i) {
-				double p = Math.pow(i + 1, -k);
-				sum += p;
-				d.add(p);
-			}
-			double iSum = 1.0 / sum;
-			for (int i = 0; i <= max; ++i)
-				d.set(i, d.get(i) * iSum);
-		}
-		public double density(int x) {
-			if (x > max)
-				return 0.0;
-			return d.get(x);
-		}
-		//public double logDensity(int x) {
-		//	return ld.get(x);
-		//}
-	}
-	
-	private double likelihood(boolean verbose) {
-		Gaussian g[] = new Gaussian[numCategories];
-
-		/*double rate1 = count[0] / (double) count[1];
-		double rate2 = count[0] / (double) count[2];
-		double rate3 = count[0] / (double) count[3];
-		double k1 = Math.log(rate1) / Math.log(2.0);
-		double k2 = Math.log(rate2) / Math.log(3.0);
-		double k3 = Math.log(rate3) / Math.log(4.0);
-		k = Math.min(k1, k2, k3);
-		if (k > 1.0)
-			;
-		else k = 1.0;*/
-		//double k = 1.2;
-		
-		Zeta z = new Zeta(zetaK, maxDepth);
-		if (verbose)
-			System.err.println("Zeta parameter " + zetaK);
-		
-		{ // Initialisation
-			for (int j = 0; j < numCategories; ++j) {
-				double mean = (normalDepth * (j + 1)) / (double) numCategories;
-				g[j] = new Gaussian(mean, Math.sqrt(normalDepth) * Math.exp(2.0 * Math.random() - 1.0));
-			}
-			double sum = 0.0;
-			for (int j = 0; j <= numCategories; ++j) {
-				double r = Math.random(); 
-				freq[j] = r;
-				sum += r;
-			}
-			double iSum = 1.0 / sum;
-			for (int j = 0; j <= numCategories; ++j)
-				freq[j] *= iSum;
-		}
-
-		double d[] = new double[numCategories + 1];
-
-		double likelihood = 0.0;
-		for (int iteration = 0; iteration < MAX_ITERATIONS; ++iteration) {
-			double qFreq[] = new double[numCategories + 1];
-			double qVar[] = new double[numCategories];
-			double qSum[] = new double[numCategories];
-
-			//System.err.println(freq[0] + "\t" + freq[1] + "\t" + freq[2]);
-			likelihood = 0.0;
-			for (int i = 0; i <= maxDepth; ++i) {
-
-				double sum = 0.0;
-				for (int j = 0; j <= numCategories; ++j) {
-					double p = 0.0;
-					if (j < numCategories)
-						p = g[j].density(i) * freq[j];
-					else 
-						p = z.density(i) * freq[j];
-					d[j] = p;
-					sum += p;
-				}
-				//System.err.println("Sum " + sum);
-				double iSum = 1.0 / sum;
-				
-				for (int j = 0; j <= numCategories; ++j) {
-					double q = d[j] * iSum * count[i];
-					qFreq[j] += q;
-					if (j < numCategories) {
-						double diff = (i - g[j].mean);
-						qVar[j] += q * diff * diff;
-						qSum[j] += q;
-					}
-				}
-				likelihood += Math.log(sum) * count[i];
-			}
-			double sum = 0.0;
-			for (int j = 0; j <= numCategories; ++j)
-				sum += qFreq[j];
-			//for (int j = 0; j <= numCategories; ++j)
-			//	if (qFreq[j] < 0.1 * sum)
-			//		qFreq[j] = 0.1 * sum;
-			//sum = 0.0;
-			//for (int j = 0; j <= numCategories; ++j)
-			//	sum += qFreq[j];
-			
-			double iSum = 1.0 / sum;
-			for (int j = 0; j <= numCategories; ++j)
-				freq[j] = qFreq[j] * iSum;
-
-			//variance in gaussians must be non-decreasing 
-			for (int j = numCategories - 1; j >= 1; --j) {
-				if (qVar[j] * qSum[j - 1] < qVar[j - 1] * qSum[j]) {
-					double qs = qSum[j] + qSum[j - 1];
-					double qv = qVar[j] + qVar[j - 1];
-					qSum[j] = qs;
-					qSum[j - 1] = qs;
-					qVar[j] = qv;
-					qVar[j - 1] = qv;
-				}
-			}
-			for (int j = 0; j < numCategories; ++j) {
-				double sdev = Math.sqrt(qVar[j] / qSum[j]);
-				if (sdev < 1.0)
-					sdev = 1.0;
-				//System.err.println(freq[j] + "\t" + sdev);
-				g[j] = new Gaussian((normalDepth * (j + 1)) / (double) numCategories, sdev);
-				//System.err.println("mean=" + g[j].mean);
-			}
-			//System.err.println(freq[numCategories]);
-			// System.err.println(Math.sqrt(iSum * qVar[0]) + "\t" +
-			// Math.sqrt(iSum * qVar[1]) + "\t" + Math.sqrt(iSum * qVar[2]));
-			if (verbose)
-				System.err.println("logL=" + likelihood);
-		}
-		long totalCount = 0;
-		for (int i = 0; i <= maxDepth; ++i) {
-			totalCount += count[i];
-		}
-		if (verbose)
-			System.err.println(freq[0] + "\t" + freq[1] + "\t" + g[0].getStdev() + "\t" + g[1].getStdev());
-
-		for (int i = 0; i <= maxDepth; ++i) {
-			
-			double tmp[] = new double[numCategories + 2];
-			for (int j = 0; j < numCategories; ++j)
-				tmp[j] = g[j].density(i);
-
-			//split zeta distribution to 0 (<=normalDepht/numCategories) and repeat (>=normalDepht)
-			double zf = z.density(i);
-			if (i <= g[0].mean)
-				tmp[numCategories] = zf;
-			else if (i >= g[numCategories - 1].mean)
-				tmp[numCategories + 1] = zf;
-			else {
-				double t = (i - g[0].mean) / (g[numCategories - 1].mean - g[0].mean);
-				tmp[numCategories] = zf * (1.0 - t);
-				tmp[numCategories + 1] = zf * t;
-			}
-
-			double sum = 0.0;
-			double max = 0.0;
-			for (int j = 0; j <= numCategories + 1; ++j) {
-				double p = tmp[j] * freq[Math.min(j, numCategories)];
-				sum += p;
-				max = Math.max(max, tmp[j]);
-			}
-			if (verbose) {
-				System.out.print(i + "\t" + count[i] + "\t" + (totalCount * sum) );
-			
-				double iMax = 1.0 / max;
-				System.out.print("\t" + tmp[numCategories] * iMax);
-				for (int j = 0; j <= numCategories + 1; ++j)
-					if (j != numCategories)
-						System.out.print("\t" + tmp[j] * iMax);
-				
-				System.out.println();
-			}
-		}
-
-		
-		//System.err.println(num[0] + "\t" + num[1] + "\t" + num[2] + "\t" + num[3]);
-		return likelihood;
-	}
-
-	
-	public void analyse() {
-		if (findNormal) {
-			// Find normalDepth and other parameters...
-			System.err.println("Estimating normal depth parameter...");
-			double maxL = Double.NEGATIVE_INFINITY;
-			int maxNd = 1;
-			for (int nd = 1; nd + nd <= maxDepth; ++nd) {
-				normalDepth = nd;
-				double ll = likelihood(false);
-				if (ll > maxL) {
-					System.err.println(nd + "\t" + ll + "\t*");
-					maxL = ll;
-					maxNd = nd;
-				} else
-					System.err.println(nd + "\t" + ll);
-			}
-			normalDepth = maxNd;
-			System.err.println("Value " + maxNd + " chosen for normal depth");
-		}
-		likelihood(true);
-	}
-
-	public void setNumCategories(int value) {
-		numCategories = value;
-		freq = new double[numCategories + 1];
-
-
-		for (int i = 0; i <= numCategories; ++i)
-			freq[i] = Math.random();
-	}
-
-	public void setNormalDepth(double value) {
-		normalDepth = value;
-		maxDepth = (int)(3 * value + 0.99);
-		setNumCategories(numCategories);
-	}
-
-	public void setColumn(int value) {
-		column = value;
-	}
-
-	public void setMaxDepth(int value) {
-		maxDepth = value;
-		findNormal = true;
-	}
-
-	public void setZeta(double value) {
-		zetaK = value;
-	}
-
-	public static void usageInfo() {
-//		pp.warning(new String[] { "depth", "numCategories", "normalDepth",
-//				"column", "sample", "maxDepth", "zeta"});
-		System.err.println("Usage: java CoverageAnalyser depth=depth.txt [parameters] ");
-		System.err.println("       depth=file           output from samtools -a depth");
-		System.err.println("       numCategories=NUM    the ploidy [2]");
-		System.err.println("       normalDepth=NUM      the normal depth [not set, ML value searched]");
-		System.err.println("       maxDepthDepth=NUM    search normalDepth between 1..NUM, applies only when normalDepth is not set [1000]");
-        System.err.println("       column=NUM           Take column NUM from depth file [3]");
-        System.err.println("       zeta=NUM             Zeta distribution parameter [1.5]");
-		
-		System.exit(0);
-	}
-
-	public static void main(String args[]) {
-		ParameterParser pp = new ParameterParser();
-
-		String extraParameters = "";
-		for (int i = 0; i < args.length; ++i) {
-			extraParameters += " " + args[i];
-		}
-		if (args.length == 0 || !pp.init(extraParameters)) {
-			usageInfo();
-		}
-		System.out.println("#java CoverageAnalyser " + extraParameters);
-		
-		pp.warning(new String[] { "depth", "numCategories", "normalDepth",
-				"column", "maxDepth", "zeta"});
-
-		String depthFile = pp.getValueAsString("depth", null);
-		if (depthFile == null)
-			usageInfo();
-
-		CoverageAnalyser ca = new CoverageAnalyser();
-		int column = Integer.parseInt(pp.getValueAsString("column", "3"));
-		ca.setColumn(column - 1);
-		ca.setNumCategories(Integer.parseInt(pp.getValueAsString(
-				"numCategories", "2")));
-
-		String normalD = pp.getValueAsString("normalDepth", null);
-		if (normalD != null) {
-			ca.setNormalDepth(Double.parseDouble(normalD));
-			//ca.setMaxDepth();
-			String md = pp.getValueAsString("maxDepth", null);
-			if (md != null)
-				ca.setMaxDepth(Integer.parseInt(md));
-		}
-		else
-			ca.setMaxDepth(Integer.parseInt(pp.getValueAsString("maxDepth",
-					"1000")));
-
-		ca.setZeta(Double.parseDouble(pp.getValueAsString("zeta", "1.5")));
-		
-		ca.loadDepth(depthFile);
-		ca.analyse();
-
-	}
-}
diff --git a/software/LepAnchor/src/CoverageHMM.java b/software/LepAnchor/src/CoverageHMM.java
deleted file mode 100644
index a03e111..0000000
--- a/software/LepAnchor/src/CoverageHMM.java
+++ /dev/null
@@ -1,571 +0,0 @@
-/**
-    This file is part of Lep-Anchor.
-
-    Lep-Anchor is free software: you can redistribute it and/or modify
-    it under the terms of the GNU General Public License as published by
-    the Free Software Foundation, either version 3 of the License, or
-    (at your option) any later version.
-
-    Lep-Anchor is distributed in the hope that it will be useful,
-    but WITHOUT ANY WARRANTY; without even the implied warranty of
-    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-    GNU General Public License for more details.
-
-    You should have received a copy of the GNU General Public License
-    along with Lep-Anchor.  If not, see <http://www.gnu.org/licenses/>.
-
-	Copyright (C) 2019 Pasi Rastas, pasi.rastas@gmail.com, University of Helsinki
-	
-*/
-//User interface and implementation of ScaffoldHMM  
-import java.io.BufferedReader;
-import java.io.FileReader;
-import java.io.InputStreamReader;
-import java.text.DecimalFormat;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collections;
-import java.util.HashMap;
-
-public class CoverageHMM {
-
-	private int column = 2;
-	private int numMixture = 0;
-	private int MAX_ITERATIONS = 1000;
-	private int numScaffolds;
-	
-	private double minProb = 0.001;
-	private double scale = 0.001;
-	private double sample = 0.1;
-	
-	private ArrayList<String> scaffolds = new ArrayList<String>();
-	
-	public void setColumn(int value) 
-	{
-		column = value;
-	}
-
-	public void setMinProb(double value) 
-	{
-		minProb = value;
-	}
-
-	public void setSample(double value) 
-	{
-		sample = value;
-	}
-
-	public void setScale(double value) 
-	{
-		scale = value;
-	}
-
-	private ArrayList<double[]> mixture = new ArrayList<double[]>();
-	private HashMap<String, ArrayList<Integer>> scaffoldMap = new HashMap<String, ArrayList<Integer>>();
-	
-	public void loadMixture(String mixtureFile)
-	{
-		numMixture = 0;
-		try {
-			BufferedReader br = new BufferedReader(new FileReader(mixtureFile));
-			
-			ArrayList<String> line = Input.loadTableRow(br, " \t");
-			while (line != null) {
-				if (numMixture == 0)
-					numMixture = line.size() - 3;
-				else
-					if (numMixture != line.size() - 3) {
-						System.err.println("Error: Different number of columns in the input");
-						System.exit(-1);
-					}
-				int value = Integer.parseInt(line.get(0));
-				if (mixture.size() != value) {
-					System.err.println("Error: Incorrect mixture file");
-					System.exit(-1);
-				}
-				double m[] = new double[numMixture];
-				for (int i = 0; i < numMixture; ++i)
-					m[i] = Double.parseDouble(line.get(i + 3));
-				mixture.add(m);
-				line = Input.loadTableRow(br, " \t");
-			}
-		} catch (Exception e) {
-			e.printStackTrace();
-			System.exit(-1);
-		}
-	}
-	
-	
-	public void loadDepth(String depthFile)
-	{
-		try {
-			BufferedReader br = null;
-			if (depthFile.equals("-"))	
-				br = new BufferedReader(new InputStreamReader(System.in));
-			else
-				br = new BufferedReader(new FileReader(depthFile));
-			
-			ArrayList<String> line = Input.loadTableRow(br, " \t");
-			double pick = 0.0;
-			while (line != null) {
-				if (line.size() <= column) {
-					System.err.println("Warning: skipping " + line); 
-					continue; 
-				}
-				pick += sample;
-				if (pick >= 1.0) {
-					pick -= 1.0;
-					String scaffold = line.get(0);
-					long position = Long.parseLong(line.get(1));
-					if (position > 0xffffffffl) {
-						System.err.println("Error: Too long scaffold");
-						System.exit(-1);
-					}
-					int cov = Integer.parseInt(line.get(column));
-	
-					if (!scaffoldMap.containsKey(scaffold))
-						scaffoldMap.put(scaffold, new ArrayList<Integer>());
-					ArrayList<Integer> list = scaffoldMap.get(scaffold);
-					list.add((int) position);
-					list.add(cov);
-				}
-				line = Input.loadTableRow(br, " \t");
-			}
-		} catch (Exception e) {
-			e.printStackTrace();
-			System.exit(-1);
-		}
-		
-		numScaffolds = scaffoldMap.keySet().size();
-//		double markerDensityScales[][] = new double[numScaffolds][]; 
-		scaffolds = new ArrayList<String>();
-		for (String scaffold : scaffoldMap.keySet())
-			scaffolds.add(scaffold);
-
-		for (String scaffold : scaffolds) {
-			ArrayList<Integer> positionsAndCov = scaffoldMap.get(scaffold); 
-			int numM = positionsAndCov.size();
-			for (int i = 2; i < numM; i+=2) {
-				if (positionsAndCov.get(i - 2) > positionsAndCov.get(i)) {
-					System.err.println("physical positions must be increasing...");
-					System.exit(0);
-				}
-			}
-		}
-		System.err.println("Number of scaffolds = " + numScaffolds);
-	}
-	
-	public void hmm()
-	{
-		DecimalFormat df = new DecimalFormat("#0.000"); 
-		
-		for (double m[] : mixture)
-			for (int i = 0; i < numMixture; ++i) {
-				double v = m[i];
-				if (v < minProb)
-					m[i] = minProb;
-				m[i] = Math.pow(m[i], scale);
-			}
-		
-		//Init transition
-		double t[][] = new double[numMixture][numMixture];
-	
-		for (double tmp[] : t)
-			Arrays.fill(tmp, 1.0 / numMixture);
-		
-		for (int i = 0; i < numMixture; ++i) {
-			double sum = 0.0;
-			for (int j = 0; j < numMixture; ++j) {
-				double r = (i == j) ? 1.0 : 0.1 * scale * Math.random();
-				sum += r;
-				t[i][j] = r;
-			}
-			double iSum = 1.0 / sum;
-			for (int j = 0; j < numMixture; ++j)
-				t[i][j] *= iSum;
-		}
-
-		boolean converge = false;
-		double oldLogL = Double.NEGATIVE_INFINITY;
-		for (int iterations = 0; iterations <= MAX_ITERATIONS; ++iterations) {			
-			int maxCount = mixture.size() - 1;
-			double QT[][] = new double[numMixture][numMixture];
-			double logL = 0.0;
-			double l = 1.0;
-			for (int scaffold=0; scaffold < numScaffolds; ++scaffold) {
-				String scaffoldS = scaffolds.get(scaffold);
-				ArrayList<Integer> positionsAndCov = scaffoldMap.get(scaffoldS);
-
-				int numM = positionsAndCov.size() / 2;
-				double forward[][] = new double[numM + 1][numMixture];
-				double scale[] = new double[numM + 1];
-				scale[0] = 1.0;
-				
-				double iM = 1.0 / numMixture;
-				for (int i = 0; i < numMixture; ++i)
-					forward[0][i] = iM;
-
-				for (int p = 0; p < numM; ++p) {
-					int cov = positionsAndCov.get(p + p + 1);
-					if (cov >= maxCount)
-						cov = maxCount;
-					
-					double m[] = mixture.get(cov); 
-					
-					for (int j = 0; j < numMixture; ++j) {
-						double fp1j = 0.0;
-						double f_[] = forward[p];
-						for (int i = 0; i < numMixture; ++i)
-							fp1j += f_[i] * t[i][j];
-						forward[p + 1][j] = fp1j * m[j]; 
-					}
-					
-					
-					double sum = 0.0;
-					for (int j = 0; j < numMixture; ++j)
-						sum += forward[p + 1][j];
-					double isum = 1.0 / sum;
-					
-					for (int j = 0; j < numMixture; ++j)
-						forward[p + 1][j] *= isum;
-					scale[p + 1] = isum;
-					
-					l *= sum;
-					if (l < 1e-100) {
-						logL += Math.log10(l); 
-						l = 1.0;
-					}
-				}
-				double backward[][] = new double[numM + 1][numMixture];
-				for (int j = 0; j < numMixture; ++j)
-					backward[numM][j] = 1.0;
-
-				for (int p = numM - 1; p >= 0; --p) {
-					int cov = positionsAndCov.get(p + p + 1);
-					if (cov >= maxCount)
-						cov = maxCount;
-					
-					double m[] = mixture.get(cov);
-
-					
-					for (int j = 0; j < numMixture; ++j) {
-						double tmp = backward[p + 1][j] * m[j] * scale[p + 1];
-						for (int i = 0; i < numMixture; ++i)
-							backward[p][i] += t[i][j] * tmp;
-					}
-				}
-				//double sum = 0.0;
-				//for (int j = 0; j < numMixture; ++j)
-				//	sum += backward[1][j] * forward[1][j];
-				//System.err.println(sum);
-				
-				if (iterations == MAX_ITERATIONS || converge) {
-					for (int p = 0; p < numM; ++p) {
-						long pos = positionsAndCov.get(p + p) & 0xffffffffl;
-						int cov = positionsAndCov.get(p + p + 1);
-						double max = 0.0;
-						double max2 = 0.0;
-						int maxj = 0;
-						for (int j = 0; j < numMixture; ++j) {
-							double pj = forward[p][j] * backward[p][j];
-							if (pj > max) {
-								max2 = max;
-								max = pj;
-								maxj = j;
-							} else if (pj > max2)
-								max2 = pj;
-						}
-						StringBuilder sb = new StringBuilder();
-						sb.append(scaffoldS);
-						sb.append('\t');
-						sb.append(pos);
-						sb.append('\t');
-						sb.append(cov);
-						sb.append('\t');
-						sb.append(maxj);
-						sb.append('\t');
-						sb.append(df.format(Math.log10(max) - Math.log10(max2)));
-						System.out.println(sb.toString());
-					}
-					
-				} else
-				for (int p = 1; p < numM; ++p) {
-					int cov = positionsAndCov.get(p + p + 1);
-					if (cov >= maxCount)
-						cov = maxCount;
-					double m[] = mixture.get(cov);
-					for (int j = 0; j < numMixture; ++j) {
-						double tmp = scale[p + 1] * backward[p + 1][j] * m[j];
-						for (int i = 0; i < numMixture; ++i)
-							QT[i][j] += forward[p][i] * t[i][j] * tmp;
-					}
-				}
-				
-			}
-			if (iterations == MAX_ITERATIONS || converge)
-				break;
-			
-			for (int i = 0; i < numMixture; ++i) {
-				double sum = 0.0;
-				for (double q : QT[i])
-					sum += q;
-				double iSum = 1.0 / sum;
-				for (int j = 0; j < numMixture; ++j)
-					t[i][j] = QT[i][j] * iSum;
-			}
-			
-			//for (int i = 0; i < numMixture; ++i) {
-			//	for (int j = 0; j < numMixture; ++j)
-			//		System.err.println(i + "\t" + j + "\t" + t[i][j]);
-			//}
-
-			logL = logL + Math.log10(l);
-			System.err.println("logL = " + logL);
-			if (oldLogL > logL - 0.01)
-				converge = true;
-					
-			oldLogL = logL;
-		}
-
-				
-/*
-				//backward
-				double backward[][] = new double[numM + 1][numChromosomes];
-				for (int j = 0; j < numChromosomes; ++j)
-					backward[numM][j] = 1.0;
-
-				for (int i = numM - 1; i >= 0; --i) {
-					long pos = positionsAndChr.get(3 * i);
-					int chr = positionsAndChr.get(3 * i + 1).intValue();
-					int density = positionsAndChr.get(3 * i + 2).intValue();
-					double p1 = 1.0;
-					if (i > 0) {
-							prevPos = positionsAndChr.get(3 * i - 3);
-							p1 = transition(pos - prevPos);
-					}
-					double p2 = (1.0 - p1) / numChromosomes;
-
-					double sum = 0.0;
-					for (int j = 0; j < numChromosomes; ++j)
-						sum += backward[i + 1][j];
-					
-					double sump2 = sum * p2;
-					
-					for (int j = 0; j < numChromosomes; ++j)
-						backward[i][j] = (sump2 + p1 * backward[i + 1][j]) * scale[i + 1] * emission(chr, j, density);
-				}
-				//for (int j = 0; j < numChromosomes; ++j) {
-				//	System.err.println(backward[0][j]);
-				//}
-
-				//QE
-				for (int i = 0; i < numM; ++i) {
-					//int pos = positionsAndChr.get(3 * i);
-					int chr = positionsAndChr.get(3 * i + 1).intValue();
-					int density = positionsAndChr.get(3 * i + 2).intValue();
-					for (int j = 0; j < numChromosomes; ++j) {
-						if (chr < 0) {
-							//QE[0] += ?
-							//QE[1] += ?
-						} else {
-							if (chr == j)
-								QE[0] += backward[i + 1][j] * forward[i + 1][j] / density;
-							else
-								QE[1] += backward[i + 1][j] * forward[i + 1][j] / density;
-						}
-					}
-				}
-
-				//QT
-				for (int i = 0; i < numM; ++i) {
-					long pos = positionsAndChr.get(3 * i);
-					if (i > 0) {
-						int chr = positionsAndChr.get(3 * i + 1).intValue();
-						int density = positionsAndChr.get(3 * i + 2).intValue();
-
-						double sum  = 0.0;
-						for (int j = 0; j < numChromosomes; ++j)
-							sum += backward[i + 1][j];
-
-						double p1 = transition(pos - prevPos);
-						double p2 = (1.0 - p1) / numChromosomes;
-						//if (ts != 1.0)
-						//	System.err.println(ts);
-						for (int j = 0; j < numChromosomes; ++j) {
-								
-							double se = scale[i + 1] * emission(chr, j, density);
-							QT[0] += p1 * forward[i][j] * backward[i + 1][j] * se;
-							QT[1] += p2 * forward[i][j] * sum * se; 
-						}
-						
-					}
-					prevPos = pos;
-				}
-				
-				if (iterations == MAX_ITERATIONS) {
-					// Viterbi
-					double viterbi[][] = new double[numM + 1][numChromosomes];
-					int path[][] = new int[numM + 1][numChromosomes];
-
-					for (int j = 0; j < numChromosomes; ++j)
-						viterbi[0][j] = 1.0 / numChromosomes;
-					
-					prevPos = 0;
-
-					for (int i = 0; i < numM; ++i) {
-						long pos = positionsAndChr.get(3 * i);
-						int chr = positionsAndChr.get(3 * i + 1).intValue();
-						int density = positionsAndChr.get(3 * i + 2).intValue();
-
-						double p1 = 1.0;
-						if (i > 0)
-							p1 = transition((int)(pos - prevPos));
-
-						double p2 = (1.0 - p1) / numChromosomes;
-						
-						int maxj = 0;
-						for (int j = 1; j < numChromosomes; ++j)
-							if (viterbi[i][j] > viterbi[i][maxj])
-								maxj = j;
-
-						double sump2 = p2 * viterbi[i][maxj];
-						
-						for (int j = 0; j < numChromosomes; ++j) {
-							double sump1 = p1 * viterbi[i][j]; 
-							if (sump2 > sump1) {
-								viterbi[i + 1][j] = sump2 * emission(chr, j, density);
-								path[i + 1][j] = maxj;
-							}
-							else {
-								viterbi[i + 1][j] = sump1 * emission(chr, j, density);;
-								path[i + 1][j] = j;
-							}
-						}
-
-						double max = 0.0;
-						for (int j = 0; j < numChromosomes; ++j)
-							max = Math.max(max, viterbi[i + 1][j]);
-						
-						double imax = 1.0 / max;
-						for (int j = 0; j < numChromosomes; ++j)
-							viterbi[i + 1][j] *= imax;
-
-						prevPos = pos;
-					}
-					//backtrack path
-					int finalPath[] = new int[numM];
-
-					int maxj = 0;
-					for (int j = 1; j < numChromosomes; ++j)
-						if (viterbi[numM][j] > viterbi[numM][maxj])
-							maxj = j;
-					
-					for (int i = numM; i >= 1; --i) {
-						finalPath[i - 1] = maxj;
-						maxj = path[i][maxj];
-					}
-					
-					for (int i = 0; i < numM; ++i) {
-						int maxJ = finalPath[i]; // Viterbi path
-						double max2 = Double.NEGATIVE_INFINITY;
-						for (int j = 0; j < numChromosomes; ++j) {
-							if (j != maxJ) {
-								max2 = Math.max(max2, backward[i + 1][j] * forward[i + 1][j]);
-							}
-						}
-						max2 = Math.log10(backward[i + 1][maxJ] * forward[i + 1][maxJ]) - Math.log10(max2);
-						long pos = positionsAndChr.get(3 * i);
-						int chr = positionsAndChr.get(3 * i + 1).intValue();
-						if (chr >= 0) // do not print padding markers
-							System.out.println(scaffolds.get(scaffold) + "\t" + pos + "\t" + (maxJ + 1) + "\t" + (chr + 1) + "\t" + max2);
-					}
-				}
-	
-				//System.err.println(scaffolds.get(scaffold) + "\t" + logScale + "\t" + QE[0] + "\t" + QE[1]);
-			}
-			logL = logL + Math.log10(l);
-			System.err.println("logL = " + logL);
-			System.err.println(P_ERROR + "\t" + P_CHIMERA);
-			P_ERROR = QE[1] / (QE[0] + QE[1]);
-			P_CHIMERA = QT[1] / (QT[0] + QT[1]);*/
-	}
-
-	private double emissionTable1[] = new double[1000]; 
-	private double emissionTable2[] = new double[1000]; 
-	
-	private void initParameters()
-	{
-		//double e = P_ERROR / (double) (numChromosomes - 1); // P_ERROR/0 does not matter!
-		for (int i = 0; i < emissionTable1.length; ++i) {
-			//emissionTable1[i] = Math.pow(e, 1.0 / i);
-			//emissionTable2[i] = Math.pow(1.0 - P_ERROR, 1.0 / i);
-		}
-		
-	}
-	
-	private double emission(int chr, int state, int density){
-		if (chr < 0)
-			return 1;
-
-		assert(density >= 1);
-		
-		if (density < emissionTable1.length) {
-			if (chr != state)
-				return emissionTable1[density];
-			else
-				return emissionTable2[density];
-			
-		}
-		return	Math.pow(emission(chr, state, 1), 1.0 / density); 
-	}
-
-	private static void usageInfo()
-	{
-		System.err.println("Usage: java CoverageHMM depth=depth.txt mixture=mixture.txt [options]");
-		System.err.println("options:");
-		System.err.println("       depth=file            output from samtools -a depth");
-        System.err.println("       mixture=file          output from CoverageAnalyser");
-        System.err.println("       column=NUM            Take column NUM from depth file [3]");
-        System.err.println("       scale=NUM             One position counts this much [0.01]");
-        System.err.println("       sample=NUM            Take only NUM fraction of data [0.1]");
-        System.err.println("       (default scale*sample=0.001, 1 per 1kb)");
-        System.err.println("       minProb=NUM           One position can be this sure [0.001] (1:1000)");
-	}
-	
-	
-	public static void main(String args[])
-	{
-		ParameterParser pp = new ParameterParser();
-
-		String extraParameters = "";
-	    for (int i = 0; i < args.length; ++i) {
-	            extraParameters +=  " " + args[i];
-	    }
-	    
-		if (args.length == 0 || !pp.init(extraParameters)) {
-			usageInfo();
-            System.exit(0);
-		}
-		pp.warning(new String[]{"depth", "mixture", "column", "scale", "minProb", "sample"});
-		
-		
-		System.out.println("#java CoverageHMM" + extraParameters);
-			
-		int column = Integer.parseInt(pp.getValueAsString("column", "3"));
-		CoverageHMM ch = new CoverageHMM();
-		ch.setColumn(column - 1);
-		String df = pp.getValueAsString("depth", null);
-		String mf = pp.getValueAsString("mixture", null);
-		if (df == null || mf == null) {
-			usageInfo();
-            System.exit(0);
-		}
-		ch.setScale(Double.parseDouble(pp.getValueAsString("scale", "0.001")));
-		ch.setMinProb(Double.parseDouble(pp.getValueAsString("minProb", "0.001")));
-		ch.setSample(Double.parseDouble(pp.getValueAsString("sample", "0.1")));
-
-		ch.loadMixture(mf);
-		ch.loadDepth(df);
-		ch.hmm();
-	}
-}
diff --git a/software/LepAnchor/src/FindContigErrors.java b/software/LepAnchor/src/FindContigErrors.java
deleted file mode 100644
index ad1ebdf..0000000
--- a/software/LepAnchor/src/FindContigErrors.java
+++ /dev/null
@@ -1,557 +0,0 @@
-/**
-    This file is part of Lep-Anchor.
-
-    Lep-Anchor is free software: you can redistribute it and/or modify
-    it under the terms of the GNU General Public License as published by
-    the Free Software Foundation, either version 3 of the License, or
-    (at your option) any later version.
-
-    Lep-Anchor is distributed in the hope that it will be useful,
-    but WITHOUT ANY WARRANTY; without even the implied warranty of
-    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-    GNU General Public License for more details.
-
-    You should have received a copy of the GNU General Public License
-    along with Lep-Anchor.  If not, see <http://www.gnu.org/licenses/>.
-
-	Copyright (C) 2019 Pasi Rastas, pasi.rastas@gmail.com, University of Helsinki
-	
-*/
-
-import java.io.BufferedReader;
-
-import java.io.FileReader;
-import java.io.InputStreamReader;
-import java.util.*;
-
-//Calculate score over positions of each contig (paf + ?)
-//...and to different position...
-
-public class FindContigErrors {
-	//calculate coverage for read mapping intervals...
-	//could be used to find (about) exact cut positions
-	
-	//prox, use borderScore
-	//map,
-
-	private void addPositions(String contig, HashMap<String, ArrayList<long[]>> positionHash, long start, long end, long weight)
-	{
-		ArrayList<long[]> list = positionHash.get(contig);
-		if (list == null) {
-			list = new ArrayList<long[]>();
-			positionHash.put(contig, list);
-		}
-		list.add(new long[]{start, end, weight});
-	}
-	
-	ArrayList<String> contigs = new ArrayList<String>();
-	ArrayList<Long> contigLengths = new ArrayList<Long>();
-	
-	HashMap<String, Integer> contigHash = new HashMap<String, Integer>();
-	
-	private void addContig(String name, long length){
-		if (!contigHash.containsKey(name)) {
-			contigHash.put(name, contigs.size());
-			contigs.add(name);
-			contigLengths.add(length);
-		}
-	}
-
-	//TODO: is this needed? Could we use cov instead?
-	private void mergeCovs(String contig, ArrayList<Long> cov, ArrayList<Long> cov2) {
-		System.out.println(contig);
-		int covi = 0;
-		int cov2i = 0;
-		//merge in cov and cov2
-
-		long pos = 0;
-		long cp = 0;
-		long cp2 = 0;
-		while (covi < cov.size() || cov2i < cov2.size()) {
-			if (covi >= cov.size() ) {
-				pos = cov2.get(cov2i);
-				cp2 = cov2.get(cov2i + 1);
-				cov2i+=2;
-			}
-			else if (cov2i >= cov2.size() ) {
-				pos = cov.get(covi);
-				cp = cov.get(covi + 1);
-				covi+=2;
-			}
-			else {
-				if (cov.get(covi) <= cov2.get(cov2i)) {
-						pos = cov.get(covi);
-						cp = cov.get(covi + 1);
-						covi+=2;
-				}
-				else {
-					pos = cov2.get(cov2i);
-					cp2 = cov2.get(cov2i + 1);
-					cov2i+=2;
-				}
-			}
-			System.out.println(pos + "\t" + cp + "\t" + cp2);
-		}
-	}
-	
-	HashMap<String, ArrayList<long[]>> pafPositions = new HashMap<String, ArrayList<long[]>>();
-	HashMap<String, ArrayList<long[]>> pafPositions2 = new HashMap<String, ArrayList<long[]>>();
-	public void processErrorsFromPaf(String fn)
-	{
- 		System.err.println("loading paf...");
- 		ArrayList<ArrayList<String>> rows = new ArrayList<ArrayList<String>>(); 
-		try {
-			BufferedReader br = null;
-			if (fn.equals("-"))
-				br = new BufferedReader(new InputStreamReader(System.in));
-			else
-				br = new BufferedReader(new FileReader(fn));
-			
-			do {
-				ArrayList<String> row = Input.loadTableRow(br, "\t ");
-				if (row == null)
-					break;
-				if (rows.size() == 0 || rows.get(0).get(0).equals(row.get(0)))
-					rows.add(row);
-				else {
-					processPAF(rows);
-					rows.clear();
-					rows.add(row);
-				}
-
-			} while (true);
-			processPAF(rows);
-
-			for (String contig : contigs) {
-				ArrayList<long[]> list = pafPositions.get(contig);
-				ArrayList<Long> cov = null;
-				if (list != null)
-					cov = Misc.cov(list);
-				else {
-					cov = new ArrayList<Long>();
-					cov.add(0L);
-					cov.add(0L);
-				}
-
-				ArrayList<long[]> list2 = pafPositions2.get(contig);
-				ArrayList<Long> cov2 = null;
-				if (list2 != null)
-					cov2 = Misc.cov(list2);
-				else {
-					cov2 = new ArrayList<Long>();
-					cov2.add(0L);
-					cov2.add(0L);
-				}
-
-				mergeCovs(contig, cov, cov2);
-				//for (int i = 0; i < cov.size(); i+=2) {
-				//	System.out.println(cov.get(i) + "\t" + cov.get(i + 1));
-				//}
-			}
-
-		}
-		catch (Exception e) {
-			e.printStackTrace();
-			System.err.println("Error in file " + fn);
-  		}
-	}
-	
-	private void processPAF(ArrayList<ArrayList<String>> rows) {
-		for (ArrayList<String> row : rows) {
-			String contig = row.get(5); 
-			long length = Long.parseLong(row.get(6));
-			addContig(contig, length);
-			long start = Long.parseLong(row.get(7)) + 1;
-			long end = Long.parseLong(row.get(8));
-			addPositions(contig, pafPositions, start, end, 1); // calculate coverage...
-		}
-		//take two longest alignments to two different contigs...  
-		long maxL = 0;
-		ArrayList<String> maxRow = null;
-		for (ArrayList<String> row : rows) {
-			long aLen = Long.parseLong(row.get(8)) - Long.parseLong(row.get(7));
-			if (aLen > maxL) {
-				maxL = aLen;
-				maxRow = row;
-			}
-		}
-		long maxL2 = 0;
-		ArrayList<String> maxRow2 = null;
-		for (ArrayList<String> row : rows)
-			if (!row.get(5).equals(maxRow.get(5))) {
-				long aLen = Long.parseLong(row.get(8)) - Long.parseLong(row.get(7));
-				if (aLen > maxL2) {
-					maxL2 = aLen;
-					maxRow2 = row;
-				}
-			}
-		if (maxRow2 != null) { // two aligments found to two contigs
-			long rstart1 =  Long.parseLong(maxRow.get(2));
-			long rstart2 =  Long.parseLong(maxRow2.get(2));
-			if (rstart1 > rstart2) { // make sure maxRow starts first...
-				long tmp = rstart2;
-				rstart2 = rstart1;
-				rstart1 = tmp;
-				
-				tmp = maxL;
-				maxL = maxL2;
-				maxL2 = tmp;
-				
-				ArrayList<String> tmp2 = maxRow;
-				maxRow = maxRow2;
-				maxRow2 = tmp2;
-			}
-			long rend1 =  Long.parseLong(maxRow.get(3));
-			//long rend2 =  Long.parseLong(maxRow2.get(3));
-			
-			long distance = rstart2 - rend1 + 2; //
-			
-			long minL = Math.min(maxL, maxL2);
-			
-			if (distance < -minL || distance > 2 * minL) // no overlap distance 2 x the length of the shorter alignment
-				return;
-			if (distance < 0)
-				distance = 0;
-//			TODO: figure out what happens if distance < 0, maybe distance can be -2 minL
-			
-			String o1 = maxRow.get(4);
-			if ("+".equals(o1)) {
-				long end1 = Long.parseLong(maxRow.get(8));
-				long length1 = Long.parseLong(maxRow.get(6));
-				addPositions(maxRow.get(5), pafPositions2, end1 + 1, Math.min(length1 + 1, end1 + 1 + distance), 1); // calculate coverage...
-			} else {
-				long start1 = Long.parseLong(maxRow.get(7));
-				addPositions(maxRow.get(5), pafPositions2, Math.max(0, start1 - distance), start1, 1); // calculate coverage...
-			}
-			String o2 = maxRow2.get(4);
-			if ("+".equals(o2)) {
-				long start2 = Long.parseLong(maxRow2.get(7));
-				addPositions(maxRow2.get(5), pafPositions2, Math.max(0, start2 - distance), start2, 1); // calculate coverage...
-			} else {
-				long end2 = Long.parseLong(maxRow2.get(8));
-				long length2 = Long.parseLong(maxRow2.get(6));
-				addPositions(maxRow2.get(5), pafPositions2, end2 + 1, Math.min(length2 + 1, end2 + 1 + distance), 1); // calculate coverage...
-			}
-			
-		}
-	}
-
-	HashMap<String, ArrayList<long[]>> chainPositions = new HashMap<String, ArrayList<long[]>>(); 
-	public void processErrorsFromChain(String fn)
-	{
- 		System.err.println("loading chain...");
-		try {
-			BufferedReader br = null;
-			if (fn.equals("-"))
-				br = new BufferedReader(new InputStreamReader(System.in));
-			else
-				br = new BufferedReader(new FileReader(fn));
-			
-			do {
-				ArrayList<String> row = Input.loadTableRow(br, "\t ");
-				if (row == null)
-					break;
-				if (row.get(4).equals("+")) {
-					String contig1 = row.get(2);
-					long start1 = Long.parseLong(row.get(5)) + 1;
-					long end1 = Long.parseLong(row.get(6));
-					long aScore = Long.parseLong(row.get(1));
-
-					long length1 = Long.parseLong(row.get(3));
-
-					addContig(contig1, length1);
-					addPositions(contig1, chainPositions, start1, end1, aScore / length1);
-
-					String contig2 = row.get(7);
-					long length2 = Long.parseLong(row.get(8));
-					addContig(contig2, length2);
-					long start2 = Long.parseLong(row.get(10));
-					long end2 = Long.parseLong(row.get(11));
-					if (row.get(9).equals("+"))
-						addPositions(contig2, chainPositions, start2 + 1, end2, aScore / length2);
-					else {
-						addPositions(contig2, chainPositions, length2 - end2 + 1, length2 - start2, aScore / length2);
-					}
-				}
-			} while (true);
-
-		}
-		catch (Exception e) {
-			e.printStackTrace();
-			System.err.println("Error in file " + fn);
-  		}
-	}
-
-//	1 (n starts)
-//	2,3 (n/2)
-//	4,5,6,7 (n/4)
-//	8,9,10,11,12,13,14,15 (n/8)
-// 16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31 (n/16)
-// ...
-
-	private int getPosition(Marker m, boolean plusOrientation) {
-		if (plusOrientation)
-			return m.pPlus;
-		else
-			return m.pMinus;
-	}
-	
-	HashMap<String, ArrayList<long[]>> proximityPositions = new HashMap<String, ArrayList<long[]>>(); 
-	HashMap<String, ArrayList<long[]>> proximityPositions2 = new HashMap<String, ArrayList<long[]>>(); 
-	public void processErrorsFromProximity(String fn, int bin, int maxD, double scale)
-	{
- 		System.err.println("loading proximity data...");
- 		long maxDistance = bin * maxD;
-		try {
-			BufferedReader br = null;
-			if (fn.equals("-"))
-				br = new BufferedReader(new InputStreamReader(System.in));
-			else
-				br = new BufferedReader(new FileReader(fn));
-			
-			do {
-				ArrayList<String> row = Input.loadTableRow(br, "\t ");
-				if (row == null)
-					break;
-				if (row.size() < 5) {
-					System.err.println("Warning: skipping " + row);
-					continue;
-				}
-				
-				String contig1 = row.get(0);
-				String contig2 = row.get(2);
-				long pos1 = Long.parseLong(row.get(1));
-				long pos2 = Long.parseLong(row.get(3));
-				long weight = (long) Double.parseDouble(row.get(4));
-				if (contig1.equals(contig2)) {
-					if (pos1 < pos2 && pos2 - pos1 < maxDistance) {
-						addPositions(contig1, proximityPositions, pos1, pos2, weight);
-					}
-				} else {
-					addPositions(contig1, proximityPositions2, pos1, pos1 + bin, weight);
-					addPositions(contig2, proximityPositions2, pos2, pos2 + bin, weight);
-				}
-			} while (true);
-
-			for (String key : proximityPositions.keySet())
-				if (!contigHash.containsKey(key))
-					addContig(key, 0);
-
-			for (String key : proximityPositions2.keySet())
-				if (!contigHash.containsKey(key))
-					addContig(key, 0);
-				
-			
-			for (String contig : contigs) {
-				ArrayList<long[]> list = proximityPositions.get(contig);
-				ArrayList<Long> cov = null;
-				if (list != null)
-					cov = Misc.cov(list);
-				else {
-					cov = new ArrayList<Long>();
-					cov.add(0L);
-					cov.add(0L);
-				}
-
-				ArrayList<long[]> list2 = proximityPositions2.get(contig);
-				ArrayList<Long> cov2 = null;
-				if (list2 != null)
-					cov2 = Misc.cov(list2);
-				else {
-					cov2 = new ArrayList<Long>();
-					cov2.add(0L);
-					cov2.add(0L);
-				}
-
-				mergeCovs(contig, cov, cov2);
-				//for (int i = 0; i < cov.size(); i+=2) {
-				//	System.out.println(cov.get(i) + "\t" + cov.get(i + 1));
-				//}
-			}
-
-		}
-		catch (Exception e) {
-			e.printStackTrace();
-			System.err.println("Error in file " + fn);
-  		}
-		
-		
-	}
-		
-	public void findErrors() {
-		int numContigs = contigs.size();
-		for (int ci = 0; ci < numContigs; ++ci) {
-			String contig = contigs.get(ci);
-			long length = contigLengths.get(ci);
-			ArrayList<long[]> list = pafPositions.get(contig);
-		}
-		
-		/*ArrayList<Long> t = new ArrayList<Long>();
-		t.add(-2l);
-		t.add(-2l);
-		t.add(-1l);
-		t.add(-1l);
-		t.add(-1l);
-		t.add(10l);
-		t.add(10l);
-		t.add(10l);
-		t.add(11l);
-		t.add(12l);
-		cov(t);*/
-		//paf
-		//for (String contig: contigs) {
-		//	ArrayList<Long> list = pafCoverage.get(contig);
-		//	if (list != null) {
-		//		Collections.sort(list);
-				//System.err.println(list);
-				//cov(list);
-				//ArrayList<Long> new_list = new ArrayList<Long>();
-		//	}
-		//}
-		//chain
-		
-		//prox
-		
-		//map
-		
-	}
-	/*
-	if (processErrors) {
-		for (int c1 = 0; c1 < numContigs; ++c1) {
-			String contig1 = contigs.get(c1); 
-			ArrayList<Long> list = pafCoverage.get(contig1);
-			if (list == null) {
-				list = new ArrayList<Long>();
-				pafCoverage.put(contig1, list);
-			}
-			ArrayList<ArrayList<String>> rows1 = alignmentHash.get(contig1);
-			
-			for (ArrayList<String> row1 : rows1) {
-				long start1 = Long.parseLong(row1.get(7)) + 1;
-				long end1 = Long.parseLong(row1.get(8));
-				list.add(-start1); // add -start
-				list.add(end1);    // and end position
-			}
-
-			//TODO: Try joining adjacent aligment blocks if the gap <= min{maxBridge, length1, length2} 
-			/*ArrayList<Long> comp = new ArrayList<Long>(); // sort row by start position... 
-			/for (ArrayList<String> row1 : rows1)
-				comp.add(Long.parseLong(row1.get(7))); // start
-		    Misc.ArrayIndexComparator<Long> comparator = new Misc.ArrayIndexComparator<Long>(comp);
-		    Integer[] indexes = comparator.createIndexArray();
-		    Arrays.sort(indexes, comparator);
-		    
-			ArrayList<Long> list = pafCoverage.get(contig1);
-			if (list == null) {
-				list = new ArrayList<Long>();
-				pafCoverage.put(contig1, list);
-			}
-		    
-			for (int orientation = 0; orientation < 2; ++orientation) {
-		    	long minStart = Long.MAX_VALUE;
-		    	long maxEnd = 0;
-
-		    	long minRStart = Long.MAX_VALUE;
-		    	long maxREnd = 0;
-			    for (int i : indexes) {
-			    	ArrayList<String> row1 = rows1.get(i);
-			    	
-			    	if ((orientation != 0) ^ ("+".equals(row1.get(4)))) { // take only + or - orientation...
-				    	long start1 = Long.parseLong(row1.get(7)) + 1;
-						long end1 = Long.parseLong(row1.get(8));
-						
-						long oldStart = minStart;
-						long oldEnd = maxEnd;
-						
-						minStart = Math.min(minStart, start1);
-						maxEnd = Math.max(maxEnd, end1);
-
-						long rstart1 = Long.parseLong(row1.get(2));
-						long rend1 = Long.parseLong(row1.get(3));
-
-						minRStart = Math.min(minRStart, rstart1);
-						maxREnd = Math.max(maxREnd, rend1);
-						
-						long RL = maxREnd - minRStart; // read length
-						long L = maxEnd - minStart;    // contig length
-						
-						if (oldEnd == 0 || RL <= 1.5 * L && L <= 1.5 * RL) {
-							 
-						} else {
-							list.add(-oldStart); // add -start
-							list.add(oldEnd);    // and end position
-						}
-						
-			    	}
-				}
-			}*/
-
-	
-	private static void usageInfo()
-	{
-        System.err.println("usage: java FindContigErrors [options]");        
-        System.err.println("       chain=file                  chain file ");
-        
-        System.err.println("       paf=file                    load alignment file in paf (minimap2) format");
-
-        System.err.println("       proximity=file NUM1 NUM2 NUM3  load proximity data, NUM1=bin size [10000]");
-        System.err.println("                                      NUM2=max distance in bins[25], NUM3=scale score [1.0]");
-	}
-	
-	private static void test()
-	{
-		ArrayList<long[]> list = new ArrayList<long[]>();
-		list.add(new long[]{0, 9, 1});
-		list.add(new long[]{0, 10, 1});
-		list.add(new long[]{0, 11, 1});
-		list.add(new long[]{5, 10, 1});
-		FindContigErrors fce = new FindContigErrors(); 
-		System.err.println(Misc.cov(list));
-	}
-	
-	public static void main(String[] args)
-	{
-		//FindContigErrors.test();
-		
-        if (args.length == 0) {
-        	usageInfo();
-            System.exit(0);
-        }
-	    String extraParameters = "";
-	    for (int i = 0; i < args.length; ++i) {
-	            extraParameters +=  " " + args[i];
-	    }
-		ParameterParser pp = new ParameterParser();
-		if (!pp.init(extraParameters)) {
-        	usageInfo();
-            System.exit(0);
-		}
-		pp.warning(new String[]{"paf", "chain", "proximity"});
-				
-		FindContigErrors fe = new FindContigErrors();
-		System.out.println("#java FindContigErrors" + extraParameters);
-		
-		//for (int i = 0; i < pp.getNumberOfValues("map"); ++i) {
-		//	fe.processErrorsFromMap(pp.getValueAsString("map", i, null), pp.getValueAsString("noIntervals", "0").equals("1"));
-		//}
-
-		String chain = pp.getValueAsString("chain", null);
-		if (chain != null) {
-			fe.processErrorsFromChain(chain);
-		}
-
-		String paf = pp.getValueAsString("paf", null);
-		if (paf != null)
-			fe.processErrorsFromPaf(paf);
-
-		String prox = pp.getValueAsString("proximity", 0, null);
-		if (prox != null) {
-			int bin = Integer.parseInt(pp.getValueAsString("proximity", 1, "10000"));
-			int maxD = Integer.parseInt(pp.getValueAsString("proximity", 2, "25"));
-			double scale = Double.parseDouble(pp.getValueAsString("proximity", 3, "1.0"));
-			fe.processErrorsFromProximity(prox, bin, maxD, scale);
-		}
-		fe.findErrors();
-	}
-
-}
diff --git a/software/LepAnchor/src/Input.java b/software/LepAnchor/src/Input.java
deleted file mode 100644
index 0d57214..0000000
--- a/software/LepAnchor/src/Input.java
+++ /dev/null
@@ -1,209 +0,0 @@
-/**
-    This file is part of Lep-Anchor.
-
-    Lep-Anchor is free software: you can redistribute it and/or modify
-    it under the terms of the GNU General Public License as published by
-    the Free Software Foundation, either version 3 of the License, or
-    (at your option) any later version.
-
-    Lep-Anchor is distributed in the hope that it will be useful,
-    but WITHOUT ANY WARRANTY; without even the implied warranty of
-    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-    GNU General Public License for more details.
-
-    You should have received a copy of the GNU General Public License
-    along with Lep-Anchor.  If not, see <http://www.gnu.org/licenses/>.
-
-	Copyright (C) 2019 Pasi Rastas, pasi.rastas@gmail.com, University of Helsinki
-
-*/
-/**
-    This file is part of Lep-MAP.
-
-    Lep-MAP is free software: you can redistribute it and/or modify
-    it under the terms of the GNU General Public License as published by
-    the Free Software Foundation, either version 3 of the License, or
-    (at your option) any later version.
-
-    Lep-MAP is distributed in the hope that it will be useful,
-    but WITHOUT ANY WARRANTY; without even the implied warranty of
-    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-    GNU General Public License for more details.
-
-    You should have received a copy of the GNU General Public License
-    along with Lep-MAP.  If not, see <http://www.gnu.org/licenses/>.
-
-	Copyright (C) 2013 Pasi Rastas, pasi.rastas@gmail.com, University of Helsinki
-*/
-
-//Reads files to ArrayLists of Strings 
-import java.io.*;
-import java.util.*;
-
-public class Input {
-  private Input() { };
-
-  private static boolean keepComments = false;
-  private static StringBuilder comments = new StringBuilder();
-  public static String getComments()
-  {
-	  return comments.toString();
-  }
-  public static void setKeepComments(boolean value)
-  {
-	  keepComments = value;
-  }
-  
-  public static String loadRow(BufferedReader br) throws Exception
-  {
-	  String s = "";
-	  do { 
-		  s = br.readLine();
-		  //System.err.println(s);
-		  if (s != null) {
-			  int index = s.indexOf('#');
-			  if (index >= 0) {
-				  s = s.substring(0, index);
-				  if (keepComments) {
-					  comments.append(s.substring(index + 1));
-					  comments.append('\n');
-				  }
-			  }
-		  }
-	  }	while ( s != null && (s.length() == 0) );
-	  return s;
-  }
-  
-  public static ArrayList<String> splitRow(String s, String delim)
-  {
-	  StringTokenizer st = new StringTokenizer(s, delim, false);
-	  ArrayList<String> row = new ArrayList<String>(); 
-	  while (st.hasMoreTokens()) {
-		  String nt = st.nextToken();
-		  row.add(nt);
-	  }
-	  return row;
-  }
-  
-  
-  public static ArrayList<String> loadTableRow(BufferedReader br, String delim) throws Exception
-  {
-	  String s = loadRow(br);
-	  if (s == null)
-		  return null;
-	  
-	  /*String sa[] = s.split(delim);
-	  ArrayList<String> row = new ArrayList<String>();
-	  for (String tmp : sa) 
-		  row.add(tmp);*/
-	  return splitRow(s, delim);
-  }
-
-  public static ArrayList<ArrayList<String>> loadTable(BufferedReader br, String delim) throws Exception {
-	  ArrayList<ArrayList<String>> ret = new ArrayList<ArrayList<String>>();
-	  //ArrayList<String> comments = new ArrayList<String>(); 
-	  while (true) {
-		  ArrayList<String> row =  loadTableRow(br, delim);
-		  if (row == null)
-			  break;
-		  else
-			  ret.add(row);
-	  }
-	  return ret;
-  }  
-  
-  public static ArrayList<ArrayList<String>> loadTable(BufferedReader br, String delim, String returnDelim) throws Exception {
-	  ArrayList<ArrayList<String>> ret = new ArrayList<ArrayList<String>>();
-	  
-	  //ArrayList<String> comments = new ArrayList<String>(); 
-	  while (true) {
-		  StringTokenizer st = null;
-		  String s = null;
-		  do { 
-			  s = loadRow(br);
-			  if (s != null)
-				  st = new StringTokenizer(s, delim, true);
-		  }	while ( s != null && !st.hasMoreTokens());
-		  if (s == null)
-			  break;
-		  ArrayList<String> row = new ArrayList<String>(); 
-		  while (st.hasMoreTokens()) {
-			  String nt = st.nextToken();
-			  if (delim.indexOf(nt) >= 0) {
-				  if (returnDelim.indexOf(nt) >= 0)
-					  row.add(nt);
-			  } else
-				  row.add(nt);
-		  }
-		  ret.add(row);
-	  }
-	  return ret;
-  }
- 
-  public static ArrayList<ArrayList<String>> loadTable(String filename, String delim, String returnDelim) {
-	    try {
-	      BufferedReader br = new BufferedReader(new FileReader(filename));
-	      ArrayList<ArrayList<String>> t = loadTable(br, delim, returnDelim);
-	      br.close();
-	      return t;
-
-	    } catch (Exception e) {
-	      System.err.println(e);
-	      return null;
-	    }
-	  }
-  
-  
-  public static ArrayList<ArrayList<String>> loadTable(String filename, String delim) {
-	    try {
-	      BufferedReader br = new BufferedReader(new FileReader(filename));
-	      ArrayList<ArrayList<String>> t = loadTable(br, delim);
-	      br.close();
-	      return t;
-
-	    } catch (Exception e) {
-	      System.err.println(e);
-	      return null;
-	    }
-	  }
-  
-  public static int[][] loadIntTable(String filename, String delim) {
-	  	
-	  ArrayList<int[]> ret = new ArrayList<int[]>(); 
-	    try {
-	      BufferedReader br = new BufferedReader(new FileReader(filename));
-	      while (true) {
-	    	  ArrayList<String> t = loadTableRow(br, delim);
-	    	  if (t == null)
-	    		  break;
-	    	  else {
-	    		  int it[] = new int[t.size()];
-	    		  int i = 0;
-	    		  for (String s : t)
-	    			  it[i++] = Integer.parseInt(s);
-	    		  ret.add(it);
-	    	  }
-	    		  
-	      }
-	      br.close();
-	      return ret.toArray(new int[ret.size()][]);
-
-	    } catch (Exception e) {
-	      System.err.print(e);
-	      return null;
-	    }
-	  }
-
-  public static void main(String args[])
-  {
-	  ArrayList<ArrayList<String>> test = Input.loadTable("pedigree.txt", " \t");
-	  for (ArrayList<String> row : test) {
-		  for (String item : row)
-			  System.err.print(item + " ");
-		  System.err.println();
-	  }
-		  
-	  
-  }
- 
-}
diff --git a/software/LepAnchor/src/InputData.java b/software/LepAnchor/src/InputData.java
deleted file mode 100644
index 0e257fc..0000000
--- a/software/LepAnchor/src/InputData.java
+++ /dev/null
@@ -1,452 +0,0 @@
-/**
-    This file is part of Lep-Anchor.
-
-    Lep-Anchor is free software: you can redistribute it and/or modify
-    it under the terms of the GNU General Public License as published by
-    the Free Software Foundation, either version 3 of the License, or
-    (at your option) any later version.
-
-    Lep-Anchor is distributed in the hope that it will be useful,
-    but WITHOUT ANY WARRANTY; without even the implied warranty of
-    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-    GNU General Public License for more details.
-
-    You should have received a copy of the GNU General Public License
-    along with Lep-Anchor.  If not, see <http://www.gnu.org/licenses/>.
-
-	Copyright (C) 2019 Pasi Rastas, pasi.rastas@gmail.com, University of Helsinki
-	
-*/
-import java.io.BufferedReader;
-import java.io.FileReader;
-import java.io.InputStreamReader;
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.HashMap;
-
-
-
-public class InputData {
-	
-	public static long myParseLong(String s)
-	{
-		if (s.charAt(s.length() - 1) == '*')
-			return Long.parseLong(s.substring(0, s.length() - 1));
-		else
-			return Long.parseLong(s);
-			 
-	}
-	private static long[] myParseLongInterval(String s)
-	{
-		long ret[] = null;
-		int pos = s.indexOf('-');
-		if (pos < 0) {
-			long p = myParseLong(s);
-			return new long[]{p, p};		
-		}
-		if (s.charAt(s.length() - 1) == '*') {
-			ret = new long[3];
-			ret[1] =  Long.parseLong(s.substring(pos + 1, s.length() - 1));			
-		}
-		else {
-			ret = new long[2];
-			ret[1] =  Long.parseLong(s.substring(pos + 1));
-		}
-		ret[0] =  Long.parseLong(s.substring(0, pos));
-		return ret;
-	}
-	
-	public static HashMap<ContigInterval, ArrayList<ArrayList<String>>> loadRaw(String fn, HashMap<String, ArrayList<ContigInterval>> haplotypeHash)
-	{
-		HashMap<ContigInterval, ArrayList<ArrayList<String>>> ret = new HashMap<ContigInterval, ArrayList<ArrayList<String>>>();
-		try {
-			
-			int numMarkers = 0;
-
-			BufferedReader br = null;
-			if (fn.equals("-"))
-				br = new BufferedReader(new InputStreamReader(System.in));
-			else
-				br = new BufferedReader(new FileReader(fn));
-			
-			do {
-				String row = Input.loadRow(br);
-				if (row == null)
-					break;
-				ArrayList<String> srow = Input.splitRow(row, "[\t ]");
-				if (srow.size() >= 3) {
-					String contig = srow.get(0);
-					boolean added = false;
-					if (haplotypeHash != null && haplotypeHash.containsKey(contig)) {  
-						long pos = myParseLong(srow.get(1));
-						for (ContigInterval ci : haplotypeHash.get(contig)) {
-							if (ci.inside(pos)) {
-								ArrayList<ArrayList<String>> list = ret.get(ci);
-								if (list == null) {
-									list = new ArrayList<ArrayList<String>>();
-									ret.put(ci, list);
-								}
-								list.add(srow);
-								++numMarkers;
-								added = true;
-								break;
-							}
-						}
-					}
-					if (!added)
-						System.out.println(row);
-				} else
-					System.err.println("Warning: skipping " + row);
-			} while (true);
-			
-			System.err.println("Liftover for " + numMarkers + " markers over " + ret.size() + " regions");
-			return ret;
-		} catch (Exception e) {
-	     	e.printStackTrace();
-			System.err.println("Error in file " + fn);
-			return null;
-      	}
-	}
-	
-	public static ArrayList<Marker> loadMap(String fn, boolean nochromosome, boolean nointervals, boolean compressMap)
-	{
-		ArrayList<Double> pos = new ArrayList<Double>(); 
-		ArrayList<Integer> chr = new ArrayList<Integer>(); 
-
-		ArrayList<Marker> ret = new ArrayList<Marker>(); 
-		try {
-			BufferedReader br = null;
-			if (fn.equals("-"))
-				br = new BufferedReader(new InputStreamReader(System.in));
-			else
-				br = new BufferedReader(new FileReader(fn));
-			
-			do {
-				ArrayList<String> row = Input.loadTableRow(br, "[\t ]");
-				if (row == null)
-					break;
-				if (row.size() > 0) {
-					if (nochromosome)
-						row.add(2, "1");
-					
-					if (row.size() >= 4 && (nointervals || (row.size() & 1) == 1) || row.size() == 4) {
-						int intervals[] = new int[Math.max(2, row.size() - 3)];
-						if (row.size() == 4 || nointervals) {
-							if (nointervals) {
-								intervals = new int[2];
-								double p = Double.parseDouble(row.get(3));
-								if (row.size() >= 5)
-									p += Double.parseDouble(row.get(4));
-								pos.add(p);
-								chr.add(Integer.parseInt(row.get(2)));
-							}
-							else
-								try {
-									intervals[0] = intervals[1] =  Integer.parseInt(row.get(3));
-								} catch (NumberFormatException e) {
-									System.err.println("Error: non-integer value for interval (check parameter noIntervals=1)" + row);
-									System.exit(-1);
-								}
-						}
-						else
-							for (int i = 3; i < row.size(); i+=2) {
-								try {
-									intervals[i-3] = Integer.parseInt(row.get(i));
-									intervals[i-2] = Integer.parseInt(row.get(i + 1));
-								} catch (NumberFormatException e) {
-									System.err.println("Error: non-integer value for interval (check parameter noIntervals=1) " + row);								
-									System.exit(-1);
-								}
-							}
-						ret.add(new Marker(row.get(0), myParseLong(row.get(1)), Integer.parseInt(row.get(2)), intervals));
-					} else
-						System.err.println("Warning: skipping " + row);
-				}
-			} while (true);
-			br.close();
-			if (nointervals) {
-				//put markers in each chr to separate list... and sort...
-				HashMap<Integer, ArrayList<Double>> chrMarkers = new HashMap<Integer, ArrayList<Double>>(); // store chromosome info
-				HashMap<Integer, ArrayList<Integer>> indexMarkers = new HashMap<Integer, ArrayList<Integer>>(); // store original index in ret...
-
-				for (int mi = 0; mi < chr.size(); ++mi) {
-					int c = chr.get(mi);
-					ArrayList<Double> list = chrMarkers.get(c); 
-					ArrayList<Integer> list2 = indexMarkers.get(c); 
-					if (list == null) {
-						list = new ArrayList<Double>();
-						chrMarkers.put(c, list);
-						list2 = new ArrayList<Integer>();
-						indexMarkers.put(c, list2);
-					}
-					list.add(pos.get(mi));
-					list2.add(mi);
-				}
-				for (int c : chrMarkers.keySet()) {
-					ArrayList<Double> list = chrMarkers.get(c); 
-					ArrayList<Integer> list2 = indexMarkers.get(c); 
-				    Misc.ArrayIndexComparator<Double> comparator = new Misc.ArrayIndexComparator<Double>(list);
-				    Integer[] indexes = comparator.createIndexArray();
-				    java.util.Arrays.sort(indexes, comparator);
-				    
-				    double prev = Double.NEGATIVE_INFINITY;
-				    int ip = -1;
-				    for (int i : indexes) {
-				    	double p = list.get(i); 
-				    	if (p > prev)
-				    		++ip;
-				    	Marker m = ret.get(list2.get(i));
-				    	m.intervals[0] = ip;
-				    	m.intervals[1] = ip;
-				    	prev = p;
-				    }
-					
-				}
-			} else if (compressMap){ // no noIntervals && compress map positions
-
-				// compressing map speeds up computation... 
-				HashMap<Integer, ArrayList<Marker>> chrMarkers = new HashMap<Integer, ArrayList<Marker>>();
-
-				for (Marker m : ret) {
-					int c = m.getChromosome();
-					ArrayList<Marker> list = chrMarkers.get(c); 
-					if (list == null) {
-						list = new ArrayList<Marker>();
-						chrMarkers.put(c, list);
-					}
-					list.add(m);
-				}
-				for (ArrayList<Marker> markers: chrMarkers.values()) {
-					ArrayList<Integer> positions = new ArrayList<Integer>(); 
-					for (Marker m : markers) {
-						int[] interval = m.getIntervals();
-						for (int i : interval)  
-							positions.add(i);
-					}
-					Collections.sort(positions);
-					HashMap<Integer, Integer> compressHash = new HashMap<Integer, Integer>();
-					int numPositions = 0;
-					for (int i : positions) {
-						if (!compressHash.containsKey(i))
-							compressHash.put(i, numPositions++);
-					}
-					for (Marker m : markers) {
-						int[] interval = m.getIntervals();
-						for (int ii = 0; ii < interval.length; ++ii)  
-							interval[ii] = compressHash.get(interval[ii]); 
-					}
-				}
-			}
-			return ret;
-	    } catch (Exception e) {
-	     	e.printStackTrace();
-			System.err.println("Error in file " + fn);
-			return null;
-      	}
-  	}
-	public static ArrayList<ContigInterval> loadBedAndComments(String fn, StringBuilder comments)
-	{
-		Input.setKeepComments(true);
-		ArrayList<ContigInterval> ret = loadBed(fn, -1);
-		Input.setKeepComments(false);
-		comments.append(Input.getComments());
-		return ret;
-	}
-	
-	public static ArrayList<ContigInterval> loadBed(String fn)
-	{
-		return loadBed(fn, -1);
-	}
-	public static ArrayList<ContigInterval> loadBed(String fn, int chr)
-	{
-		ArrayList<ContigInterval> ret = new ArrayList<ContigInterval>(); 
-		try {
-			BufferedReader br = null;
-			if (fn.equals("-"))
-				br = new BufferedReader(new InputStreamReader(System.in));
-			else
-				br = new BufferedReader(new FileReader(fn));
-			
-			do {
-				ArrayList<String> row = Input.loadTableRow(br, "[\t ]");
-				if (row == null)
-					break;
-					if (row.size() >= 3) {
-						String start = row.get(1);
-						String end = row.get(2);
-						ContigInterval ci = null;
-						if (start.indexOf('-') >= 0 || end.indexOf('-') >= 0)
-							ci = new ContigInterval(row.get(0), myParseLongInterval(start), myParseLongInterval(end));
-						else
-							ci = new ContigInterval(row.get(0), myParseLong(start), myParseLong(end));
-						if (row.size() >= 4 && (row.get(3).equals("-")  || row.get(3).equals("--")  || row.get(3).equals("---")))
-							ci.flipOrientation();
-						
-						if (row.size() >= 5) {
-							int bChr = Integer.parseInt(row.get(4));
-							ci.setChromosome(bChr);
-						}
-						if (chr < 0 || ci.getChromosome() == chr)
-							ret.add(ci);
-					}
-					else
-						System.err.println("Warning: skipping " + row);
-			} while (true);
-			
-			int prevC = 0;
-			for (ContigInterval ci : ret) {
-				if (prevC != 0 && ci.getChromosome() != prevC) {
-					System.err.println("Error: multiple cromosomes in the bed");
-					System.err.println("Try providing parameter chromosome or split bed into chromosomes");
-					System.exit(-1);
-				}
-			}
-			br.close();
-			return ret;
-	    } catch (Exception e) {
-	     	e.printStackTrace();
-			System.err.println("Error in file " + fn);
-			return null;
-      	}
-	}
-	
-	public static ArrayList<ContigInterval> loadLa(String fn)
-	{
-		ArrayList<ContigInterval> ret = new ArrayList<ContigInterval>(); 
-		try {
-			BufferedReader br = null;
-			if (fn.equals("-"))
-				br = new BufferedReader(new InputStreamReader(System.in));
-			else
-				br = new BufferedReader(new FileReader(fn));
-			
-			do {
-				ArrayList<String> row = Input.loadTableRow(br, "[\t ]");
-				if (row == null)
-					break;
-					if (row.size() >= 3) {
-						String start = row.get(1);
-						String end = row.get(2);
-						if (row.size() >= 8) {
-							start = row.get(6);
-							int sis = start.indexOf('/');
-							if (sis >= 0)
-								start = start.substring(0, sis);
-							end = row.get(7);
-							int sie = end.indexOf('/');
-							if (sie >= 0)
-								end = end.substring(0, sie);
-						}
-						ContigInterval ci = null;
-						if (start.indexOf('-') >= 0 || end.indexOf('-') >= 0)
-							ci = new ContigInterval(row.get(0), myParseLongInterval(start), myParseLongInterval(end));
-						else
-							ci = new ContigInterval(row.get(0), myParseLong(start), myParseLong(end));
-						if (row.size() >= 4 && (row.get(3).equals("-")  || row.get(3).equals("--")  || row.get(3).equals("---")))
-							ci.flipOrientation();
-						
-						if (row.size() >= 5) {
-							int bChr = Integer.parseInt(row.get(4));
-							ci.setChromosome(bChr);
-						}
-						ret.add(ci);
-					}
-					else
-						System.err.println("Warning: skipping " + row);
-			} while (true);
-			
-			int prevC = 0;
-			for (ContigInterval ci : ret) {
-				if (prevC != 0 && ci.getChromosome() != prevC) {
-					System.err.println("Error: multiple cromosomes in the bed");
-					System.err.println("Try providing parameter chromosome or split bed into chromosomes");
-					System.exit(-1);
-				}
-			}
-			br.close();
-			return ret;
-	    } catch (Exception e) {
-	     	e.printStackTrace();
-			System.err.println("Error in file " + fn);
-			return null;
-      	}
-	}
-
-	
-	public static ArrayList<ContigInterval> loadHaplotypes(String fn)
-	{
-		ArrayList<ContigInterval> ret = new ArrayList<ContigInterval>(); 
-		try {
-			BufferedReader br = null;
-			if (fn.equals("-"))
-				br = new BufferedReader(new InputStreamReader(System.in));
-			else
-				br = new BufferedReader(new FileReader(fn));
-			
-			do {
-				ArrayList<String> row = Input.loadTableRow(br, "[\t ]");
-				if (row == null)
-					break;
-					if (row.size() >= 4) {
-						ContigInterval ci = new ContigInterval(row.get(1), myParseLong(row.get(2)), myParseLong(row.get(3)));
-						ret.add(ci);
-					}
-					else
-						System.err.println("Warning: skipping haplotype " + row);
-			} while (true);
-			br.close();
-			return ret;
-	    } catch (Exception e) {
-	     	e.printStackTrace();
-			System.err.println("Error in file " + fn);
-			return null;
-      	}
-	}
-	
-
-	public ArrayList<Marker> loadLGMap(String fn)
-	{
-		ArrayList<Marker> ret = new ArrayList<Marker>(); 
-		try {
-			BufferedReader br = null;
-			if (fn.equals("-"))
-				br = new BufferedReader(new InputStreamReader(System.in));
-			else
-				br = new BufferedReader(new FileReader(fn));
-			String line = null;
-			do {
-				line = br.readLine();
-				if (line == null)
-					break;
-		
-				int ic = line.indexOf('#');
-				if (ic >= 0)
-					line = line.substring(0, ic); 
-				
-				if (line.length() > 0) {
-					String[] row = line.split("\t");
-					if (row.length > 2 || row.length == 3 || (row.length & 1) == 0) {
-						int intervals[] = new int[Math.max(2, row.length - 2)];
-						if (row.length == 3)
-							intervals[0] = intervals[1] =  Integer.parseInt(row[2]);
-						else
-							for (int i = 2; i < row.length; i+=2) {
-									intervals[i-2] = Integer.parseInt(row[i]);
-									intervals[i-1] = Integer.parseInt(row[i + 1]);
-							}
-						//ret.add(new Marker(row[0], myParseInt(row[1]), intervals));
-					} else
-						System.err.println("Warning: skipping " + line);
-				}
-			} while (true);
-			br.close();
-			return ret;
-	    } catch (Exception e) {
-	     	e.printStackTrace();
-			System.err.println("Error in file " + fn);
-			return null;
-      	}
-  	}
-	
-
-}
diff --git a/software/LepAnchor/src/LiftoverHaplotypes.java b/software/LepAnchor/src/LiftoverHaplotypes.java
deleted file mode 100644
index 7edd03c..0000000
--- a/software/LepAnchor/src/LiftoverHaplotypes.java
+++ /dev/null
@@ -1,44 +0,0 @@
-
-public class LiftoverHaplotypes {
-	private static void usageInfo()
-	{
-        System.err.println("usage: java LiftoverHaplotypes haplotypes=haplo.bed map=mapX.txt chain=all.chain >mapX_liftover.txt");
-        System.err.println("       haplotypes=FILE      try liftover for markers in removed haplotypes listed in FILE (from findFullHaplotypes or from PlaceAndOrientContigs)");
-        System.err.println("       map=FILE2            any file with contig and pos in the first columns, typically the map file");
-        System.err.println("       chain=FILE3          the chain file");
-	}
-	
-	public static void main(String[] args)
-	{
-		
-        if (args.length == 0) {
-        	usageInfo();
-            System.exit(0);
-        }
-	    String extraParameters = "";
-	    for (int i = 0; i < args.length; ++i) {
-	            extraParameters +=  " " + args[i];
-	    }
-		ParameterParser pp = new ParameterParser();
-		if (!pp.init(extraParameters)) {
-        	usageInfo();
-            System.exit(0);
-		}
-		pp.warning(new String[]{"map", "chain", "haplotypes"});
-		
-		String haplotypes = pp.getValueAsString("haplotypes", null);
-		String chain = pp.getValueAsString("chain", null);
-		String map = pp.getValueAsString("map", null);
-		if (map == null || chain == null || haplotypes == null){
-        	usageInfo();
-            System.exit(0);
-		}
-		
-		
-		System.out.println("#java LiftoverHaplotypes" + extraParameters);
-		
-		PlaceAndOrientContigs poc = new PlaceAndOrientContigs();
-		poc.liftover(haplotypes, chain, map);
-	}
-
-}
diff --git a/software/LepAnchor/src/Map2Bed.java b/software/LepAnchor/src/Map2Bed.java
deleted file mode 100644
index 6759df9..0000000
--- a/software/LepAnchor/src/Map2Bed.java
+++ /dev/null
@@ -1,334 +0,0 @@
-import java.io.BufferedReader;
-import java.io.FileReader;
-import java.util.ArrayList;
-import java.util.HashMap;
-
-/**
-    This file is part of Lep-Anchor.
-
-    Lep-Anchor is free software: you can redistribute it and/or modify
-    it under the terms of the GNU General Public License as published by
-    the Free Software Foundation, either version 3 of the License, or
-    (at your option) any later version.
-
-    Lep-Anchor is distributed in the hope that it will be useful,
-    but WITHOUT ANY WARRANTY; without even the implied warranty of
-    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-    GNU General Public License for more details.
-
-    You should have received a copy of the GNU General Public License
-    along with Lep-Anchor.  If not, see <http://www.gnu.org/licenses/>.
-
-	Copyright (C) 2019 Pasi Rastas, pasi.rastas@gmail.com, University of Helsinki
-	
-*/
-public class Map2Bed {
-	private int markerSupport = 2;
-	private int splitLength = 10000;
-	private double minQuality = 2;
-	
-	public static void usage()
-	{
-		System.err.println("Usage: java Map2Bed map=contig_pos_map.txt contigLengths=contig.sizes [options] >map_clean.bed");
-        System.err.println("       map=file           a map file containing columns contig, position and chromosome ");
-        System.err.println("                          in sorted order (typically from CleanMap)");
-
-        System.err.println("       contigLength=file  a file containing columns contig name and its length");
-        
-        System.err.println("       markerSupport=NUM  at least NUM markers are needed for splitting a contig [2]");
-        System.err.println("       minSplitLength=NUM do not split shorter regions than NUM [10000]");
-        System.err.println("       minQuality=NUM     only consider markers with quality >= NUM [2]");
-        System.err.println("                          (column 5 from CleanMap)");
-	}
-	private void makeBed(String mapFile, String lengthFile)
-	{
-		
-		HashMap<String, Long> scaffoldLength = new HashMap<String, Long>();
-		try {
-			BufferedReader br = new BufferedReader(new FileReader(lengthFile));
-			
-			ArrayList<String> line = Input.loadTableRow(br, " \t");
-			while (line != null) {
-				String scaffold = line.get(0);
-				long length = Long.parseLong(line.get(1));
-				scaffoldLength.put(scaffold, length);
-				line = Input.loadTableRow(br, " \t");
-			}
-		} catch (Exception e) {
-			System.err.println("Error loading contig lengths");
-			e.printStackTrace();
-			System.exit(-1);
-		}
-		
-		int numChromosomes = 0;
-		String prevScaffold = "";
-		ArrayList<Long> list = new ArrayList<Long>();
-		
-		HashMap<String, Long> scaffoldMap = new HashMap<String, Long>();
-		try {
-			BufferedReader br = new BufferedReader(new FileReader(mapFile));
-			
-			ArrayList<String> line = Input.loadTableRow(br, " \t");
-			while (line != null) {
-				if (!line.get(0).equals("CHR") && !line.get(0).equals("CHROM")) { 
-					String scaffold = line.get(0);
-					long position = Long.parseLong(line.get(1));
-					int chr = Integer.parseInt(line.get(2));
-					double quality = minQuality;
-					if (line.size() >= 5)
-						quality = Double.parseDouble(line.get(4));
-					if (chr > 0 && quality >= minQuality) {
-						if (scaffoldMap.containsKey(scaffold) && scaffoldMap.get(scaffold) > position) {
-							System.err.println("Error: map file must be sorted");
-							System.exit(-1);
-						}
-						if (!scaffoldLength.containsKey(scaffold)) {
-							System.err.println("Error: contig " + scaffold + " does not have length in " + lengthFile);
-							System.exit(-1);
-						}
-							
-						if (!prevScaffold.equals("") && !prevScaffold.equals(scaffold)) {
-							processScaffold(prevScaffold, scaffoldLength.get(prevScaffold), list);
-							list.clear();
-						}
-						scaffoldMap.put(scaffold, position);
-						prevScaffold = scaffold;
-
-						list.add(position);
-						list.add((long)chr);
-						list.add((long)(100 * quality));
-						numChromosomes = Math.max(numChromosomes, chr);
-					}
-				}
-				line = Input.loadTableRow(br, " \t");
-			}
-			processScaffold(prevScaffold, scaffoldLength.get(prevScaffold), list);
-		} catch (Exception e) {
-			System.err.println("Error loading map file");
-			e.printStackTrace();
-			System.exit(-1);
-		}
-	}
-	private class Interval{
-		int startIndex;
-		int endIndex;
-		long quality;
-		long position;
-		long startPosition;
-		long chr;
-		int markers;
-		public Interval(int startIndex, long position, long quality, long chr){
-			this.startIndex = startIndex;
-			this.endIndex = startIndex;
-			this.quality = quality;
-			this.chr = chr;
-			this.position = position;
-			startPosition = position;
-			markers = 1;
-		}
-		public void addMarker(int index, long position, long quality) {
-			endIndex = index;
-			this.quality += quality;
-			this.position = position;
-			++markers;
-		}
-
-		public void addMarkerLeft(int index, long position, long quality) {
-			startIndex = index;
-			this.quality += quality;
-			this.startPosition = position;
-			++markers;
-		}
-
-		public void addInterval(Interval i) {
-			endIndex = i.endIndex;
-			quality += i.quality;
-			position = i.position;
-			markers += i.markers;
-		}
-		public int getMarkers() {
-			return markers;
-		}
-		public long getLength() {
-			return position - startPosition + 1;
-		}
-		public long getQuality() {
-			return quality;
-		}
-		public long getChr() {
-			return chr;
-		}
-		public int getStartIndex() {
-			return startIndex;
-		}
-		public int getEndIndex() {
-			return endIndex;
-		}
-		public long getStartPosition() {
-			return startPosition;
-		}
-
-		public long getPosition() {
-			return position;
-		}
-		public String toString()
-		{
-			//return chr + "\t" + markers + "\t" + quality;
-			return startPosition + "\t" + position + "\t" + chr;
-		}
-	}
-	
-	private void processScaffold(String scaffold, long scaffoldLength, ArrayList<Long> list)
-	{
-		
-		//create intervals of adjacent markers in the same chromosome
-		ArrayList<Interval> intervals = new ArrayList<Interval>();
-		long prevChr = 0;
-		for (int i = 0; i < list.size(); i+=3) {
-			long position = list.get(i);
-			long chr = list.get(i + 1);
-			long quality = list.get(i + 2);
-			if (i == 0 || prevChr != chr)
-				intervals.add(new Interval(i, position, quality, chr));
-			else
-				intervals.get(intervals.size() - 1).addMarker(i, position, quality);
-			prevChr = chr;
-		}
-		
-		if (intervals.size() > 1) { //more than one interval, prune
-			do {
-				int removed = -1;
-				for (int ii = 0; ii < intervals.size(); ++ii) {
-					Interval i = intervals.get(ii);
-					if (i.getMarkers() < markerSupport || i.getLength() < splitLength) { // < markerSupport markers and/or length < splitLength
-						if (removed < 0)
-							removed = ii;
-						else {
-							long l = i.getLength();
-							long lr = intervals.get(removed).getLength();
-							if (l < lr || (l == lr && i.getQuality() < intervals.get(removed).getQuality()))
-								removed = ii;
-						}
-					}
-				}
-				
-				if (removed >= 0) { //remove removed (too short and/or too few markers)
-					if (removed > 0 && removed + 1 < intervals.size() && intervals.get(removed - 1).getChr() == intervals.get(removed + 1).getChr()) {
-						Interval prev = intervals.get(removed - 1);
-						Interval next = intervals.get(removed + 1);
-						for (int li = prev.getEndIndex() + 3; li < next.getStartIndex(); li+=3) {
-							long chr = list.get(li + 1);
-							if (chr == prev.getChr()) {
-								long position = list.get(li);
-								long quality = list.get(li + 2);
-								prev.addMarker(li, position, quality);
-							}
-						}
-						prev.addInterval(next);	
-						intervals.remove(removed + 1);
-						intervals.remove(removed);
-					} else
-						intervals.remove(removed);
-				}
-				else
-					break;
-			} while (true);
-
-			//try to extend intervals
-			for (int ii = 0; ii + 1 < intervals.size(); ++ii) {
-				Interval prev = intervals.get(ii);
-				Interval next = intervals.get(ii + 1);
-				
-				for (int li = prev.getEndIndex() + 3; li < next.getStartIndex(); li+=3) {
-					long chr = list.get(li + 1);
-					if (chr == next.getChr()) // conflict
-						break;
-					if (chr == prev.getChr()) {
-						//System.err.println("Extend");
-						long position = list.get(li);
-						long quality = list.get(li + 2);
-						prev.addMarker(li, position, quality);
-					}
-				}
-
-				for (int li = next.getStartIndex() - 3; li > prev.getEndIndex(); li-=3) {
-					long chr = list.get(li + 1);
-					if (chr == prev.getChr()) // conflict
-						break;
-					if (chr == next.getChr()) {
-						//System.err.println("Extend");
-						long position = list.get(li);
-						long quality = list.get(li + 2);
-						next.addMarkerLeft(li, position, quality);
-					}
-				}
-			}
-			
-		}
-		
-		for (int ii = 0; ii < intervals.size(); ++ii) {
-			Interval i = intervals.get(ii);
-			long start = 1;
-			if (ii > 0)
-				start =  intervals.get(ii - 1).getPosition() + 1;
-
-			String end = scaffoldLength + "*";
-			if (ii + 1 < intervals.size())
-				end = "" + (intervals.get(ii + 1).getStartPosition() - 1);
-			System.out.println(scaffold + "\t" + start + "-" + i.getStartPosition() + "\t" + i.getPosition() + "-" + end + "\t?\t" + i.getChr());
-		}
-		
-		//System.err.println(scaffold + "\t" +  intervals);
-	}
-	
-	private void setMarkerSupport(int parseInt) {
-		markerSupport = parseInt;
-	}
-	private void setSplitLength(int parseInt) {
-		splitLength = parseInt;
-	}
-	private void setMinQuality(double parseDouble) {
-		minQuality = parseDouble;
-	}
-	
-	public static void main(String args[])
-	{
-		ParameterParser pp = new ParameterParser();
-
-		String extraParameters = "";
-	    for (int i = 0; i < args.length; ++i) {
-	            extraParameters +=  " " + args[i];
-	    }
-		if (args.length == 0 || !pp.init(extraParameters)) {
-			usage();
-            System.exit(0);
-		}
-		
-		
-		String mapFile = pp.getValueAsString("map", null);
-		String lengthFile = pp.getValueAsString("contigLength", null);
-		if (mapFile == null) {
-			System.err.println("Please specify a map file");
-			usage();
-            System.exit(0);
-			
-		}
-		if (lengthFile == null) {
-			System.err.println("Please specify a contig length file");
-			usage();
-            System.exit(0);
-			
-		}
-
-		pp.warning(new String[]{"map", "contigLength", "markerSupport", "minSplitLength", "minQuality"});
-
-		
-		Map2Bed m2p = new Map2Bed();
-		m2p.setMarkerSupport(Integer.parseInt(pp.getValueAsString("markerSupport", "2")));
-		m2p.setSplitLength(Integer.parseInt(pp.getValueAsString("minSplitLength", "10000")));
-		m2p.setMinQuality(Double.parseDouble(pp.getValueAsString("minQuality", "2.0")));
-
-		System.out.println("#java Map2Bed" + extraParameters);
-		m2p.makeBed(mapFile, lengthFile);
-	}
-}
diff --git a/software/LepAnchor/src/Marker.java b/software/LepAnchor/src/Marker.java
deleted file mode 100644
index 181da59..0000000
--- a/software/LepAnchor/src/Marker.java
+++ /dev/null
@@ -1,139 +0,0 @@
-/**
-    This file is part of Lep-Anchor.
-
-    Lep-Anchor is free software: you can redistribute it and/or modify
-    it under the terms of the GNU General Public License as published by
-    the Free Software Foundation, either version 3 of the License, or
-    (at your option) any later version.
-
-    Lep-Anchor is distributed in the hope that it will be useful,
-    but WITHOUT ANY WARRANTY; without even the implied warranty of
-    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-    GNU General Public License for more details.
-
-    You should have received a copy of the GNU General Public License
-    along with Lep-Anchor.  If not, see <http://www.gnu.org/licenses/>.
-
-	Copyright (C) 2019 Pasi Rastas, pasi.rastas@gmail.com, University of Helsinki
-	
-*/
-public class Marker implements Comparable<Marker>{
-	String contig;
-	int chromosome;
-	long position;
-	int intervals[];
-	ContigInterval ci;
-	
-	int pPlus;
-	int pMinus;
-
-
-	public Marker(String contig, long position, int chromosome, int intervals[])
-	{
-		this.contig = contig;
-		this.position = position;
-		this.chromosome = chromosome;
-		//TODO: consider cloning intervals...
-		this.intervals = intervals;
-	}
-
-	public Marker(Marker m, long position)
-	{
-		this(m.contig, position, m.chromosome, m.intervals);
-	}
-
-	public Marker(Marker m)
-	{
-		this(m.contig, m.position, m.chromosome, m.intervals);
-	}
-
-	public Marker(Marker m, ContigInterval ci)
-	{
-		this(m.contig, m.position, m.chromosome, m.intervals);
-		this.ci = ci;
-	}
-
-	//return next position inside from p or p + 1 if p is inside
-	public int nextInside(int p) {
-		int min = Integer.MAX_VALUE;
-        for (int j = 0; j < intervals.length; j+=2)
-            if (p <= intervals[j + 1] && min > intervals[j])
-            	min = intervals[j];
-        if (min <= p)
-        	return p + 1;
-        return min;
-	}
-	
-	public int inside(int p)
-	{
-        for (int j = 0; j < intervals.length; j+=2)
-            if (p >= intervals[j] && p <= intervals[j + 1])
-                return 1;
-        return 0;
-	}
-	@Override
-	public String toString()
-	{
-		return contig + "\t" + position + "\t" + chromosome;
-	}
-	//orders first by contig and then by position...
-	@Override
-	public int compareTo(Marker o) {
-		int ret = getContig().compareTo(o.getContig());
-		if (ret != 0)
-			return ret;
-		if (position < o.position)
-			return -1;
-		if (position > o.position)
-			return 1;
-		return 0;
-	}
-	public String getName(){
-		return contig + '\t' +  position;
-	}
-	public String getContig(){
-		return contig;
-	}
-	public long getPosition(){
-		return position;
-	}
-	
-	public int getChromosome(){
-		return chromosome;
-	}
-	public int[] getIntervals() {
-		return intervals;
-	}
-	
-	public int maxBin() // get maximum bin value...
-	{
-		int ret = 0;
-        for (int j = 1; j < intervals.length; j+=2)
-            ret = Math.max(ret, intervals[j]);
-        return ret;
-	}
-	public int minBin() // get minimum bin value...
-	{
-		int ret = Integer.MAX_VALUE;
-        for (int j = 0; j < intervals.length; j+=2)
-            ret = Math.min(ret, intervals[j]);
-        return ret;
-	}
-	public void flip(int maxBin)
-	{
-		int i[] = new int[intervals.length];
-        for (int j = 0; j < intervals.length; ++j)
-        	i[j] = maxBin - intervals[j ^ 1];
-        intervals = i;
-	}
-
-	public ContigInterval getContigInterval() {
-		return ci;
-	}
-	public static void main(String args[]){
-		Marker m = new Marker("Contig", 1, 1, new int[]{10,20,40,60});
-		for (int i = 0; i <= 61; ++i)
-			System.out.println(i + ":" + m.nextInside(i));
-	}
-
-}
diff --git a/software/LepAnchor/src/Misc.java b/software/LepAnchor/src/Misc.java
deleted file mode 100644
index 2c7ffe0..0000000
--- a/software/LepAnchor/src/Misc.java
+++ /dev/null
@@ -1,224 +0,0 @@
-/**
-    This file is part of Lep-Anchor.
-
-    Lep-Anchor is free software: you can redistribute it and/or modify
-    it under the terms of the GNU General Public License as published by
-    the Free Software Foundation, either version 3 of the License, or
-    (at your option) any later version.
-
-    Lep-Anchor is distributed in the hope that it will be useful,
-    but WITHOUT ANY WARRANTY; without even the implied warranty of
-    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-    GNU General Public License for more details.
-
-    You should have received a copy of the GNU General Public License
-    along with Lep-Anchor.  If not, see <http://www.gnu.org/licenses/>.
-
-	Copyright (C) 2019 Pasi Rastas, pasi.rastas@gmail.com, University of Helsinki
-	
-*/
-/**
-    This file is part of Lep-MAP.
-
-    Lep-MAP is free software: you can redistribute it and/or modify
-    it under the terms of the GNU General Public License as published by
-    the Free Software Foundation, either version 3 of the License, or
-    (at your option) any later version.
-
-    Lep-MAP is distributed in the hope that it will be useful,
-    but WITHOUT ANY WARRANTY; without even the implied warranty of
-    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-    GNU General Public License for more details.
-
-    You should have received a copy of the GNU General Public License
-    along with Lep-MAP.  If not, see <http://www.gnu.org/licenses/>.
-
-	Copyright (C) 2013 Pasi Rastas, pasi.rastas@helsinki.fi, University of Helsinki
-*/
-
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.Comparator;
-
-public class Misc {
-	
-	//compare based on first element of long[]
-	private static class LongComparator0 implements Comparator<long[]>
-	{
-		@Override
-		public int compare(long[] l1, long[] l2){
-			return Long.compare(l1[0], l2[0]);
-		}
-	}
-
-	//compare based on second element of long[]
-	private static class LongComparator1 implements Comparator<long[]>
-	{
-		@Override
-		public int compare(long[] l1, long[] l2){
-			return Long.compare(l1[1], l2[1]);
-		}
-	}
-	//list elements contains 3 values, start, end and weight as long[3]
-	//dynamic programming for finding coverage of multiple weighted intervals
-	public static ArrayList<Long> cov(ArrayList<long[]> list_)
-	{
-		ArrayList<long[]> listStop = new ArrayList<long[]>();
-		listStop.addAll(list_);
-		ArrayList<long[]> list = new ArrayList<long[]>();
-		list.addAll(list_);
-		Collections.sort(list, new LongComparator0());
-		Collections.sort(listStop, new LongComparator1());
-		
-		ArrayList<Long> ret = new ArrayList<Long>(); 
-		int n = list.size();
-		int end = 0;
-		int start = 0;
-		long pos = 0;
-
-		long cov = 0;
-		long ps = list.get(start)[0]; // start
-		long pe = listStop.get(end)[1]; // end
-
-		long prevP = 0;
-		long prevC = 0;
-		while (end < n) {
-			if (start < n && ps <= pe) {
-				pos = ps;
-				while (start < n && pos == list.get(start)[0]) { // take all intervals with same start
-					cov += list.get(start)[2];
-					++start;
-					if (start < n)
-						ps = list.get(start)[0];
-				}
-			} else {
-				pos = pe;
-				while (end < n && pos == listStop.get(end)[1]) { // teka all intervals with same end
-					cov -= listStop.get(end)[2];
-					++end;
-					if (end < n)
-						pe = listStop.get(end)[1];
-				}
-				++pos;
-			}
-			if (pos != prevP) {
-				//System.err.println(prevP + "\t" + prevC);
-				ret.add(prevP);
-				ret.add(prevC);
-			}
-			prevP = pos;
-			prevC = cov;
-		}
-		ret.add(pos);
-		ret.add(0L);
-		//System.err.println(pos + "\t0");
-		return ret;
-	}
-
-	
-	public static boolean intersectIntervals(long b1, long e1, long b2, long e2){
-		if (e1 < b2 || e2 < b1)
-			return false;
-		return true;
-	}
-
-	public static long intersectIntervalsLength(long b1, long e1, long b2, long e2){
-		if (e1 <= b2 || e2 <= b1)
-			return 0;
-		return Math.min(e1 - b2, e2 - b1);
-	}
-	
-	private static final double LN10 = Math.log(10.0);
-
-	public static double exp10(double a)
-	{
-		return Math.exp(a * LN10);
-	}
-	
-    public static class ArrayIndexComparator<T extends Comparable<T>> implements Comparator<Integer>
-    {
-            private final T[] array;
-
-            public ArrayIndexComparator(T[] array)
-        {
-            this.array = array;
-        }
-        @SuppressWarnings("unchecked")
-            public ArrayIndexComparator(ArrayList<T> alArray)
-        {
-                this.array = (T[]) alArray.toArray(new Comparable[0]);
-        }       
-
-        public Integer[] createIndexArray()
-        {
-            Integer[] indexes = new Integer[array.length];
-            for (int i = 0; i < array.length; i++)
-            {
-                indexes[i] = i;
-            }
-            return indexes;
-        }
-
-            public int compare(Integer index1, Integer index2)
-        {
-            return array[index1].compareTo(array[index2]);
-        }
-    }       
-    //Misc.ArrayIndexComparator<Double> comparator = new Misc.ArrayIndexComparator<Double>(table);
-    //Integer[] indexes = comparator.createIndexArray();
-    //Arrays.sort(indexes, comparator);     
-
-    public static class ArrayIndexComparator2<T> implements Comparator<Integer>
-    {
-        private final T[] array;
-        private Comparator<T> C;
-
-        public ArrayIndexComparator2(T[] array, Comparator<T> C)
-        {
-            this.array = array;
-            this.C = C;
-        }
-        @SuppressWarnings("unchecked")
-        public ArrayIndexComparator2(ArrayList<T> alArray, Comparator<T> C)
-        {
-        	this.array = (T[]) alArray.toArray(new Comparable[0]);
-            this.C = C;
-        }       
-
-        public Integer[] createIndexArray()
-        {
-            Integer[] indexes = new Integer[array.length];
-            for (int i = 0; i < array.length; i++)
-            {
-                indexes[i] = i;
-            }
-            return indexes;
-        }
-
-        public int compare(Integer index1, Integer index2)
-        {
-            return C.compare(array[index1], array[index2]);
-        }
-    }       
-    //Misc.ArrayIndexComparator2<Double> comparator = new Misc.ArrayIndexComparator2<Double>(table, customDoubleComparator);
-    //Integer[] indexes = comparator.createIndexArray();
-    //Arrays.sort(indexes, comparator);     
-    
-    //returns random merge of two lists...
-    public static <T> ArrayList<T> randomMerge(ArrayList<T> l1, ArrayList<T> l2)
-    {
-    	ArrayList<T> ret = new ArrayList<T>();
-		int n = l1.size();
-		int m = l2.size();
-		int j = 0;
-		int k = 0;
-		for (int i = 0; i < n + m; ++i) {
-			if (j < n && (k == m || Math.random() * (n - j) > (m - k) * 0.5))
-				ret.add(l1.get(j++));
-			else
-				ret.add(l2.get(k++));
-		}
-    	return ret;
-    }
-    
-}
diff --git a/software/LepAnchor/src/ParameterParser.java b/software/LepAnchor/src/ParameterParser.java
deleted file mode 100644
index 555b64f..0000000
--- a/software/LepAnchor/src/ParameterParser.java
+++ /dev/null
@@ -1,231 +0,0 @@
-/**
-    This file is part of Lep-Anchor.
-
-    Lep-Anchor is free software: you can redistribute it and/or modify
-    it under the terms of the GNU General Public License as published by
-    the Free Software Foundation, either version 3 of the License, or
-    (at your option) any later version.
-
-    Lep-Anchor is distributed in the hope that it will be useful,
-    but WITHOUT ANY WARRANTY; without even the implied warranty of
-    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-    GNU General Public License for more details.
-
-    You should have received a copy of the GNU General Public License
-    along with Lep-Anchor.  If not, see <http://www.gnu.org/licenses/>.
-
-	Copyright (C) 2019 Pasi Rastas, pasi.rastas@gmail.com, University of Helsinki
-	
-*/
-/**
-    This file is part of Lep-MAP.
-
-    Lep-MAP is free software: you can redistribute it and/or modify
-    it under the terms of the GNU General Public License as published by
-    the Free Software Foundation, either version 3 of the License, or
-    (at your option) any later version.
-
-    Lep-MAP is distributed in the hope that it will be useful,
-    but WITHOUT ANY WARRANTY; without even the implied warranty of
-    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-    GNU General Public License for more details.
-
-    You should have received a copy of the GNU General Public License
-    along with Lep-MAP.  If not, see <http://www.gnu.org/licenses/>.
-
-	Copyright (C) 2013 Pasi Rastas, pasi.rastas@helsinki.fi, University of Helsinki
-*/
-//Parses parameters given as "x=a y=b c d z = e"
-import java.util.StringTokenizer;
-import java.util.ArrayList;
-import java.util.HashMap;
-
-public class ParameterParser {
-	private HashMap<String, ArrayList<String>> hm;
-
-	public ParameterParser()
-	{
-		
-	}
-	public ParameterParser(String parameters)
-	{
-		if (!init(parameters))
-			hm = null;
-	}
-	
-	public boolean init(ArrayList<String> tokens) 
-	{
-		hm = new HashMap<String, ArrayList<String>>();
-		int n = tokens.size();
-		int i = 0;
-		while (i < n) {
-			String key = tokens.get(i);
-			if (key.equals("="))
-				return false;
-			++i;
-			if (i < n - 1)  {
-				if (!tokens.get(i).equals("="))
-					return false;
-				++i;
-			} else
-				return false;
-			
-			ArrayList<String> value = new ArrayList<String>();
-			while (i == n - 1 || (i < n - 1 && !tokens.get(i + 1).equals("="))) {
-				String nv = tokens.get(i);
-				if (nv.equals("="))
-					return false;
-				value.add(nv);
-				++i;
-			}
-			if (hm.containsKey(key))
-				return false;
-			hm.put(key, value);
-		}
-		return true;
-	}
-	public boolean init(String parameters)
-	{
-		String delims = "\t =;";
-		StringTokenizer st = new StringTokenizer(parameters, delims, true);
-		
-		ArrayList <String> tokens = new ArrayList <String>();  
-		while (st.hasMoreTokens()) {
-			String nt = st.nextToken();
-			if (delims.indexOf(nt) >= 0) {
-				if (nt.equals("=") || nt.equals(";"))
-					tokens.add(nt);
-			  } else
-				  tokens.add(nt);
-			
-		}
-		return init(tokens);
-	}
-	public ArrayList<String> getValue(String variable)
-	{
-		return hm.get(variable);
-	}
-	public String getValueAsString(String variable, String defaultValue)
-	{
-		ArrayList<String> ret = getValue(variable);
-		if (ret != null) {
-			String rets = "";
-			for (String s : ret)
-				rets += " " + s;
-			return rets.substring(Math.min(1, rets.length())); // remove first space
-		}
-		return defaultValue;
-	}
-	public int getNumberOfValues(String variable)
-	{
-		ArrayList<String> ret = getValue(variable);
-		if (ret != null)
-			return ret.size();
-		else
-			return 0;
-	}
-	public String getValueAsString(String variable, int index, String defaultValue)
-	{
-		ArrayList<String> ret = getValue(variable);
-		if (ret != null && index < ret.size()) 
-				return ret.get(index);
-		return defaultValue;
-	}
-	public ArrayList<String> getValuesAsList(String variable)
-	{
-		return getValuesAsList(variable, 1, null);
-	}
-	
-	public ArrayList<String> getValuesAsList(String variable, int size, String defaultValue)
-	{
-		ArrayList<String> ret = new ArrayList<String>(); 
-		if (getNumberOfValues(variable) == 1 && getValueAsString(variable, null).startsWith("file:")) {
-			ArrayList<ArrayList<String>> matrix = Input.loadTable(getValueAsString(variable, null).substring(5), "[\t ]");
-			if (matrix.size() == 1)
-				ret.addAll(matrix.get(0));
-			if (matrix.size() > 1) { // transpose  matrix
-				ArrayList<String> tp = new ArrayList<String>();
-				boolean ok = true;
-//				System.err.println("Reading matrix");
-				for (ArrayList<String> als : matrix) {
-					if (als.size() != 1)
-						ok = false;
-					else
-						tp.add(als.get(0));
-				}
-				if (ok)
-					ret.addAll(tp);
-//				System.err.println("Reading matrix ok" + ok);
-			}
-		} else
-			for (int i = 0; i < getNumberOfValues(variable); ++i)
-				ret.add(getValueAsString(variable, i, null));
-		if (ret.size() == 0)
-			ret.add(defaultValue);
-		if (ret.size() == 1)
-			for (int i = 0; i < size - 1; ++i)
-				ret.add(new String(ret.get(0)));
-		return ret;
-	}
-	
-
-	public ArrayList<ArrayList<String>> getValuesAsMatrix(String variable)
-	{
-		if (getNumberOfValues(variable) == 1 && getValueAsString(variable, null).startsWith("file:")) {
-//			System.err.println("loading matrix " + getValueAsString(variable, null).substring(5));
-			ArrayList<ArrayList<String>> matrix = Input.loadTable(getValueAsString(variable, null).substring(5), "[\t ]");
-			return matrix;
-		}
-		ArrayList<ArrayList<String>> ret = new ArrayList<ArrayList<String>>();
-		if (getNumberOfValues(variable) > 0)
-			ret.add(new ArrayList<String>());
-		int line = 0;
-
-		for (int i = 0; i < getNumberOfValues(variable); ++i) {
-			if (getValueAsString(variable, i, null).equals(";")) {
-				++line;
-				ret.add(new ArrayList<String>());
-			} else
-			ret.get(line).add(getValueAsString(variable, i, null));
-		}
-		return ret;
-	}
-	public boolean warning(String keyWords[])
-	{
-		HashMap<String, Integer> hm2 = new HashMap<String, Integer>();
-		
-		for (String s : hm.keySet())
-			hm2.put(s, 1);
-		
-		for (String s : keyWords)
-			hm2.remove(s);
-		
-		if (hm2.size() > 0) {
-			System.err.println("Error! Unknown parameters: "); 
-			for (String s : hm2.keySet())
-				System.err.print(s + " ");
-			System.err.println();
-			System.exit(-1);
-		}
-
-		return false;
-	}
-	
-	public static void main(String args[])
-	{
-		ParameterParser pp = new ParameterParser("a=40 10 30 b=10 d = 1 2;3 4 6 e=file:ped1");
-		System.err.println("a = " + pp.getValueAsString("a", 0, "null"));
-		
-		System.err.println("a = " + pp.getValue("a"));
-		System.err.println("b = " + pp.getValue("b"));
-		System.err.println("c = " + pp.getValue("c"));
-		System.err.println("d = " + pp.getValue("d"));
-		System.err.println("number of values for a = " + pp.getNumberOfValues("a"));
-		System.err.println("number of values for b = " + pp.getNumberOfValues("b"));
-		System.err.println("number of values for c = " + pp.getNumberOfValues("c"));
-		System.err.println(pp.getValuesAsList("d"));
-		System.err.println(pp.getValuesAsMatrix("d"));
-		System.err.println(pp.getValuesAsMatrix("e"));
-	}
-	
-}
diff --git a/software/LepAnchor/src/PlaceAndOrientContigs.java b/software/LepAnchor/src/PlaceAndOrientContigs.java
deleted file mode 100644
index 551edd3..0000000
--- a/software/LepAnchor/src/PlaceAndOrientContigs.java
+++ /dev/null
@@ -1,4821 +0,0 @@
-/**
-    This file is part of Lep-Anchor.
-
-    Lep-Anchor is free software: you can redistribute it and/or modify
-    it under the terms of the GNU General Public License as published by
-    the Free Software Foundation, either version 3 of the License, or
-    (at your option) any later version.
-
-    Lep-Anchor is distributed in the hope that it will be useful,
-    but WITHOUT ANY WARRANTY; without even the implied warranty of
-    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-    GNU General Public License for more details.
-
-    You should have received a copy of the GNU General Public License
-    along with Lep-Anchor.  If not, see <http://www.gnu.org/licenses/>.
-
-	Copyright (C) 2019 Pasi Rastas, pasi.rastas@gmail.com, University of Helsinki
-	
-*/
-
-import java.io.BufferedReader;
-import java.io.FileOutputStream;
-import java.io.FileReader;
-import java.io.InputStreamReader;
-import java.io.PrintStream;
-import java.util.*;
-import java.util.concurrent.atomic.AtomicBoolean;
-import java.util.concurrent.atomic.AtomicInteger;
-
-public class PlaceAndOrientContigs {
-	
-	private ArrayList<ContigInterval> bed = null; // store bed file 
-	private HashMap<String, ArrayList<ContigInterval>> bedHash = new HashMap<String, ArrayList<ContigInterval>>(); // get intervals for each contig
-
-	private HashMap<String, ArrayList<ContigInterval>> haplotypeHash = new HashMap<String, ArrayList<ContigInterval>>(); // get intervals for each haplotype contig
-
-	private HashMap<String, Integer> chainLinkHash = new HashMap<String, Integer>(); // get score for each chain link...
-	private HashMap<String, Long> chainLinkHashCut1 = new HashMap<String, Long>(); // get cut point for each link
-	private HashMap<String, Long> chainLinkHashCut2 = new HashMap<String, Long>(); // get cut point for each link
-
-	private HashMap<String, Long> chainLinkHashCut1a = new HashMap<String, Long>(); // get alternative cut point for each link
-	private HashMap<String, Long> chainLinkHashCut2a = new HashMap<String, Long>(); // get alternative cut point for each link
-
-	private HashMap<String, Integer> chainHaplotypeHash = new HashMap<String, Integer>(); // get score for each contig pair for second being haplotype of the first...
-	private HashMap<String, long[]> chainHaplotypeCut = new HashMap<String, long[]>(); // get haplotype alignment end points 
-
-	private HashMap<String, Integer> scaffoldingLink_tmp = new HashMap<String, Integer>(); // get scaffolding score linking contigs... 
-	private HashMap<String, Integer> scaffoldingLink = new HashMap<String, Integer>(); // get scaffolding score linking contigs... 
-
-	private HashMap<String, String> scaffoldingLinkInfo = new HashMap<String, String>(); // get scaffolding score linking contigs... 
-	
-	private ArrayList<String> contigs = new ArrayList<String>(); // store contigs
-	
-	//private HashMap<String, ArrayList<Long>> pafCoverage = new HashMap<String, ArrayList<Long>>();
-
-	private int numErrorsPerContig = 3;
-	private int numErrors = 40;
-
-	private int numMaps = 0;
-	private ArrayList<ContigInterval> intervalsInChr = null;
-	
-	private double scaleScore = 0.00001;
-	private double orientationPenalty = 0.5;
-	private double cutPenalty = 0.001;
-	
-	private double liftoverScoreDiff = 0.5;
-	
-	private boolean useChainAndPaf = false;
-	
-	private String printAnimation = "";
-	
-	private int maxBridge = 50000;
-	private int maxIntersect = 2000;
-	
-	private int numRuns = 5;
-	
-	private int numThreads = 8;
-	
-	private int minHaplotypeAlignmentScore = -10;
-	private int minLinkAlignmentScore = -10;
-	private boolean keepEmptyIntervals;
-	
-	private boolean commentOutput; 
-	private boolean compressMap;
-
-	private Proximity prox = null;
-
-	
-	private void setCommentOutput(boolean commentOutput) {
-		this.commentOutput = commentOutput;
-	}
-	public void setCompressMap(boolean value) {
-		compressMap = value;
-	}
-	public void setPrintAnimation(String fn) {
-		printAnimation = fn;
-	}
-	
-	public void setUseChainAndPaf(boolean value) {
-		useChainAndPaf = value;
-	}
-
-	public void setNumRuns(int runs) {
-		numRuns = runs;
-	}
-
-	public void setNumErrors(int errors) {
-		numErrors = errors;
-	}
-
-	public void setNumErrorsPerContig(int errors) {
-		numErrorsPerContig = errors;
-	}
-	
-	public void setKeepEmptyIntervals(boolean value) {
-		keepEmptyIntervals = value;
-	}
-
-	public ArrayList<ArrayList<Marker>> getMarkers(ContigInterval ci_result){
-		ArrayList<ArrayList<Marker>> ret =  new ArrayList<ArrayList<Marker>>();
-		for (int map = 0; map < numMaps; ++map)
-			ret.add(new ArrayList<Marker>());
-		
-		ArrayList<ContigInterval> cis = bedHash.get(ci_result.getContig());
-		if (cis != null) {
-			for (ContigInterval c2 : cis) {
-				if (Misc.intersectIntervals(c2.getStart(), c2.getEnd(), ci_result.getStart(), ci_result.getEnd()))
-					for (int map = 0; map < numMaps; ++map)
-						ret.get(map).addAll(c2.getMarkers(map, ci_result.getOrientation()));
-			}
-		}
-		return ret;
-	}
-	
-	// forward calculation, increasing map positions
-	private void forward1(ArrayList<Marker> markers, int S[][], int P[][], int startBin, int endBin) {
-		forward1(markers, S, P, startBin, endBin, 0, markers.size());
-	}
-	
-	private void forward1(ArrayList<Marker> markers, int S[][], int P[][], int startBin, int endBin, int start, int end)
-	{
-		for (int mi = start; mi < end; ++mi) {
-			Marker m = markers.get(mi);
-
-			//substract startBin
-			int maxI  = 0;
-			int Si[] = S[mi];
-			int Si1[] = S[mi + 1];
-			int Pi1[] = P[mi + 1];
-			for (int b = 0; b <= endBin - startBin; ++b) { 
-                if (Si[b] > Si[maxI])
-                    maxI = b;
-                Si1[b] = Si[maxI];// + m.inside(b + startBin); 
-                Pi1[b] = maxI + startBin; 
-            }
-			int b = startBin;
-			while (b <= endBin) {
-				Si1[b - startBin] += m.inside(b);
-				b = m.nextInside(b);
-			}
-		}		
-	}
-	
-	private void forwardFast1(ArrayList<Marker> markers, int S[][], int startBin, int endBin) {
-		forwardFast1(markers, S, startBin, endBin, 0, markers.size());
-	}
-	
-	private void forwardFast1(ArrayList<Marker> markers, int S[][], int startBin, int endBin, int start, int end)
-	{
-		for (int mi = start; mi < end; ++mi) {
-			Marker m = markers.get(mi);
-
-			//substract startBin
-			int maxS  = 0;
-			int Si[] = S[mi];
-			int Si1[] = S[mi + 1];
-			for (int b = 0; b <= endBin - startBin; ++b) {
-				int s = Si[b]; 
-                if (s > maxS)
-                    maxS = s;
-                Si1[b] = maxS;// + m.inside(b + startBin); 
-            }
-			int b = startBin;
-			while (b <= endBin) {
-				Si1[b - startBin] += m.inside(b);
-				b = m.nextInside(b);
-			}
-
-		}		
-	}
-
-	private void forward2(ArrayList<Marker> markers, int S[][], int P[][], int startBin, int endBin) {
-		forward2(markers, S, P, startBin, endBin, 0, markers.size());
-	}
-	// forward calculation, decreasing map positions
-	private void forward2(ArrayList<Marker> markers, int S2[][], int P2[][], int startBin, int endBin, int start, int end)
-	{
-		for (int mi = start; mi < end; ++mi) {
-			Marker m = markers.get(mi);
-			int maxI2  = endBin - startBin;
-			int S2i[] = S2[mi];
-			int S2i1[] = S2[mi + 1]; 
-			int P2i1[] = P2[mi + 1];
-			
-			for (int b = endBin - startBin; b >= 0; --b) { 
-                  
-                if (S2i[b] > S2i[maxI2])
-                    maxI2 = b;
-              
-                S2i1[b] = S2i[maxI2];// + m.inside(b + startBin); // add startBin as we subtract it from b 
-                P2i1[b] = maxI2 + startBin; 
-            }
-			int b = startBin;
-			while (b <= endBin) {
-				S2i1[b - startBin] += m.inside(b);
-				b = m.nextInside(b);
-			}
-
-		}		
-	}
-
-	private void forwardFast2(ArrayList<Marker> markers, int S[][], int startBin, int endBin) {
-		forwardFast2(markers, S, startBin, endBin, 0, markers.size());
-	}
-	// forward calculation, decreasing map positions
-	private void forwardFast2(ArrayList<Marker> markers, int S2[][], int startBin, int endBin, int start, int end)
-	{
-		for (int mi = start; mi < end; ++mi) {
-			Marker m = markers.get(mi);
-			int maxS = 0;
-			int S2i[] = S2[mi];
-			int S2i1[] = S2[mi + 1]; 
-			
-			for (int b = endBin - startBin; b >= 0; --b) { 
-                int s = S2i[b]; 
-                if (s > maxS)
-                    maxS = s;
-                S2i1[b] = maxS;// + m.inside(b + startBin); // add startBin as we subtract it from b 
-            }
-			int b = startBin;
-			while (b <= endBin) {
-				S2i1[b - startBin] += m.inside(b);
-				b = m.nextInside(b);
-			}
-
-		}		
-	}
-
-	//positions increasing
-	private int solveForward(ArrayList<Marker> markers) {
-		return solveForward(markers, getMinBin(markers), getMaxBin(markers));
-	}
-	private int solveForward(ArrayList<Marker> markers, int startBin, int endBin) {
-		//System.err.println(startBin);
-		//System.err.println(endBin);
-		
-		int numMarkers = markers.size();
-		int S[][] = new int[numMarkers + 1][endBin - startBin + 1];
-		int P[][] = new int[numMarkers + 1][endBin - startBin + 1];
-
-		forward1(markers, S, P, startBin, endBin);
-
-		int maxI = startBin;
-		for (int i = startBin; i <= endBin; ++i) { 
-            if (S[numMarkers][i - startBin] > S[numMarkers][maxI - startBin])
-                maxI = i;
-		}
-		
-		int ret = S[numMarkers][maxI - startBin];
-		
-		 // + orientation
-		for (int mi = numMarkers; mi > 0; --mi) {
-			markers.get(mi - 1).pPlus = maxI;
-			//System.err.println(markers.get(mi - 1) + "\t" + maxI);
-			maxI = P[mi][maxI - startBin];
-		}
-		return ret;
-	}
-	private int solveForwardFast(ArrayList<Marker> markers) {
-		return solveForwardFast(markers, getMinBin(markers), getMaxBin(markers));
-	}
-	private int solveForwardFast(ArrayList<Marker> markers, int startBin, int endBin) {
-		//System.err.println(startBin);
-		//System.err.println(endBin);
-		
-		int numMarkers = markers.size();
-		int S[][] = new int[numMarkers + 1][endBin - startBin + 1];
-
-		forwardFast1(markers, S, startBin, endBin);
-
-		int ret = 0;
-		int SnM[] = S[numMarkers];
-		for (int b = startBin; b <= endBin; ++b) {
-			int s = SnM[b - startBin];
-            if (s > ret)
-                ret = s;
-		}
-		
-		return ret;
-	}
-
-	
-	//positions decreasing
-	private int solveBackward(ArrayList<Marker> markers) {
-		return solveBackward(markers, getMinBin(markers), getMaxBin(markers));
-	}
-	private int solveBackward(ArrayList<Marker> markers, int startBin, int endBin) {
-		//System.err.println(startBin);
-		//System.err.println(endBin);
-		
-		int numMarkers = markers.size();
-
-		int S2[][] = new int[numMarkers + 1][endBin - startBin + 1];
-		int P2[][] = new int[numMarkers + 1][endBin - startBin + 1];
-		
-		forward2(markers, S2, P2, startBin, endBin);
-		
-		int maxI2 = endBin;
-		for (int i = endBin; i >= startBin; --i) { 
-            if (S2[numMarkers][i - startBin] > S2[numMarkers][maxI2 - startBin])
-                maxI2 = i;
-		}
-		
-		int ret = S2[numMarkers][maxI2 - startBin];
-		
-		 // - orientation
-		for (int mi = numMarkers; mi > 0; --mi) {
-			markers.get(mi - 1).pMinus = maxI2;
-			//System.err.println(markers.get(mi - 1) + "\t" + maxI2);
-			maxI2 = P2[mi][maxI2 - startBin];
-		}
-		return ret;
-	}
-	
-	public static int[] markerScore(ArrayList<Marker> markers)
-	{
-		PlaceAndOrientContigs poc = new PlaceAndOrientContigs();
-		return poc.solve(markers);
-	}
-	
-	private int[] solve(ArrayList<Marker> markers)
-	{
-		int scorePlus = solveForward(markers);
-		int scoreMinus = solveBackward(markers);
-		int ret[] = new int[]{scorePlus, scoreMinus};
-		return ret;
-	}
-	
-	public void loadBed(String fn, int chromosome)
-	{
-		bed = InputData.loadBed(fn, chromosome);
-		for (ContigInterval ci : bed) {
-			if (!bedHash.containsKey(ci.getContig())) {
-				bedHash.put(ci.getContig(), new ArrayList<ContigInterval>());
-				contigs.add(ci.getContig());
-			}
-			bedHash.get(ci.getContig()).add(ci);
-		}
-		for (String c: contigs) {
-			ArrayList<ContigInterval> aci = bedHash.get(c);
-			Collections.sort(aci); // Put positions into physical order
-			long prev = 0;
-			for (ContigInterval ci: aci) {
-				if (ci.getStart() > 0 && ci.getStart() > ci.getEnd() || ci.getStart() <= prev) { // check the consistency of the bed...
-					System.err.println(c + "\t" + ci.getStart() + "\t" + ci.getEnd());
-					System.err.println("Error: erroneous or overlapping intervals in the bed file");
-					System.exit(-1);
-				}
-				prev = ci.getEnd();
-			}
-		}
-		System.err.println(contigs.size() + " contigs loaded from the bed file");
-		//TODO: 
-	}
-
-	//reverse map
-	private void flip(ArrayList<Marker> markers) {
-		int max = getMaxBin(markers);
-		for (Marker m : markers)
-			m.flip(max);
-	}
-
-	private long[] chain2OneBase(String length, String orientation, String start, String stop)
-	{
-		if ("+".equals(orientation)) {
-			return new long[]{Long.parseLong(start) + 1, Long.parseLong(stop)};
-		}
-		else {
-			long l = Long.parseLong(length);
-			return new long[]{l - Long.parseLong(stop) + 1, l - Long.parseLong(start)};
-		}
-	}
-	
-	// first coordinate system to second
-	private long mapPosition12(ArrayList<long[]> alignment, long pos1, boolean sameOrientation){
-		int low = 0;
-		int high = alignment.size() - 1;
-		
-		while (low <= high) {
-			int mid = (low + high) / 2;
-			long a[] = alignment.get(mid);
-			long mpos = a[0];
-			long len = a[2];
-			
-			if (mpos > pos1)
-				high = mid - 1;
-			else if (mpos <= pos1 && mpos + len > pos1)
-				return a[1] + (sameOrientation ? (pos1 - mpos) : (mpos - pos1));
-			else if (mpos < pos1)
-				low = mid + 1;
-			else
-				return -1;
-		}
-		return -1; 
-	}
-
-	// second coordinate system to first
-	private long mapPosition21(ArrayList<long[]> alignment, long pos2, boolean sameOrientation){
-		int low = 0;
-		int high = alignment.size() - 1;
-		
-		while (low <= high) {
-			int mid = (low + high) / 2;
-			long a[] = alignment.get(mid);
-			long mpos = a[1];
-			long len = a[2];
-			if (sameOrientation) {
-				if (mpos > pos2)
-					high = mid - 1;
-				else if (mpos <= pos2 && mpos + len > pos2)
-					return a[0] + (pos2 - mpos);
-				else if (mpos < pos2)
-					low = mid + 1;
-				else
-					return -1;
-			} else {
-				if (mpos < pos2)
-					high = mid - 1;
-				else if (mpos >= pos2 && mpos - len < pos2)
-					return a[0] + (pos2 - mpos);
-				else if (mpos > pos2)
-					low = mid + 1;
-				else
-					return -1;
-			}
-		}
-		return -1; 
-	}
-	
-	//c2 is full haplotype of ofHaplotype?
-	private int calculateLiftOverHaplotype(ContigInterval ofHaplotype, int ofHaplotypeOrientation1, ContigInterval c2, ArrayList<long[]> alignment, boolean sameOrientation)
-	{
-		int score = 0;
-		for (int map = 0; map < numMaps; ++map) {
-			int numM2 = c2.getMarkers(map).size();
-
-			if (numM2 > 0) {
-				ArrayList<Marker> markers = new ArrayList<Marker>();
-				markers.addAll(ofHaplotype.getMarkers(map, ofHaplotypeOrientation1));
-
-				int score1 = solveForward(markers);
-
-				ArrayList<Marker> markers2 = c2.getMarkers(map);
-				for (Marker m: markers2) {
-					long p21 = mapPosition21(alignment, m.getPosition(), sameOrientation);
-					if (p21 > 0)
-						markers.add(new Marker(m, p21));
-				}
-				Collections.sort(markers);
-				if (ofHaplotypeOrientation1 != 0)
-					Collections.reverse(markers);
-				
-				score += solveForward(markers) - score1;
-			}
-		}
-		return score;
-	}	
-
-	private int[] calculateLiftOver(ContigInterval c1, int orientation1, ContigInterval c2, int orientation2, ArrayList<long[]> alignment, boolean sameOrientation, long interval1[], long interval2[])
-	{
-		int score1 = 0;
-		int score2 = 0;
-		for (int map = 0; map < numMaps; ++map) {
-			int numM1 = c1.getMarkers(map).size();
-			int numM2 = c2.getMarkers(map).size();
-			if (numM2 > 0 || numM1 > 0){ // markers in one or both contigs...
-				int start1 = 0;
-				int end1 = numM1 - 1;
-				if (orientation1 != 0) {
-					end1 = 0;
-					start1 = numM1 - 1;
-				}
-				
-				int start2 = 0;
-				int end2 = numM2 - 1;
-				if (orientation2 != 0) {
-					end2 = 0;
-					start2 = numM2 - 1;
-				}
-				
-				// c1|----------------|
-				//              ||||| (interval 1&2 markers put to am1 and am2)
-				//          c2|-------------|
-				
-				ArrayList<Marker> am1 = new ArrayList<Marker>(); 
-				ArrayList<Marker> am2 = new ArrayList<Marker>(); 
-				
-				while (orientation1 == 0 && end1 >= start1 && c1.getMarker(map, end1).position >= interval1[0]) {
-					if (c1.getMarker(map, end1).position <= interval1[1])
-						am1.add(c1.getMarker(map, end1));
-					--end1;
-				}
-
-				while (orientation1 != 0 && end1 <= start1 && c1.getMarker(map, end1).position <= interval1[1]) {
-					if (c1.getMarker(map, end1).position >= interval1[0])
-						am1.add(c1.getMarker(map, end1));
-					++end1;
-				}
-
-				while (orientation2 == 0 && end2 >= start2 && c2.getMarker(map, start2).position <= interval2[1]) {
-					if (c2.getMarker(map, start2).position >= interval2[0])
-						am2.add(c2.getMarker(map, start2));
-					++start2;
-				}
-
-				while (orientation2 != 0 && end2 <= start2 && c2.getMarker(map, start2).position >= interval2[0]) {
-					if (c2.getMarker(map, start2).position <= interval2[1])
-						am2.add(c2.getMarker(map, start2));
-					--start2;
-				}
-				
-				ArrayList<Marker> test1 = new ArrayList<Marker>();
-				if (orientation1 == 0) 
-					for (int i = start1; i <= end1; ++i)
-						test1.add(c1.getMarker(map, i));
-				else
-					for (int i = start1; i >= end1; --i)
-						test1.add(c1.getMarker(map, i));
-				
-				//DO MAGIC HERE...
-				Collections.reverse(am1);
-
-				ArrayList<Marker> mid1 = new ArrayList<Marker>();
-				ArrayList<Marker> mid2 = new ArrayList<Marker>();
-				ArrayList<Marker> merge1 = new ArrayList<Marker>();
-				ArrayList<Marker> merge2 = new ArrayList<Marker>();
-				
-				//merge1
-				for (Marker m : am1) {
-					long p2 = mapPosition12(alignment, m.getPosition(), sameOrientation);
-					if (p2 > 0) { // liftover possible
-						Marker m2 = new Marker(m, p2);
-						mid2.add(m2);
-					}
-				}
-				merge1.addAll(mid2);
-				merge1.addAll(am2);
-				Collections.sort(merge1);
-				if (orientation2 != 0)
-					Collections.reverse(merge1);
-				
-				//merge2
-				for (Marker m : am2) {
-					long p1 = mapPosition21(alignment, m.getPosition(), sameOrientation);
-					if (p1 > 0) { // liftover possible
-						Marker m2 = new Marker(m, p1);
-						mid1.add(m2);
-					}
-				}
-
-				merge2.addAll(mid1);
-				merge2.addAll(am1);
-				Collections.sort(merge2);
-
-				if (orientation1 != 0)
-					Collections.reverse(merge2);
-				
-				//System.err.println(numM2 + "\t" + start2 + "\t" + end2 + "\t" +  numM1 + "\t" + start1 + "\t" + end1 );
-				
-				ArrayList<Marker> test3 = new ArrayList<Marker>();
-				if (orientation2 == 0) 
-					for (int i = start2; i <= end2; ++i)
-						test3.add(c2.getMarker(map, i));
-				else
-					for (int i = start2; i >= end2; --i)
-						test3.add(c2.getMarker(map, i));
-
-				ArrayList<Marker> test = new ArrayList<Marker>();
-
-				// c1 + c2 
-				test.addAll(c1.getMarkers(map, orientation1));
-				test.addAll(c2.getMarkers(map, orientation2));
-				int s0 = solveForward(test);
-			
-				score1 -= s0;
-				score2 -= s0;
-
-				//System.err.println(solve(test)[0] + "\t(" + test.size() + ")\t");
-				
-				test.clear();
-				test.addAll(test1);
-				test.addAll(merge1);
-				test.addAll(test3);
-						
-				// c1 + merge1 + c2
-				int s1 = solveForward(test);
-				score1 += s1;
-				
-				//System.err.print(c1.getContig() + "_" + orientation1 + "\t" + c2.getContig() + "_" + orientation2);
-				
-				//System.err.print("\tscores\t" + solve(test)[0] + "\t(" + test.size() + ")\t");
-
-				test.clear();
-				test.addAll(test1);
-				test.addAll(merge2);
-				test.addAll(test3);
-				//System.err.print(solve(test)[0] + "\t(" + test.size() + ")\t");
-
-				// c1 + merge2 + c2
-				int s2 = solveForward(test);
-				score2 += s2;
-
-				//System.out.println(s0 + "\t" + s1 + "\t" + s2);
-				
-			}
-		}
-		return new int[]{score1, score2};
-	}
-	
-	// change alignment from contig1=>contig2 to contig2=>contig1
-	private ArrayList<long[]> reverseAlignment(ArrayList<long[]> a, boolean sameOrientation){
-		ArrayList<long[]> ret = new ArrayList<long[]>();
-		if (sameOrientation) {
-			for (long[] aa : a)
-				ret.add(new long[]{aa[1],aa[0], aa[2]});
-		} else {
-			int n = a.size();
-			for (int i = n - 1; i>=0; --i) { // reverse and add length for each block
-				long[] aa = a.get(i);
-				ret.add(new long[]{aa[1] - aa[2] + 1, aa[0] + aa[2] - 1, aa[2]});
-			}
-		}
-		return ret;
-	}
-	
-	public void loadProximity(String fn, int bin, int maxDistance, double scale){
-		prox = new Proximity(bin, maxDistance, scale);
-		boolean nempty = prox.loadData(fn, bedHash);
-		if (!nempty)
-			prox = null;
-	}
-	
-	public void loadPaf(String fn, int maxScore, double scalePaf){
- 		System.err.println("loading paf...");
-		try {
-			BufferedReader br = null;
-			if (fn.equals("-"))
-				br = new BufferedReader(new InputStreamReader(System.in));
-			else
-				br = new BufferedReader(new FileReader(fn));
-			
-			ArrayList<ArrayList<String>> rows = new ArrayList<ArrayList<String>>(); 
-			
-			do {
-				ArrayList<String> row = Input.loadTableRow(br, "\t ");
-				if (row == null)
-					break;
-
-				if (row.size() < 9) {
-					System.err.println("Warning: skipping row " + row);
-					continue;
-				}
-				
-				if (!bedHash.containsKey(row.get(0)) && bedHash.containsKey(row.get(5))) { // find "extra" contigs or single reads for scaffolding...
-					if (rows.size() == 0 || rows.get(0).get(0).equals(row.get(0)))
-						rows.add(row);
-					else {
-						processPAF(rows);
-						rows.clear();
-						rows.add(row);
-					}
-				}
-				
-			} while (true);
-			processPAF(rows);
-			System.err.println("Scaffolding links:"); 
-			for (String key: scaffoldingLink.keySet()) {
-				int value = (int)(0.5 + scalePaf * scaffoldingLink.get(key));
-				if (value > maxScore) {
-					value = maxScore;
-				}
-				scaffoldingLink.put(key, value);
-				System.err.println(key + "\t" +  value);
-			}
-			
-			br.close();
-	    } catch (Exception e) {
-	     	e.printStackTrace();
-			System.err.println("Error in file " + fn);
-      	}
-	}
-	
-	//int tmps = 0;
-	
-	private void helperPAF1(ContigInterval ci1, ContigInterval ci2, ArrayList<String> row1, ArrayList<String> row2) {
-
-		//check that alignments are in right order in the read...
-		
-		long rstart1 = Long.parseLong(row1.get(2));
-		long rend1 = Long.parseLong(row1.get(3));
-		
-		long rstart2 = Long.parseLong(row2.get(2));
-		long rend2 = Long.parseLong(row2.get(3));
-
-		// require non-intersecting intervals...		
-		if (Misc.intersectIntervalsLength(rstart1, rend1, rstart2, rend2) > maxIntersect)
-			return;
-			
-		boolean plus = row1.get(4).equals("+");
-		boolean r1first = rstart1 < rstart2;
-		
-		long start1 = Long.parseLong(row1.get(7));
-		long end1 = Long.parseLong(row1.get(8));
-
-		long start2 = Long.parseLong(row2.get(7));
-		long end2 = Long.parseLong(row2.get(8));
-		
-		//++ orientation
-		long gap1 = ci1.calculateGapLength(0, start1 + 1, end1);
-		long gap2 = ci2.calculateGapLength(1, start2 + 1, end2);
-		
-		long length1 = end1 - start1;
-		long length2 = end2 - start2;
-		
-		if (length1 - gap1 > 0 && length2 - gap2 > 0 ) {
-			if (plus ^ !r1first) {
-				//System.err.println(ci1.getContig() + "->" + ci2.getContig());
-				String key = ci1.toString() + '+' + ci2.toString() + '+';
-				scaffoldingLink_tmp.put(key, 1);
-				scaffoldingLinkInfo.put(key, row1.get(0));
-			} else { // read is not consistent
-				//System.err.println("*");
-				//System.err.println(row1);
-				//System.err.println(ci1);
-				//System.err.println(row2);
-				//System.err.println(ci2);			
-				//System.err.println("*");
-			}
-		}
-		//-- orientation
-		gap1 = ci1.calculateGapLength(1, start1 + 1, end1);
-		gap2 = ci2.calculateGapLength(0, start2 + 1, end2);
-
-		if (length1 - gap1 > 0 && length2 - gap2 > 0) {
-			if  (plus ^ r1first) {
-				//System.err.println(ci1.getContig() + "->" + ci2.getContig());
-				String key = ci1.toString() + '-' + ci2.toString() + '-';
-				scaffoldingLink_tmp.put(key, 1);
-				scaffoldingLinkInfo.put(key, row1.get(0));
-				
-			} else { // read is not consistent
-				//System.err.println("*");
-				//System.err.println(row1);
-				//System.err.println(ci1);
-				//System.err.println(row2);
-				//qSystem.err.println(ci2);			
-				//System.err.println("*");
-			}
-		}
-	}
-
-	private void helperPAF2(ContigInterval ci1, ContigInterval ci2, ArrayList<String> row1, ArrayList<String> row2) {
-		//check that alignments are in right order in the read...
-		long rstart1 = Long.parseLong(row1.get(2));
-		long rend1 = Long.parseLong(row1.get(3));
-		long rstart2 = Long.parseLong(row2.get(2));
-		long rend2 = Long.parseLong(row2.get(3));
-
-		// require non-intersecting intervals...		
-		if (Misc.intersectIntervalsLength(rstart1, rend1, rstart2, rend2) > maxIntersect)
-			return;
-			
-		boolean plus = row1.get(4).equals("+");
-		boolean r1first = rstart1 < rstart2;
-		
-		long start1 = Long.parseLong(row1.get(7));
-		long end1 = Long.parseLong(row1.get(8));
-
-		long start2 = Long.parseLong(row2.get(7));
-		long end2 = Long.parseLong(row2.get(8));
-		
-		//+- orientation
-		long gap1 = ci1.calculateGapLength(0, start1 + 1, end1);
-		long gap2 = ci2.calculateGapLength(0, start2 + 1, end2);
-		
-		long length1 = end1 - start1;
-		long length2 = end2 - start2;
-		
-		if (length1 - gap1 > 0 && length2 - gap2 > 0) {
-		 	if (plus ^ !r1first) {
-				//System.err.println(ci1.getContig() + "->" + ci2.getContig());
-				String key = ci1.toString() + '+' + ci2.toString() + '-';
-				scaffoldingLink_tmp.put(key, 1);
-				scaffoldingLinkInfo.put(key, row1.get(0));
-			} else { // read is not consistent
-				//System.err.println("*");
-				//System.err.println(row1);
-				//System.err.println(ci1);
-				//System.err.println(row2);
-				//System.err.println(ci2);
-				//System.err.println("*");
-			}
-		}
-		//-+ orientation
-		gap1 = ci1.calculateGapLength(1, start1 + 1, end1);
-		gap2 = ci2.calculateGapLength(1, start2 + 1, end2);
-
-		if (length1 - gap1 > 0 && length2 - gap2 > 0) {
-		 	if (plus ^ r1first) {
-				//System.err.println(ci1.getContig() + "->" + ci2.getContig());
-				String key = ci1.toString() + '-' + ci2.toString() + '+';
-				scaffoldingLink_tmp.put(key, 1);
-				scaffoldingLinkInfo.put(key, row1.get(0));
-			
-			} else { // read is not consistent
-				//System.err.println("*");
-				//System.err.println(row1);
-				//System.err.println(ci1);
-				//System.err.println(row2);
-				//System.err.println(ci2);
-				//System.err.println("*");
-			}
-		}
-	}	
-
-	private void processPAF(ArrayList<ArrayList<String>> rows)
-	{
-		HashMap<String, ArrayList<ArrayList<String>>> alignmentHash = new HashMap<String, ArrayList<ArrayList<String>>>();
-		for (ArrayList<String> row : rows) {
-			ArrayList<ArrayList<String>> a = alignmentHash.get(row.get(5));
-			if (a == null) {
-				a = new ArrayList<ArrayList<String>>();
-				alignmentHash.put(row.get(5), a);
-			}
-			a.add(row);
-		}
-		ArrayList<String> contigs = new ArrayList<String>();
-		
-		contigs.addAll(alignmentHash.keySet());
-		
-		int numContigs = contigs.size();
-		
-		for (int c1 = 0; c1 < numContigs; ++c1) {
-			String contig1 = contigs.get(c1); 
-			//for (int c2 = c1 + 1; c2 < numContigs; ++c2) {
-			for (int c2 = c1; c2 < numContigs; ++c2) { //allow links between same contig...
-
-				if (c1 == c2 && bedHash.get(contig1).size() <= 1) // no need to go further if only one possible ContigInterval and contig...
-					continue;
-				
-				String contig2 = contigs.get(c2);
-				
-				
-				ArrayList<ArrayList<String>> rows1 = alignmentHash.get(contig1); 
-				ArrayList<ArrayList<String>> rows2 = alignmentHash.get(contig2);
-
-				
-				for (ArrayList<String> row1 : rows1)
-					for (ArrayList<String> row2 : rows2) {
-						long rstart1 = Long.parseLong(row1.get(2));
-						long rend1   = Long.parseLong(row1.get(3));
-						long rstart2 = Long.parseLong(row2.get(2));
-						long rend2   = Long.parseLong(row2.get(3));
-						
-						// require non-intersecting intervals...		
-						long il = Misc.intersectIntervalsLength(rstart1, rend1, rstart2, rend2);
-
-						if (il > maxIntersect || il > 0.5 * Math.min(rend1 - rstart1, rend2 - rstart2))
-							continue;
-
-						//TODO: Take into account useChainAndPaf in the calculation of bridgeLength and other...
-						//TODO: Have to take into account the contig overlap...
-
-						//read  [rs1  re1] [rs2   re2], bridgeLength = rs2-re1
-						//read  [rs2  re2] [rs1   re1], bridgeLength = rs1-re2
-						long bridgeLength = Math.max(rstart2 - rend1, rstart1 - rend2);
-						if (bridgeLength > maxBridge)
-							continue;
-					
-						if (row1.get(4).equals(row2.get(4))) { // same orientation
-							for (ContigInterval ci1 : bedHash.get(contig1)) {
-								for (ContigInterval ci2 : bedHash.get(contig2)) {
-									if (ci1 != ci2) {
-										helperPAF1(ci1, ci2, row1, row2);
-										helperPAF1(ci2, ci1, row2, row1);
-									}
-								}
-							}
-								
-						} else { // different orientation
-							for (ContigInterval ci1 : bedHash.get(contig1)) {
-								for (ContigInterval ci2 : bedHash.get(contig2)) {
-									if (ci1 != ci2) {
-										helperPAF2(ci1, ci2, row1, row2);
-										helperPAF2(ci2, ci1, row2, row1);
-									}
-								}
-							}
-						}
-					}
-			}
-		}
-		
-		for (String key : scaffoldingLink_tmp.keySet()) {
-			Integer os = scaffoldingLink.get(key);
-			if (os == null)
-				scaffoldingLink.put(key, scaffoldingLink_tmp.get(key));
-			else
-				scaffoldingLink.put(key, os + scaffoldingLink_tmp.get(key));
-		}
-		scaffoldingLink_tmp.clear();
-		
-		//if (numContigs > 1)
-		//	System.err.println(numContigs + "\t" + (++tmps));
-		
-		//calculate coverage for each contig (reads spanning each position...)
-	}
-	
-	private void addHaplotype(ContigInterval ofHaplotype, int ofHaplotypeOrientation, ContigInterval haplotype, long ha[], double ascore, ArrayList<long []> alignment, boolean sameOrientation)
-	{
-		
-		int haplotypeScore = (int) (ascore - haplotype.calculateGapLengthHaplotype(ha[0], ha[1]) * cutPenalty + 0.5); //+0.5 = rounding
-		if (haplotypeScore >= minHaplotypeAlignmentScore) {
-			haplotypeScore += calculateLiftOverHaplotype(ofHaplotype, ofHaplotypeOrientation, haplotype, alignment, sameOrientation);
-			if (haplotypeScore > 0) {
-				String key = ofHaplotype.toString() + ((ofHaplotypeOrientation == 0) ? '+':'-') + haplotype.toString();
-				Integer oscore = chainHaplotypeHash.get(key);
-				if (oscore == null || oscore < haplotypeScore) {
-					chainHaplotypeHash.put(key, (int) haplotypeScore);
-					chainHaplotypeCut.put(key, ha);
-				}
-	
-				//System.err.println(key + "\t" + (ascore * scaleScore - calculateGapLengthHaplotype(ci2, p2[0], p2[1])  * cutPenalty) + "\t" + haplotypeScore1 + "\thaplotype");
-			}
-		}
-	}
-
-	// add score between contigs ci1 and ci2 in these orientation based on alignment chain...
-	private void addChainLink(ContigInterval ci1, int orientation1, ContigInterval ci2, int orientation2, long ai1[], long ai2[], double ascore, ArrayList<long []> alignment, boolean sameOrientation)
-	{
-		long l1 = ci1.calculateGapLength(orientation1, ai1[0], ai1[1]);
-		long l2 = ci2.calculateGapLength(1 - orientation2, ai2[0], ai2[1]);
-		
-		double score = ascore;
-		if ((orientation1 == orientation2) != sameOrientation)
-			score *= orientationPenalty;
-		
-		score -= (l1 + l2) * cutPenalty;
-		
-		if (score >= minLinkAlignmentScore) { // is this needed?
-			int los[] = calculateLiftOver(ci1, orientation1, ci2, orientation2, alignment, sameOrientation, ai1, ai2);
-			int max1 = 0;
-			if (los[1] > los[0])
-				max1 = 1;
-
-			score += los[max1];
-			
-			if (score >= 0.5) {
-				String key = ci1.toString() + ((orientation1 == 0) ? '+':'-') + ci2.toString() + ((orientation2 == 0) ? '+':'-');
-				//System.err.println(key + "\t" + score1);
-				Integer oldScore = chainLinkHash.get(key);
-				score = (int)(score + 0.5); // round up...
-				if (oldScore == null || oldScore < score) {
-					chainLinkHash.put(key, (int) score);
-					
-					//if ((orientation1 == orientation2) != sameOrientation) { // orientation do not match... make a palindrome...
-					//	long start1 = (orientation1 == 0) ? ai1[1] : ai1[0];
-					//	chainLinkHashCut1.put(key, start1);
-					//	chainLinkHashCut1a.put(key, start1);
-					//	long end2 = (orientation2 == 0) ? ai2[0] : ai2[1];
-					//	chainLinkHashCut2.put(key, end2);
-					//	chainLinkHashCut2a.put(key, end2);
-					//} else 
-					{
-						if (orientation1 == 0) { // + orientation
-							if (max1 == 1) {
-								chainLinkHashCut1.put(key, ai1[1]); // take whole alignment
-								chainLinkHashCut1a.put(key, ai1[0] - 1);
-							}
-							else {
-								chainLinkHashCut1.put(key, ai1[0] - 1); // cut just before alignment
-								chainLinkHashCut1a.put(key, ai1[1]);
-							}
-						}
-						else { // - orientation
-							if (max1 == 1) {
-								chainLinkHashCut1.put(key, ai1[0]); // whole
-								chainLinkHashCut1a.put(key, ai1[1] + 1);
-							}
-							else {
-								chainLinkHashCut1.put(key, ai1[1] + 1); // after
-								chainLinkHashCut1a.put(key, ai1[0]);
-							}
-						}
-	 					if (orientation2 == 0) { // + orientation
-							if (max1 == 1) {
-								chainLinkHashCut2.put(key, ai2[1] + 1); // after
-								chainLinkHashCut2a.put(key, ai2[0]);
-							}
-							else {
-								chainLinkHashCut2.put(key, ai2[0]); // whole
-								chainLinkHashCut2a.put(key, ai2[1] + 1);
-							}
-						}
-						else { // - orientation
-							if (max1 == 1) {
-								chainLinkHashCut2.put(key, ai2[0] - 1); // before
-								chainLinkHashCut2a.put(key, ai2[1]);
-							}
-							else {
-								chainLinkHashCut2.put(key, ai2[1]); // whole
-								chainLinkHashCut2a.put(key, ai2[0] - 1);
-							}
-						}
-					}
-				}
-			}
-		}
-	}
-	// Find largest index i, where array[i] <= value, array sorted ascending order
-	private int binarySearchR(ArrayList<Integer> array, int value){
-		int right = array.size() - 1;
-		if (right < 0)
-			return -1;
-		int left = 0;
-		
-		while (right > left + 1) {
-			int mid = (left + right) / 2;
-			int am = array.get(mid); 
-			if (am > value)
-				right = mid - 1;
-			else
-				left = mid + ((am == value) ? 0 : 1);
-		}
-		if (array.get(right) <= value)
-			return right;
-		if (array.get(left) <= value)
-			return left;
-		return left - 1;
-	}
-	
-	// Find smallest index i, where array[i] >= value, array sorted ascending order
-	private int binarySearchL(ArrayList<Integer> array, int value){
-		int right = array.size() - 1;
-		if (right < 0)
-			return 0;
-		int left = 0;
-		
-		while (right > left + 1) {
-			int mid = (left + right) / 2;
-			int am = array.get(mid); 
-			if (am < value)
-				left = mid + 1;
-			else
-				right = mid - ((am == value) ? 0 : 1);
-		}
-		if (array.get(left) >= value)
-			return left;
-		if (array.get(right) >= value)
-			return right;
-		return right + 1;
-	}
-	
-	//calculate how many markers in array between start and stop
-	// array sorted
-	private int calculateNumMarkers(ArrayList<Integer> array, int start, int end)
-	{
-		return  (binarySearchR(array, end) - binarySearchL(array, start) + 1);
-	}
-	
-	private long[] getStartEnd1(ArrayList<long[]> alignment)
-	{
-		long first[] = alignment.get(0);
-		long last[] = alignment.get(alignment.size() - 1);
-		return new long[]{first[0], last[0] + last[2] - 1};
-	}
-
-	private long[] getStartEnd2(ArrayList<long[]> alignment, boolean sameOrientation)
-	{
-		long first[] = alignment.get(0);
-		long last[] = alignment.get(alignment.size() - 1);
-		if (sameOrientation)
-			return new long[]{first[1], last[1] + last[2] - 1};
-		else
-			return new long[]{last[1] - last[2] + 1, first[1]}; 
-	}
-	
-	//
-	private double trimChain(ArrayList<long[]> alignment, boolean sameOrientation, ContigInterval ci1, ContigInterval ci2, ArrayList<long[]> ret) {
-		if (alignment.size() == 0)
-			return 0.0;
-
-		long ap1[] = getStartEnd1(alignment); 
-		long ap2[] = getStartEnd2(alignment, sameOrientation);
-
-		// if contig intervals and alignment do not intersect, we are done here...
-		if (!Misc.intersectIntervals(ap1[0], ap1[1], ci1.getMinStart(), ci1.getMaxEnd()) || !Misc.intersectIntervals(ap2[0], ap2[1], ci2.getMinStart(), ci2.getMaxEnd()))
-			return 0.0;
-		long trimLength1[] = new long[2];
-		
-		if (ap1[0] < ci1.getMinStart()) // alignment spans too far
-			trimLength1[0] = ci1.getMinStart() - ap1[0];
-		if (ap1[1] > ci1.getMaxEnd()) // alignment spans too far
-			trimLength1[1] = ap1[1] - ci1.getMaxEnd();
-
-		long trimLength2[] = new long[2];
-		
-		
-		if (ap2[0] < ci2.getMinStart()) // alignment spans too far 
-			trimLength2[0] = ci2.getMinStart() - ap2[0];  
-		if (ap2[1] > ci2.getMaxEnd()) // alignment spans too far
-			trimLength2[1] = ap2[1] - ci2.getMaxEnd();
-
-		if (!sameOrientation) {
-			long tmp =  trimLength2[0];
-			trimLength2[0] = trimLength2[1];
-			trimLength2[1] = tmp; 
-		}
-		
-		long tl1 = trimLength1[0] + trimLength2[0];
-		long tl2 = trimLength1[1] + trimLength2[1];
-		if (tl1 + tl2 > 0) {
-			//System.err.println("Alignment of " + ci1.getContig() + " and " + ci2.getContig() + " needs trimming of " + (tl1 + tl2));
-
-			long first[] = alignment.get(0);
-			long last[] = alignment.get(alignment.size() - 1);
-			//System.err.println(first[0] + "\t" + first[1] + "\t" + last[0] + "\t" + last[1] + "\t" + last[2] + "\t" + ci1 + "\t" + ci2);
-			
-			long alignL = 0;
-			for (long[] a : alignment) 
-				alignL += a[2];
-			
-			int t1 = 0;
-			long wt1 = 0;
-			long totalW1 = 0;
-			if (tl1 > 0) {
-				for (long[] a : alignment) {
-					long w = a[2];
-					long dt1 = a[0] - ap1[0];
-					long dt2 = ((sameOrientation) ? a[1] - ap2[0] : ap2[1] - a[1]);
-					if (dt1 + w - 1 >= trimLength1[0] && dt2 + w - 1 >= trimLength2[0]) {
-						if (dt1 >= trimLength1[0] && dt2 >= trimLength2[0]) {
-							wt1 = 0;
-							//System.err.print("*full ");
-						} else {
-							wt1 = Math.max(trimLength1[0] - dt1, trimLength2[0] - dt2);
-							//System.err.print("*"+ wt1 + " of " +  w + " ");
-						}
-						totalW1 += wt1;
-						//System.err.println("trimming " + t1 + " blocks (of " + alignment.size() +  ") with length " + dt1 + "\t" + dt2 + "\t" + ((alignL - totalW1) / (double) alignL));
-						
-						break;
-					} else
-						totalW1 += w;
-					++t1;
-				}
-			}
-
-			int t2 = 0;
-			long wt2 = 0;
-			long totalW2 = 0;
-			if (tl2 > 0) {
-				for (int ai = alignment.size() - 1; ai >= 0; --ai) {
-					long[] a = alignment.get(ai);
-					long w = a[2];
-
-					long p1 = a[0] + w - 1;
-					long p2 = ((sameOrientation) ? a[1] + w - 1 : a[1] - w + 1);
-					
-					long dt1 = ap1[1] - p1;
-					long dt2 = ((sameOrientation) ? ap2[1] - p2 : p2 - ap2[0]);
-
-					if (dt1 + w - 1 >= trimLength1[1] && dt2 + w - 1 >= trimLength2[1]) {
-						if (dt1 >= trimLength1[1] && dt2 >= trimLength2[1]) {
-							wt2 = 0;
-							//System.err.print("full ");
-						} else {
-							wt2 = Math.max(trimLength1[1] - dt1, trimLength2[1] - dt2);
-							//System.err.print(wt2 + " of " +  w + " ");
-						}
-						totalW2 += wt2;
-						//System.err.println("trimming " + t2 + " blocks (of " + alignment.size() +  ") with length " + dt1 + "\t" + dt2 + "\t" + ((alignL - totalW2) / (double) alignL));
-						
-						break;
-					} else
-						totalW2 += w;
-					++t2;
-				}
-			}
-			if (totalW1 + totalW2 >= alignL) {
-				//System.err.println("all trimmed of a chain");
-				return 0.0; // all trimmed off
-			} else {
-				ret.clear();
-				int n = alignment.size();
-				for (int i = t1; i < n - t2; ++i) {
-					long a[] = alignment.get(i);
-					if (i == t1 && wt1 > 0) {
-						ret.add(new long[]{a[0] + wt1, a[1] + ((sameOrientation) ? + wt1 : -wt1), a[2] - wt1});
-					} else if (i == n - t2 - 1 && wt2 > 0) {
-						ret.add(new long[]{a[0], a[1], a[2] - wt2});
-					} else
-						ret.add(a);
-				}
-				return (alignL - totalW1 - totalW2) / (double) alignL;
-			}
-			
-		} else {
-			//System.err.println("Alignment of " + ci1.getContig() + " and " + ci2.getContig() + " does not need trimming");
-			return 1.0;
-		}
-		//total length of aligning bases...
-	}
-	
-	public void loadChain(String fn){
-		int numAlignments = 0;
-		/*
-		//calculate data structure to get the number of marker in each interval in O(log(n)) time
-		
-		HashMap<String, ArrayList<Integer>> markerHash = new HashMap<String, ArrayList<Integer>>();
-		for (ContigInterval ci : intervalsInChr) {
-			ArrayList<Integer> markers = new ArrayList<Integer>();
-			markerHash.put(ci.getContig(), markers);
-			for (int map = 0; map < numMaps; ++map)
-				for (Marker m : ci.getMarkers(map))
-					markers.add(m.getPosition());
-			Collections.sort(markers);
-		}*/
-
- 		System.err.println("loading alignment chain...");
-		try {
-			BufferedReader br = null;
-			if (fn.equals("-"))
-				br = new BufferedReader(new InputStreamReader(System.in));
-			else
-				br = new BufferedReader(new FileReader(fn));
-			do {
-				ArrayList<String> row = Input.loadTableRow(br, "\t ");
-				if (row == null)
-					break;
-				boolean skip = true;
-				if (row.size() >= 12 && "chain".equals(row.get(0))) {
-					String contig1 = row.get(2);
-					String contig2 = row.get(7);
-					
-					if (bedHash.containsKey(contig1) && bedHash.containsKey(contig2)) {
-						skip = false;
-						long p1_[] = chain2OneBase(row.get(3), row.get(4), row.get(5), row.get(6));
-						long p2_[] = chain2OneBase(row.get(8), row.get(9), row.get(10), row.get(11));
-						if ("-".equals(row.get(4))) {
-							System.err.println("Error: only ++, and +- orientation allowed in the chain file");
-							continue;
-						}
-						double ascore_ = scaleScore * Double.parseDouble(row.get(1)); // alignment score
-	
-						//int numMarkers1 = calculateNumMarkers(markerHash.get(contig1), p1[0], p1[1]);
-						//int numMarkers2 = calculateNumMarkers(markerHash.get(contig2), p2[0], p2[1]);
-						//System.err.println(contig1 + "\t" + p1[0] + " " + p1[1] + " " + numMarkers1);
-						//System.err.println(contig2 + "\t" + p2[0] + " " + p2[1] + " " + numMarkers2);
-						
-						boolean sameOrientation = row.get(4).equals(row.get(9));
-
-						// load alignment for liftover...
-						ArrayList<long[]> alignment_ = new ArrayList<long[]>();
-						ArrayList<String> row2 = null;
-						long v1 = p1_[0];
-						long v2 = ((sameOrientation) ? p2_[0] : p2_[1]);
-						int v3 = 0;
-						do {
-							row2 = Input.loadTableRow(br, "\t ");
-							
-							v3 = Integer.parseInt(row2.get(0));
-							alignment_.add(new long[]{v1, v2, v3});
-							v1 += v3;
-							v2 += ((sameOrientation) ? v3 : -v3);
-							if (row2.size() >= 3) {
-								v1 += Integer.parseInt(row2.get(1));
-								v2 += ((sameOrientation) ? Integer.parseInt(row2.get(2)) : -Integer.parseInt(row2.get(2)));
-							}
-						} while (row2 != null && row2.size() >= 3);
-						
-						ArrayList<long[]> revAlignment_ = reverseAlignment(alignment_, sameOrientation);
-
-						//System.err.println(row);
-						//for (int[] a : alignment)
-						//	System.err.println(a[0] + "\t" +  a[1] + "\t" + a[2]);
-
-						//for (int i = 1; i<=100; i+=1)
-						//	System.err.println(mapPosition12(alignment, i, sameOrientation));
-						//System.err.println("*");
-						//for (int i = 1; i<=100; i+=1)
-						//	System.err.println(mapPosition21(alignment, i, sameOrientation));
-							
-						//if (true)
-						//	System.exit(-1);
-					
-						//check here
-						
-						for (ContigInterval ci1 : bedHash.get(contig1))
-							for (ContigInterval ci2 : bedHash.get(contig2)) {
-								
-								ArrayList<long[]> alignment = new ArrayList<long[]>();
-								
-								double t = trimChain(alignment_, sameOrientation, ci1, ci2, alignment);
-								if (t == 0.0)
-									continue;
-								
-								ArrayList<long[]> revAlignment = new ArrayList<long[]>();
-								long p1[]; 
-								long p2[];
-								double ascore = t * ascore_;
-								
-								if (t < 1.0) {
-									double t2 = trimChain(revAlignment_, sameOrientation, ci2, ci1, revAlignment);
-									if (t != t2) {
-										System.err.println("Error in parsing alignment chain:" + t +"!="+  t2);
-										System.exit(-1);
-									}
-									
-									p1 = getStartEnd1(alignment);
-									p2 = getStartEnd2(alignment, sameOrientation);
-									if (p2[0] > p2[1]) {
-										long tmp = p2[0];
-										p2[0] = p2[1];
-										p2[1] = tmp; 
-									}
-									
-								} else {
-									alignment = alignment_;
-									revAlignment = revAlignment_;
-									p1 = p1_;
-									p2 = p2_;
-								}
-								for (int orientation1 = 0; orientation1 < 2; ++orientation1) { 
-									//calculate haplotype scores...
-									//ci2 is the haplotype of ci1?
-									addHaplotype(ci1, orientation1, ci2, p2, ascore, alignment, sameOrientation);
-									//ci1 is the haplotype of ci2?
-									//use orientation1 for ci2 as well... (1 - orientation is not really needed)
-									addHaplotype(ci2, 1 - orientation1, ci1, p1, ascore, revAlignment, sameOrientation);
-									
-									for (int orientation2 = 0; orientation2 < 2; ++orientation2) {  // four combinations, ++/+-/-+/--
-										//add partial haplotype link scores
-										addChainLink(ci1, orientation1, ci2, orientation2, p1, p2, ascore, alignment, sameOrientation);
-										//add partial haplotype link scores (1 - orientation is not really needed)
-										addChainLink(ci2, 1 - orientation2, ci1, 1 - orientation1, p2, p1, ascore, revAlignment, sameOrientation);
-											//System.err.println("hiphei");										
-									}
-								}
-							}
-							
-					++numAlignments;
-					}
-				} else {
-					if (skip && (row.size() == 3 || row.size() == 1))
-						;
-					else
-						System.err.println("Warning: skipping " + row);
-				}
-			} while (true);
-			br.close();
-	    } catch (Exception e) {
-	     	e.printStackTrace();
-			System.err.println("Error in file " + fn);
-      	}
-		System.err.println("loading " +  numAlignments + " alignments");
-		
-		System.err.println("Alignment links:");
-		for (String key:chainLinkHash.keySet()) 
-			System.err.println(key + "\t" + chainLinkHash.get(key));		
-	}
-
-	public void addMap(String fn, boolean flip, boolean nochromosome, boolean nointervals, int chromosome)
-	{
-		
-		ArrayList<Marker> markers = InputData.loadMap(fn, nochromosome, nointervals, compressMap);
-		
-		if (flip) {
-			flip(markers);
-		}
-
-		for (Marker m : markers) 
-			if (chromosome <= 0 || m.getChromosome() == chromosome) { 
-			boolean inside = false;
-			if (bedHash.containsKey(m.contig))
-				for (ContigInterval ci : bedHash.get(m.getContig())) {
-					if (ci.inside(m.position)) {
-						inside = true;
-						ci.addMarker(m, numMaps);
-						break;
-					}
-				}
-			if (!inside) {
-//				System.err.println(m);
-//				System.err.println("Warning: marker position not listed in the bed file");
-				//System.exit(-1);
-			}
-		}		
-		System.err.println("#map = " + fn);
-		System.err.println("contig\tstart_pos\tend_pos\tscore+orientation\tscore-orientation");
-		for (ContigInterval ci : bed) {
-			if (ci.markers.size() > numMaps) {
-				Collections.sort(ci.markers.get(numMaps)); // Put positions into physical order
-
-				int scores[] = solve(ci.markers.get(numMaps));	// Solve marker positions by dynamic programming...
-				//ci.scores.set(numMaps, scores);
-				
-				System.err.println(ci + "\t" + scores[0] + "\t" + scores[1]);
-			}
-		}
-		++numMaps;
-
-		int maxChromosome = 0;
-		for (ContigInterval ci : bed)
-			maxChromosome = Math.max(maxChromosome, ci.getChromosome());
-
-		int minChromosome = maxChromosome; 
-		for (ContigInterval ci : bed)
-			if (ci.getChromosome() > 0)
-				minChromosome = Math.min(minChromosome, ci.getChromosome());
-		
-		if (minChromosome != maxChromosome) {
-			System.err.println("Error: Only one chromosome allowed in the input maps!");
-			System.exit(-1);
-		}
-		
-		intervalsInChr = new ArrayList<ContigInterval>();
-
-		for (ContigInterval ci : bed) {
-			if (ci.getChromosome() == maxChromosome || ci.getChromosome() == 0)
-				intervalsInChr.add(ci);
-		}
-		
-	}
-	
-	public void combineMaps(boolean findOrientation, boolean randomOrder, boolean finalImprove)
-	{
-		//(remove) check intervals without any markers...
-		ArrayList<ContigInterval> contigsWithMarkers = new ArrayList<ContigInterval>(); 
-
-		ArrayList<ContigInterval> contigsWithoutMarkers = new ArrayList<ContigInterval>(); 
-
-		for (ContigInterval ci : intervalsInChr) {
-			if (ci.markers.size() > 0)
-				contigsWithMarkers.add(ci);
-			else {
-				contigsWithoutMarkers.add(ci);
-				System.err.println("Contig " + ci + " does not have any markers");
-			}
-		}
-		intervalsInChr = contigsWithMarkers;
-		if (keepEmptyIntervals)
-			for (ContigInterval ci : contigsWithoutMarkers) {
-				intervalsInChr.add(ci);
-			}
-		
-		
-		
-		if (randomOrder) { // destroy initial solution... 
-			Collections.shuffle(intervalsInChr);
-			for (ContigInterval c : intervalsInChr)
-				if (Math.random() < 0.5)
-					c.flipOrientation();
-		} else { // find contig order by ordering contigs on the most abundant marker
-
-			ArrayList<Marker> allMarkers = getMarkers(intervalsInChr, null, 0);
-			
-			int maxBin = getMaxBin(allMarkers);
-			int minBin = getMinBin(allMarkers);
-			
-			//int n = intervalsInChr.size();
-			ArrayList<Double> sortValues = new ArrayList<Double>();
-			
-			for (ContigInterval ci : intervalsInChr) {
-				ArrayList<Marker> markersInFirstMap = ((ci.markers.size() > 0) ? ci.markers.get(0) : new ArrayList<Marker>());
-				int s[] = solve(markersInFirstMap);
-				if (s[1] > s[0] || (s[1] == s[0] && Math.random() < 0.5))  
-					ci.flipOrientation();
-				
-				HashMap<Integer, Integer> hm = new HashMap<Integer, Integer>();
-				
-				for (Marker m : markersInFirstMap) {
-					int numI = m.intervals.length;
-					for (int i = 0; i < numI; i+=2)
-						for (int p = m.intervals[i]; p <= m.intervals[i + 1]; ++p) {
-							Integer oldValue = hm.get(p);
-							if (oldValue == null)
-								hm.put(p, 1);
-							else
-								hm.put(p, oldValue + 1);
-						}
-				}
-					
-				int maxCount = -1;
-				int bin = 0;
-				int numMaxCount = 0;
-				for (int p : hm.keySet()) {
-					int count = hm.get(p); 
-					if (count > maxCount) {
-						numMaxCount = 1;
-						bin = p;
-						maxCount = count;
-					} else if (count == maxCount) {
-						++numMaxCount;
-						if (Math.random() * numMaxCount < 1.0) // randomly pick one of multiple bins with maximum count
-							bin = p;
-					}
-				}
-				if (maxCount > 0) // there was at least one marker
-					sortValues.add(bin + Math.random()); //bin + rand[0,1]
-				else // no markers
-					sortValues.add(Math.random() * (maxBin - minBin + 1) + minBin);
-			}
-		    Misc.ArrayIndexComparator<Double> comparator = new Misc.ArrayIndexComparator<Double>(sortValues);
-		    Integer[] indexes = comparator.createIndexArray();
-		    Arrays.sort(indexes, comparator);
-		    
-			ArrayList<ContigInterval> cis_new = new ArrayList<ContigInterval>(); 
-		    for (int i : indexes)
-		    	cis_new.add(intervalsInChr.get(i));
-		    intervalsInChr = cis_new;
-		}
-		if (findOrientation && numMaps > 1) {
-			String orientation = "+";
-			String scores = "";
-
-			//disable chains
-			HashMap<String, Integer> oldChainLinkHash = chainLinkHash;
-			chainLinkHash = new HashMap<String, Integer>();
-			
-			//use only first map
-			int oldNumMaps = numMaps;
-			numMaps = 1;
-			
-			ArrayList<ContigInterval> cis_new = new ArrayList<ContigInterval>(); 
-
-			for (ContigInterval ci : intervalsInChr) {
-				if (ci.markers.size() > 0 && ci.markers.get(0).size() > 0)
-					cis_new.add(ci);
-			}
-			
-			//Collections.shuffle(cis_new); // random order as init (could be based on most common marker in each contig...)
-			
-			for (int map = 1; map < oldNumMaps; ++map) {
-				int oldNumRuns = numRuns;
-				if (map == 1)
-					numRuns = Math.min(2, oldNumRuns);
-				else
-					numRuns = 1; // this is probably enough...
-				improveAnchoring(cis_new, false, true);
-				numRuns = oldNumRuns;
-						
-				numMaps = map + 1;				
-
-				int score1 = calculateScore(cis_new, numMaps, false);
-
-				flip(getMarkers(intervalsInChr, null, map));
-				
-				int score2 = calculateScore(cis_new, numMaps, false);
-				
-				if (score1 >= score2) {
-					flip(getMarkers(intervalsInChr, null, map));
-					orientation += " +";
-				} else
-					orientation += " -";
-
-				scores = scores + " " + (score1 - score2);
-
-
-				//add new markers to cis_new to random places...
-
-				ArrayList<ContigInterval> cis_new2 = new ArrayList<ContigInterval>(); 
-				out: for (ContigInterval ci : intervalsInChr) {
-					if (ci.markers.size() > map && ci.markers.get(map).size() > 0) {
-						for (int m = 0; m < map; ++m)
-							if (ci.markers.get(m).size() > 0)
-								continue out;
-						cis_new2.add(ci);
-					}
-				}
-				//Collections.shuffle(cis_new2); no need to shuffle...
-				cis_new = Misc.randomMerge(cis_new, cis_new2);
-			}
-			//System.out.println(intervalsInChr.size() + "\t" + cis_new.size() );
-			
-			//intervalsInChr.clear();
-			//intervalsInChr.addAll(cis_new);
-			
-			//finally add contigs without markers 
-			for (ContigInterval ci : intervalsInChr)
-				if (ci.markers.size() == 0)
-					cis_new.add(ci);
-			
-			assert(intervalsInChr.size() == cis_new.size());
-
-			
-			intervalsInChr = cis_new;
-			
-			//enable chains
-			chainLinkHash = oldChainLinkHash;
-
-			System.out.println("#found orientation=" + orientation + " ( support " + scores + " )");
-		}
-		if (finalImprove)
-			improveAnchoring();
-	}
-	
-	private ArrayList<Marker> getMarkers(ArrayList<ContigInterval> cis, ContigInterval excluded, int map)
-	{
-		ArrayList<Marker> ret = new ArrayList<Marker>();
-		for (ContigInterval ci : cis) 
-			if (ci != excluded) 
-				ret.addAll(ci.getMarkers(map));
-		return ret;
-	}
-	
-	private String calculateKey(ContigInterval prev, boolean orientationPrev, ContigInterval ci, boolean orientationCi){
-		return prev.toString() + ((orientationPrev) ? '+':'-') + ci.toString() + ((orientationCi) ? '+':'-');
-	}
-	
-	private String calculateKey(ContigInterval prev, ContigInterval ci){
-		return calculateKey(prev, (prev.getOrientation() >= 0), ci, (ci.getOrientation() >= 0));
-	}
-
-	//chainScore with possible flips for prev and ci
-	private int calculateChainScore(ContigInterval prev, boolean flipPrev, ContigInterval ci, boolean flipCi) {
-		String key = calculateKey(prev, (prev.getOrientation() >= 0) ^ flipPrev, ci, (ci.getOrientation() >= 0) ^ flipCi);
-		return calculateChainScore(key);
-	}
-	private int calculateChainScore(ContigInterval prev, ContigInterval ci) {
-		String key = calculateKey(prev, ci);
-		return calculateChainScore(key);
-	}
-
-	private int calculateChainScore(String key) {
-		if (chainLinkHash.containsKey(key)) {
-			int ret = chainLinkHash.get(key);
-			if (useChainAndPaf && scaffoldingLink.containsKey(key))
-				ret += scaffoldingLink.get(key);
-			return ret; 
-		}
-		if (scaffoldingLink.containsKey(key))
-			return scaffoldingLink.get(key);
-		return 0;
-	}
-
-	// haplotype is haplotype of ofHaplotype?
-	private int calculateChainScoreHaplotype(ContigInterval ofHaplotype, ContigInterval haplotype) {
-		String key = calculateKey(ofHaplotype, haplotype);
-		key = key.substring(0, key.length() - 1); // last orientation 
-		
-		if (chainHaplotypeHash.containsKey(key))
-			return chainHaplotypeHash.get(key);
-		return 0;
-	}
-
-	private long[] calculateChainScoreHaplotypeCut(ContigInterval ofHaplotype, ContigInterval haplotype) {
-		String key = calculateKey(ofHaplotype, haplotype);
-		key = key.substring(0, key.length() - 1); // last orientation 
-		
-		return chainHaplotypeCut.get(key);
-	}
-	
-	private int calculateChainScore(ArrayList<ContigInterval> cis)
-	{
-		int score = 0;
-		ContigInterval prev = null;
-		for (ContigInterval ci : cis) {
-			if (prev != null)
-				score += calculateChainScore(prev, ci);
-			prev = ci;
-		}
-		return score;
-	}
-
-	private int calculateProximityScore(ArrayList<ContigInterval> cis)
-	{
-		if (prox != null)
-			return prox.score(cis);
-		return 0;
-	}
-	
-	private int evaluateScore(ArrayList<ContigInterval> eval, boolean improve)
-	{
-		ArrayList<ContigInterval> eval2 = new ArrayList<ContigInterval>(); 
-		for (ContigInterval e : eval) {
-			boolean found = false;
-			for (ContigInterval ci : intervalsInChr) {
-				if (ci.equals(e)) {
-					eval2.add(ci);
-					ci.setOrientation(e.getOrientation());
-					found = true;
-					break;
-				}
-			}
-			if (!found) {
-				System.err.println("Contig " + e +  " not found");
-			}
-		}
-
-		if (improve) {
-			int score = calculateScore(eval2, false) + calculateNonMarkerScore(eval2);
-			//System.out.print("#initial score " +  score + " ");
-			improveAnchoring(eval2, true, true);
-		} else {
-			ArrayList<Double> orderSupport = calculateSupport(eval2);
-			int score = calculateScore(eval2, false) + calculateNonMarkerScore(eval2);
-			System.out.println("#final score " +  score);
-			printAnchoring(eval2, orderSupport);
-			findLikelyAssemblyErrors(eval2);
-		}
-		//change bed to the evaluated order...
-		intervalsInChr.clear();
-		intervalsInChr.addAll(eval2);
-		
-		return calculateScore(eval2, false) + calculateNonMarkerScore(eval2);
-/*		
-		int score1 = calculateScore(eval2, true);
-		for (int map = 0; map < numMaps; ++map)
-			flip(getMarkers(intervalsInChr, null, map));
-		int score2 = calculateScore(eval2, true);
-		
-		return Math.max(score1, score2);*/ 
-	}
-
-
-	private int calculateScoreFast(ArrayList<ContigInterval> cis)
-	{
-		int score = 0;
-		for (int map = 0; map < numMaps; ++map) {				
-			int s = solveForwardFast(getMarkers(cis, null, map));
-			score += s;
-		}
-		return score;
-	}
-
-
-	private int calculateScore(ArrayList<ContigInterval> cis, boolean verbose)
-	{
-		return calculateScore(cis, numMaps, verbose);
-	}
-	
-	private int calculateScore(ArrayList<ContigInterval> cis, int numMaps, boolean verbose)
-	{
-		int score = 0;
-		for (int map = 0; map < numMaps; ++map) {				
-			int s = solveForward(getMarkers(cis, null, map));
-			if (verbose)
-				System.err.println("map " + map + " score " + s);
-			score += s;
-		}
-		return score;
-	}
-
-	private int getMaxBin(ArrayList<Marker> markers) {
-		int maxBin = Integer.MIN_VALUE;
-		for (Marker m : markers)
-			maxBin = Math.max(maxBin, m.maxBin());
-		if (maxBin != Integer.MIN_VALUE)
-			return maxBin;
-		else 
-			return 0;
-	}
-
-	private int getMinBin(ArrayList<Marker> markers) {
-		int minBin = Integer.MAX_VALUE;
-		for (Marker m : markers)
-			minBin = Math.min(minBin, m.minBin());
-		if (minBin != Integer.MAX_VALUE)
-			return minBin;
-		else 
-			return 0;
-	}
-
-	//TODO: Remove calculateChainScore(cis) and calculateChainScore(c1, c2) add calculateNonMarkerScore(...) 
-	private ArrayList<Double> calculateSupport(ArrayList<ContigInterval> cis) {
-		
-		//for (int iteration = 0; iteration < 1; ++iteration) { // add here "iteration < 2" if possible orientation errors should be corrected...
-			
-		
-		
-		//ArrayList<Integer> score1 = new ArrayList<Integer>(); 
-		ArrayList<Integer> score2 = new ArrayList<Integer>(); 
-
-		ArrayList<Integer> order1 = new ArrayList<Integer>(); 
-		ArrayList<Integer> order2 = new ArrayList<Integer>(); 
-		
-		int rank = 0;
-		for (ContigInterval ci : cis) {
-			ci.setRank(rank++);
-			score2.add(0);
-			order1.add(0);
-			order2.add(0);
-		}
-		
-		for (int map = 0; map < numMaps; ++map) {
-			ArrayList<Marker> markers = getMarkers(cis, null, map);
-
-			int endBin = getMaxBin(markers);
-			int startBin = getMinBin(markers);
-
-			int numMarkers = markers.size();
-			int S[][] = new int[numMarkers + 1][endBin - startBin + 1];
-			int P[][] = new int[numMarkers + 1][endBin - startBin + 1];
-		
-			int Sb[][] = new int[numMarkers + 1][endBin - startBin + 1];
-			//int Pb[][] = new int[numMarkers + 1][endBin - startBin + 1];
-
-			int Sc[][] = new int[numMarkers + 1][endBin - startBin + 1];
-			int Pc[][] = new int[numMarkers + 1][endBin - startBin + 1];
-
-			//simple way to calculate (about correct) backward table...
-			Collections.reverse(markers);
-			forwardFast2(markers, Sb, startBin, endBin);
-			Collections.reverse(markers);
-			
-			forward1(markers, S, P, startBin, endBin);
-			int maxScore = -1;
-			{
-				int maxI = startBin;
-				for (int i = startBin; i <= endBin; ++i) 
-		            if (S[numMarkers][i - startBin] > maxScore) {
-		            	maxScore = S[numMarkers][i - startBin];
-		                maxI = i;
-		            }
-				
-				for (int mi = numMarkers; mi > 0; --mi) {
-					markers.get(mi - 1).pPlus = maxI;
-					//System.err.println(markers.get(mi - 1) + "\t" + maxI);
-					maxI = P[mi][maxI - startBin];
-				}
-			}
-			
-			ArrayList<ArrayList<Integer>> markerIndex = new ArrayList<ArrayList<Integer>>();
-			for (ContigInterval ci : cis)
-				markerIndex.add(new ArrayList<Integer>());
-
-			for (int mi = 0; mi < numMarkers; ++mi) {
-				Marker m = markers.get(mi);
-				rank = m.ci.getRank();
-				markerIndex.get(rank).add(mi);
-			}
-			for (ContigInterval ci : cis) {
-				rank = ci.getRank();
-				
-				ArrayList<Marker> cMarkers = new ArrayList<Marker>();
-		
-				for (int i : markerIndex.get(rank))
-					cMarkers.add(markers.get(i));
-				
-				int maxB = Integer.MIN_VALUE;
-				int minB = Integer.MAX_VALUE;
-				
-				int numCMarkers = cMarkers.size(); 
-				
-				if (numCMarkers > 0) {
-					for (Marker m : cMarkers) {
-						maxB = Math.max(maxB, m.pPlus);
-						minB = Math.min(minB, m.pPlus);
-					}
-					if (maxB > minB)
-						order1.set(rank, order1.get(rank) + 1);
-					
-					Collections.reverse(cMarkers);
-					int start = markerIndex.get(rank).get(0);
-					int end = markerIndex.get(rank).get(numCMarkers - 1) + 1;
-					
-					for (int b = startBin; b <= endBin; ++b) {
-						Sc[0][b - startBin] = S[start][b - startBin];
-						Pc[0][b - startBin] = P[start][b - startBin];
-					}
-					
-					forward1(cMarkers, Sc, Pc, startBin, endBin);
-
-			
-					int Scc[] = Sc[cMarkers.size()];
-					for (int b = startBin + 1; b <= endBin; ++b) { // make table non-decreasing
-						if (Scc[b - startBin] < Scc[b - startBin - 1])
-							Scc[b - startBin] = Scc[b - startBin - 1];
-					}
-					int maxI = startBin;
-					int max = -1; 
-					for (int b = startBin; b <= endBin; ++b) {
-						int s = Scc[b - startBin] + Sb[numMarkers - end][b - startBin]; 
-						if (s > max) {
-							max = s;
-							maxI = b;
-						}
-					}
-					score2.set(rank, score2.get(rank) + max);
-					{
-						for (int mi = numCMarkers; mi > 0; --mi) {
-							cMarkers.get(mi - 1).pPlus = maxI;
-							//System.err.println(markers.get(mi - 1) + "\t" + maxI);
-							maxI = Pc[mi][maxI - startBin];
-						}
-					}
-					maxB = Integer.MIN_VALUE;
-					minB = Integer.MAX_VALUE;
-					for (Marker m : cMarkers) {
-						maxB = Math.max(maxB, m.pPlus);
-						minB = Math.min(minB, m.pPlus);
-					}
-					if (maxB > minB)
-						order2.set(rank, order2.get(rank) + 1);
-				} else {
-					score2.set(rank, score2.get(rank) + maxScore);
-				}
-			}
-		}
-		int oldNonMarkerScore = calculateNonMarkerScore(cis);
-		int oldScore = calculateScore(cis, false) + oldNonMarkerScore;
-		for (ContigInterval ci : cis) {
-			rank = ci.getRank();
-			int newNonMarkerScore = oldNonMarkerScore + nonMarkerScoreChange(cis, rank, rank, 0, true, 0);
-			score2.set(rank, score2.get(rank) + newNonMarkerScore);
-		}
-
-		ArrayList<Double> ret = new ArrayList<Double>();
-		//boolean changes = false; 
-		for (ContigInterval c : cis) {
-			rank = c.getRank();
-			int support = oldScore - score2.get(rank);
-			int order = 0;
-			if (support == 0 && order1.get(rank) > order2.get(rank)) {
-				if (c.getOrientation() >= 0)
-					order = 1;
-				else
-					order = -1;
-			}
-			else if (support == 0 && order1.get(rank) < order2.get(rank)) {
-				if (c.getOrientation() >= 0)
-					order = -1;
-				else
-					order = 1;
-			}
-			//if (support < 0) {
-			//	c.flipOrientation();
-			//	changes = true;
-			//}
-			//System.err.println("order_support\t" + c +"\t" + ((support == 0) ? 0.5 * order: support));
-			ret.add(((support == 0) ? (0.5 * order): support));
-		}
-		//if (!changes)
-		//	break;
-		//}
-		return ret;
-	}
-	
-	//flip(i..cr)
-	//move(i...cr) to new_pos w/wo flipping
-	//move cr to new position
-	
-	private int calculateNonMarkerScore(ArrayList<ContigInterval> cis)
-	{
-		return calculateChainScore(cis) + calculateProximityScore(cis);
-	}
-	
-	
-	//start...end => start+moveDirection...end+moveDirection
-	public static void changeOrder(ArrayList<ContigInterval> cis, int start, int end, int moveDirection, boolean flip)
-	{
-		int n = cis.size();
-		if (end + moveDirection >= n || start + moveDirection < 0) {
-			System.err.println("change too large");
-			return;
-		}
-		if (moveDirection == 0 && !flip) // nothing to do
-			return;
-		
-		ArrayList<ContigInterval> cis_new = new ArrayList<ContigInterval>();
-		if (moveDirection <= 0) {
-			for (int i = 0; i < start + moveDirection; ++i)
-				cis_new.add(cis.get(i));
-			
-			if (!flip)
-				for (int i = start; i <= end; ++i)
-					cis_new.add(cis.get(i));
-			else
-				for (int i = end; i >= start; --i) { //reverse and flip
-					ContigInterval ci = cis.get(i);
-					ci.flipOrientation();
-					cis_new.add(ci);
-				}
-
-			for (int i = start + moveDirection; i < start; ++i)
-				cis_new.add(cis.get(i));
-			for (int i = end + 1; i < n; ++i)
-				cis_new.add(cis.get(i));
-		} else {
-			for (int i = 0; i < start; ++i)
-				cis_new.add(cis.get(i));
-
-			for (int i = 1; i <= moveDirection; ++i)
-				cis_new.add(cis.get(i + end));
-			
-			if (!flip)
-				for (int i = start; i <= end; ++i)
-					cis_new.add(cis.get(i));
-			else
-				for (int i = end; i >= start; --i) { //reverse and flip
-					ContigInterval ci = cis.get(i);
-					ci.flipOrientation();
-					cis_new.add(ci);
-				}
-
-			for (int i = end + moveDirection + 1; i < n; ++i)
-				cis_new.add(cis.get(i));
-		}
-		cis.clear();
-		cis.addAll(cis_new);
-	}
-	
-	//reverse of changeOrder
-	public static void changeOrderReverse(ArrayList<ContigInterval> cis, int start, int end, int moveDirection, boolean flip)
-	{
-		changeOrder(cis, start + moveDirection, end + moveDirection, -moveDirection, flip);
-	}
-	public int nonMarkerScoreChange(ArrayList<ContigInterval> cis, int start, int end, int moveDirection, boolean flip, int flipScore)
-	{
-		int ret = ((flip) ? flipScore : 0);
-		if (moveDirection == 0) { // flip 
-			if (flip) {
-				if (start > 0) {
-					ret -= calculateChainScore(cis.get(start - 1), cis.get(start));
-					ret += calculateChainScore(cis.get(start - 1), false, cis.get(end), true);
-				}
-				if (end + 1 < cis.size()) {
-					ret -= calculateChainScore(cis.get(end), cis.get(end + 1));
-					ret += calculateChainScore(cis.get(start), true, cis.get(end + 1), false);
-				}
-			} // else nothing to do...
-		} else { // move one or multiple contigs...
-			ContigInterval sc = cis.get(start);
-			ContigInterval ec = cis.get(end);
-
-			if (start > 0) {
-				ret -= calculateChainScore(cis.get(start - 1), sc);
-				if (end + 1 < cis.size())
-					ret += calculateChainScore(cis.get(start - 1), cis.get(end + 1));
-			}
-			if (end + 1 < cis.size())
-				ret -= calculateChainScore(ec, cis.get(end + 1));
-			
-			if (moveDirection <= 0) {
-				if (flip) {
-					if (start + moveDirection > 0) {
-						ret -= calculateChainScore(cis.get(start + moveDirection - 1), cis.get(start + moveDirection));
-						ret += calculateChainScore(cis.get(start + moveDirection - 1), false, ec, true);
-					}
-					ret += calculateChainScore(sc, true, cis.get(start + moveDirection), false);
-				} else {
-					if (start + moveDirection > 0) {
-						ret -= calculateChainScore(cis.get(start + moveDirection - 1), cis.get(start + moveDirection));
-						ret += calculateChainScore(cis.get(start + moveDirection - 1), sc);
-					}
-					ret += calculateChainScore(ec, cis.get(start + moveDirection));
-				}
-			} else { // moveDirection > 0
-				if (flip) {
-					if (end + moveDirection + 1 < cis.size()) {
-						ret -= calculateChainScore(cis.get(end + moveDirection), cis.get(end + moveDirection + 1));
-						ret += calculateChainScore(sc, true, cis.get(end + moveDirection + 1), false);
-					}
-					ret += calculateChainScore(cis.get(end + moveDirection), false, ec, true);
-				} else {
-					if (end + moveDirection + 1 < cis.size()) {
-						ret -= calculateChainScore(cis.get(end + moveDirection), cis.get(end + moveDirection + 1));
-						ret += calculateChainScore(ec, cis.get(end + moveDirection + 1));
-					}
-					ret += calculateChainScore(cis.get(end + moveDirection), sc);
-				}
-			}
-		}
-		if (prox != null)
-			ret += prox.scoreChange(cis, start, end, moveDirection, flip);
-		return ret;
-	}
-
-	private boolean linkedIntervals(ArrayList<ContigInterval> cis, int c1, int c2)
-	{
-		return (calculateChainScore(cis.get(c1), cis.get(c2)) > 0 || (prox != null && prox.linkedIntervals(cis, c1, c2)));
-	}
-	
-	//join contig to linked contigs next to it and try to improve...
-	//not thread safe... fix?: separate scaffoldingLink initialisation
-	private int calculateBestLinkedContig(ArrayList<ContigInterval> cis, int cr, boolean verbose){
-
-		int start = cr;
-		if (start > 0 && linkedIntervals(cis, start - 1, start))
-			return 0; // only start from the first contig of each linked chain of contigs 
-	
-		int numCis = cis.size();
-
-		int end = cr;
-		while (end + 1 < numCis && linkedIntervals(cis, end, end + 1))
-			++end;
-		
-		boolean mapMarkers = false;
-		for (int i = start; i <= end; ++i)
-			if (cis.get(i).markers.size() > 0) {
-				mapMarkers = true;
-				break;
-			}
-		if (!mapMarkers) // no need to go further without markers...
-			return 0;
-
-		int numLinked = end - start + 1;
-		
-		if (start < cr || start == end || numLinked == numCis) // starts at c, at least two ContigIntervals and not connected to all
-			return 0;
-		
-		ContigInterval ci_new = new ContigInterval("\t", 1, 1); // dummy name, this cannot be loaded from a file...
-		
-		int flipScore = 0; // calculate flipsScore to take into account possible decreasing score when flipping start..end
-		for (int i = start; i < end; ++i)
-			flipScore += calculateChainScore(cis.get(i + 1), true, cis.get(i), true) - calculateChainScore(cis.get(i), cis.get(i + 1));  
-		
-		//add scaffolding links, use scaffoldingLink_tmp not to mess other links... 
-		scaffoldingLink_tmp.clear();
-		for (int i = -1; i < numCis; ++i)
-			if (i < start || i > end) {
-				int moveDirection = ((i < start) ? i - start + 1 : i - end);
-				int nmss = nonMarkerScoreChange(cis, start, end, moveDirection, false, flipScore);
-				int nmss2 = nonMarkerScoreChange(cis, start, end, moveDirection, true, flipScore);
-				if (i >= 0) {
-					ContigInterval ci = cis.get(i);
-					if (moveDirection != 0) // with links for moveDirection==0, we end up updating start-1...end as well
-						scaffoldingLink_tmp.put(calculateKey(ci, ci_new), nmss);
-					scaffoldingLink_tmp.put(calculateKey(ci, ci.getOrientation() >= 0, ci_new, false), nmss2);
-				} else { // move to the very first position...
-					int firstMarker = ((start > 0) ? 0 : end + 1);
-					ContigInterval ci = cis.get(firstMarker);
-					if (moveDirection != 0)  // with links for moveDirection==0, we end up updating start...end+1 as well
-						scaffoldingLink_tmp.put(calculateKey(ci_new, ci), nmss);
-					scaffoldingLink_tmp.put(calculateKey(ci_new, false, ci, ci.getOrientation() >= 0), nmss2);
-				}
-			}
-		
-		//and markers
-		for (int map = 0; map < numMaps; ++map) {
-			for (int i = start; i <= end; ++i) {
-				for (Marker m : cis.get(i).getMarkers(map))
-					ci_new.addMarker(new Marker(m), map);
-			}
-		}
-		
-		ArrayList<ContigInterval> cis_new = new ArrayList<ContigInterval>();
-		for (int i = 0; i < start; ++i)
-			cis_new.add(cis.get(i));
-		cis_new.add(ci_new);
-		for (int i = end + 1; i < numCis; ++i)
-			cis_new.add(cis.get(i));
-
-		//int os = this.calculateScore(cis, false) + calculateNonMarkerScore(cis);
-		//int ns2 = this.calculateScore(cis_new, false) + calculateNonMarkerScore(cis_new);
-		//int ns = this.calculateScore(cis_new, false) + calculateNonMarkerScore(cis_new);
-		//System.err.println("linked " + ret + " " + start + "," + end + " " +ns2 + " " + os + " " + ns);
-
-		Proximity tmpProx = prox;
-		prox = null; // do not use proximity
-		HashMap<String, Integer> tmpScaffoldingLink = scaffoldingLink;
-		scaffoldingLink = scaffoldingLink_tmp;
-		HashMap<String, Integer> tmpChainLink = chainLinkHash; 
-		chainLinkHash = new HashMap<String, Integer>(); //nor chainLinks
-
-		int ret = calculateBest(cis_new, ci_new, true);
-
-		prox = tmpProx;
-		scaffoldingLink = tmpScaffoldingLink;
-		chainLinkHash = tmpChainLink;
-		
-		if (ret > 0) { // update cis
-			//System.err.println("linked improvement " + ret);
-			int crn = 0;
-			for (ContigInterval ci : cis_new)
-				if (ci == ci_new)
-					break;
-				else 
-					++crn;
-			
-			cis_new.clear();
-			//int os = calculateScore(cis, false) + calculateNonMarkerScore(cis);
-			
-			for (int i = 0; i < crn; ++i)
-				if (i >= start)
-					cis_new.add(cis.get(i + numLinked));
-				else
-					cis_new.add(cis.get(i));
-			int orientation = ci_new.getOrientation();
-			if (orientation >= 0)
-				for (int i = start; i <= end; ++i)
-					cis_new.add(cis.get(i));
-			else
-				for (int i = end; i >= start; --i) {
-					cis.get(i).flipOrientation();
-					cis_new.add(cis.get(i));
-				}
-			for (int i = crn; i < numCis - numLinked; ++i)
-				if (i >= start)
-					cis_new.add(cis.get(i + numLinked));
-				else
-					cis_new.add(cis.get(i));
-			int ns = calculateScore(cis_new, false) + calculateNonMarkerScore(cis_new);
-			//if (os >= ns) {
-			//	if (orientation < 0)
-			//		for (int i = start; i <= end; ++i)
-			//			cis.get(i).flipOrientation();
-			//	System.err.println("Error: Score not improving! " + start + "-" + end + "\t" + crn + "\t" + orientation);
-			//	return 0;
-			//}
-			System.err.println("LINKED\t" + cis.get(start) + "\t" + (end - start + 1) + "\t" + ns);
-			cis.clear();
-			cis.addAll(cis_new);
-		}
-		return ret;
-	}
-	//join contig to linked contigs next to it and try to improve...
-	//thread safe version...
-	private int calculateBestLinkedContig_ts(ArrayList<ContigInterval> cis, int cr, boolean verbose){
-
-		int start = cr;
-		if (start > 0 && linkedIntervals(cis, start - 1, start))
-			return 0; // only start from the first contig of each linked chain of contigs 
-	
-		int numCis = cis.size();
-
-		int end = cr;
-		while (end + 1 < numCis && linkedIntervals(cis, end, end + 1))
-			++end;
-
-		int numLinked = end - start + 1;
-
-		if (start < cr || start == end || numLinked == numCis) // starts at c, at least two ContigIntervals and not connected to all
-			return 0;
-		
-		boolean mapMarkers = false;
-		for (int i = start; i <= end; ++i)
-			if (cis.get(i).markers.size() > 0) {
-				mapMarkers = true;
-				break;
-			}
-
-		if (!mapMarkers) // no need to go further without markers...
-			return 0;
-
-		//update rank
-		int rank = 0;
-		for (ContigInterval ci : cis)
-			ci.setRank(rank++);
-		
-		int bestRes[] = new int[numCis + 1];
-		int bestRes2[] = new int[numCis + 1];
-	
- 		for (int map = 0; map < numMaps; ++map) {
- 			
-			ArrayList<Marker> cMarkers = new ArrayList<Marker>();
-			for (int i = start; i <= end; ++i)
-				cMarkers.addAll(cis.get(i).getMarkers(map));
-
-			ArrayList<Marker> markers = new ArrayList<Marker>();
-			for (int i = 0; i < start; ++i)
-				markers.addAll(cis.get(i).getMarkers(map));
-			for (int i = end + 1; i < numCis; ++i)
-				markers.addAll(cis.get(i).getMarkers(map));
-
-			int endBin = getMaxBin(markers);
-			int startBin = getMinBin(markers);
-
-			for (Marker m : cMarkers) {
-				endBin = Math.max(endBin, m.maxBin());
-				startBin = Math.min(startBin, m.minBin());
-			}
-			//System.err.println(startBin);
-			//System.err.println(endBin);
-			
-			int numMarkers = markers.size();
-			int S[][] = new int[numMarkers + 1][endBin - startBin + 1];
-		
-			int Sb[][] = new int[numMarkers + 1][endBin - startBin + 1];
-
-			int Sc[][] = new int[1 + cMarkers.size()][endBin - startBin + 1];
-		
-			forwardFast1(markers, S, startBin, endBin);
-			//simple way to calculate (about correct) backward table...
-			Collections.reverse(markers);
-			forwardFast2(markers, Sb, startBin, endBin);
-			Collections.reverse(markers);
-			
-			int old = -1;
-			for (int mi = 0; mi <= numMarkers; ++mi) {
-				
-				if (mi < numMarkers) {  
-					Marker m = markers.get(mi); // this is the next marker
-					numCis = m.ci.getRank();
-				} else
-					numCis = cis.size();
-				
-				if (numCis != old) {
-					for (int b = 0; b <= endBin - startBin; ++b)
-						Sc[0][b] = S[mi][b];
-					
-					forwardFast1(cMarkers, Sc, startBin, endBin);
-					
-					int Scc[] = Sc[cMarkers.size()];
-					for (int b = 1; b <= endBin - startBin; ++b) { // make table non-decreasing
-						if (Scc[b] < Scc[b - 1])
-							Scc[b] = Scc[b - 1];
-					}
-					int Sbb[] = Sb[numMarkers - mi];
-					int max = -1; 
-					for (int b = 0; b <= endBin - startBin; ++b) {
-						int s = Scc[b] + Sbb[b]; 
-						if (s > max)
-							max = s;
-					}
-					//System.out.println(max);
-					for (int i = old + 1; i <= numCis; ++i)  
-						bestRes[i] += max;
-					
-					Collections.reverse(cMarkers);
-					forwardFast1(cMarkers, Sc, startBin, endBin);
-					Collections.reverse(cMarkers);
-					
-					for (int b = 1; b <= endBin - startBin; ++b) { // make table non-decreasing
-						if (Scc[b] < Scc[b - 1])
-							Scc[b] = Scc[b - 1];
-					}
-					max = -1; 
-					for (int b = 0; b <= endBin - startBin; ++b) {
-						int s = Scc[b] + Sbb[b]; 
-						if (s > max)
-							max = s;
-					}
-					//System.out.println(max);
-					for (int i = old + 1; i <= numCis; ++i)  
-						bestRes2[i] += max;
-				}
-				old = numCis;
-			}
-		}
-
- 		numCis = cis.size();
-		int flipScore = 0; // calculate flipsScore to take into account possible decreasing score when flipping start..end
-		for (int i = start; i < end; ++i)
-			flipScore += calculateChainScore(cis.get(i + 1), true, cis.get(i), true) - calculateChainScore(cis.get(i), cis.get(i + 1));  
-
-	 	int oldNonMarkerScore = calculateNonMarkerScore(cis);
-	 	int oldScore = calculateScore(cis, false) + oldNonMarkerScore;
-		for (int ci = 0; ci <= numCis; ++ci) {
-			int mD = ci - start;
-			if (ci > start)
-				if (ci > end)
-					mD = ci - end - 1;
-				else
-					mD = 0;
-			bestRes[ci] += oldNonMarkerScore + nonMarkerScoreChange(cis, start, end, mD, false, flipScore); 
-			bestRes2[ci]+= oldNonMarkerScore + nonMarkerScoreChange(cis, start, end, mD, true, flipScore); 
-		}
-		//for (int ci = 0; ci <= cis.size(); ++ci) {
-		//	System.err.print(bestRes[ci] + " ");
-		//}
-		//System.err.println();
-	
-		int max = 0;
-		for (int ci = 0; ci <= cis.size(); ++ci)
-			if (bestRes[ci] > bestRes[max]) 
-				max = ci;
-		
-		int max2 = 0;
-		for (int ci = 0; ci <= cis.size(); ++ci)
-			if (bestRes2[ci] > bestRes2[max2]) 
-				max2 = ci;
-		
-		if (bestRes[max] > oldScore || bestRes2[max2] > oldScore) {
-			int pos = max2;
-			boolean flip = true;
-			if (bestRes[max] >= bestRes2[max2]) {
-				flip = false;
-				pos = max;
-				if (verbose)
-					System.err.println("LINKED_MOVE\t" + cis.get(start) + "\t" +  numLinked + "\t" + bestRes[max]);// + "\t" + oldScore);
-
-			} else {
-				if (verbose)
-					System.err.println(((max2 == start || max2 == start + 1) ? "LINKED_FLIP\t":"LINKED_MOVE+FLIP\t") + cis.get(start) + "\t" + numLinked + "\t" + bestRes2[max2]);// + "\t" + oldScore);
-			}
-			
-			//table index is the new rank for the contig start... without flipping...
-			int mD = pos - start;
-			if (pos > start)
-				if (pos > end)
-					mD = pos - end - 1;
-				else
-					mD = 0;
-			changeOrder(cis, start, end, mD, flip);
-		}
-		//int ns = (calculateNonMarkerScore(cis) + calculateScore(cis, false));
-		//int ns2 = Math.max(bestRes[max], bestRes2[max2]);
-		//if (ns != ns2)
-		//	System.err.println("LINKED_DIFF " + oldScore + " " + ns + " " + ns2);
-		return Math.max(bestRes[max], bestRes2[max2]) - oldScore;
-	}
-
-	
-	private int calculateBest(ArrayList<ContigInterval> cis, ContigInterval c, boolean verbose) {
-		
-		//update rank
-		int numCis = 0;
-		for (ContigInterval ci : cis)
-			ci.setRank(numCis++);
-
-		boolean mapMarkers = (c.markers.size() > 0);
-
-		int oldNonMarkerScore = calculateNonMarkerScore(cis);
-		int oldScore = oldNonMarkerScore + ((mapMarkers) ? calculateScore(cis, false) : 0);
-
-		int cr = c.getRank();
-
-		//try flipping and/or moving multiple Contigs [i...cr]
-		if (cr > 0) {
-			int minFlipStart = cr - 1;
-			while (minFlipStart >= 0 && linkedIntervals(cis, minFlipStart, minFlipStart + 1)) {
-					--minFlipStart;
-			}
-			
-			int flipS = 0; //calculate this to fix the nonsymmetrical pair-wise scores...
-			for (int flipStart = cr - 1; flipStart > minFlipStart; --flipStart) {
-
-				if (!mapMarkers && cis.get(flipStart).markers.size() > 0) {
-					mapMarkers = true;
-					oldScore += calculateScore(cis, false);
-				}
-				
-				flipS -= calculateChainScore(cis.get(flipStart), cis.get(flipStart + 1)); //handles the nonsymmetrical pair-wise scores...
-				flipS += calculateChainScore(cis.get(flipStart + 1), true, cis.get(flipStart), true); //handles the nonsymmetrical pair-wise scores...
-				
-				int flipScore = nonMarkerScoreChange(cis, flipStart, cr, 0, true, flipS); 
-
-				if (flipScore >= 0) { //chainScore must not get worse, now calculate the marker score as well		
-					
-					changeOrder(cis, flipStart, cr, 0, true);
-					int nms = calculateNonMarkerScore(cis);
-					if (nms - oldNonMarkerScore != flipScore) {
-						System.err.println("Error:scores differ " + (nms - oldNonMarkerScore) + " " + flipScore);
-					}
-					int newScore = ((mapMarkers) ? calculateScoreFast(cis) + nms : nms);
-					if (newScore > oldScore) {// and the total score improves
-						if (verbose)
-							System.err.println("FLIP\t" + c + "\t" + (cr - flipStart + 1) + "\t" + (newScore));
-						return newScore - oldScore;
-					} else
-						changeOrderReverse(cis, flipStart, cr, 0, true);
-				}
-
-				//try moving multiple Contigs [i...cr] with or without flipping...
-	out:		for (int direction = -1; direction < 2;direction+=2){
-					
-					ArrayList<Integer> scores = new ArrayList<Integer>(); 
-					for (int movePosition = direction; cr + movePosition < numCis && flipStart + movePosition >= 0; movePosition+=direction) {
-						int moveScore1 = nonMarkerScoreChange(cis, flipStart, cr, movePosition, false, 0);
-						int moveScore2 = nonMarkerScoreChange(cis, flipStart, cr, movePosition, true, flipS);
-						scores.add(-Math.max(moveScore1, moveScore2));
-					}
-					//sort possible positions based on the chain (nonMarker) score... 
-				    Misc.ArrayIndexComparator<Integer> comparator = new Misc.ArrayIndexComparator<Integer>(scores);
-				    Integer[] indexes = comparator.createIndexArray();
-				    Arrays.sort(indexes, comparator);  
-
-					int maxEvaluations = 4;
-					
-					for (int i : indexes) {
-						int movePosition = (i + 1) * direction; 
-						int moveScore1 = nonMarkerScoreChange(cis, flipStart, cr, movePosition, false, 0);
-						if (moveScore1 >= 0) {
-							changeOrder(cis, flipStart, cr, movePosition, false);
-							int score = ((mapMarkers) ? calculateScoreFast(cis) + calculateNonMarkerScore(cis) : calculateNonMarkerScore(cis));
-							if (score > oldScore) {
-								if (verbose)
-									System.err.println("MOVE\t" + c + "\t" + (cr - flipStart + 1) + "\t" + score);
-								return score - oldScore;
-							} else
-								changeOrderReverse(cis, flipStart, cr, movePosition, false);
-						}
-						int moveScore2 = nonMarkerScoreChange(cis, flipStart, cr, movePosition, true, flipS);
-						if (moveScore2 >= 0) {
-							changeOrder(cis, flipStart, cr, movePosition, true);
-							int score = ((mapMarkers) ? calculateScoreFast(cis) + calculateNonMarkerScore(cis) : calculateNonMarkerScore(cis));
-							if (score > oldScore) {
-								if (verbose)
-									System.err.println("MOVE+FLIP\t" + c + "\t" + (cr - flipStart + 1) + "\t" + score);
-								return score - oldScore;
-							} else
-								changeOrderReverse(cis, flipStart, cr, movePosition, true);
-						}
-						//if (--maxEvaluations <= 0 || (moveScore1 < 0 && moveScore2 < 0)) // maximum number of evaluations reached...
-						if (--maxEvaluations <= 0) // maximum number of evaluations reached...
-							continue out;
-					}
-				}
-			}
-		}
-		//Move only contig c into new position
-		int bestRes[] = new int[cis.size() + 1];
-		int bestRes2[] = new int[cis.size() + 1];
-		
-		//System.err.println(oldScore + "\t" + oldChainScore);
-		if (c.markers.size() > 0) { // no need without markers in c...
-	 		for (int map = 0; map < numMaps; ++map) {
-				ArrayList<Marker> markers = getMarkers(cis, c, map);
-				ArrayList<Marker> cMarkers = c.getMarkers(map);
-	
-				int endBin = getMaxBin(markers);
-				int startBin = getMinBin(markers);
-	
-				for (Marker m : cMarkers) {
-					endBin = Math.max(endBin, m.maxBin());
-					startBin = Math.min(startBin, m.minBin());
-				}
-				//System.err.println(startBin);
-				//System.err.println(endBin);
-				
-				int numMarkers = markers.size();
-				int S[][] = new int[numMarkers + 1][endBin - startBin + 1];
-			
-				int Sb[][] = new int[numMarkers + 1][endBin - startBin + 1];
-	
-				int Sc[][] = new int[1 + cMarkers.size()][endBin - startBin + 1];
-			
-				forwardFast1(markers, S, startBin, endBin);
-				//simple way to calculate (about correct) backward table...
-				Collections.reverse(markers);
-				forwardFast2(markers, Sb, startBin, endBin);
-				Collections.reverse(markers);
-				
-				int old = -1;
-				for (int mi = 0; mi <= numMarkers; ++mi) {
-					
-					if (mi < numMarkers) {  
-						Marker m = markers.get(mi); // this is the next marker
-						numCis = m.ci.getRank();
-					} else
-						numCis = cis.size();
-					
-					if (numCis != old) {
-						for (int b = 0; b <= endBin - startBin; ++b)
-							Sc[0][b] = S[mi][b];
-						
-						forwardFast1(cMarkers, Sc, startBin, endBin);
-						
-						int Scc[] = Sc[cMarkers.size()];
-						for (int b = 1; b <= endBin - startBin; ++b) { // make table non-decreasing
-							if (Scc[b] < Scc[b - 1])
-								Scc[b] = Scc[b - 1];
-						}
-						int Sbb[] = Sb[numMarkers - mi];
-						int max = -1; 
-						for (int b = 0; b <= endBin - startBin; ++b) {
-							int s = Scc[b] + Sbb[b]; 
-							if (s > max)
-								max = s;
-						}
-						//System.out.println(max);
-						for (int i = old + 1; i <= numCis; ++i)  
-							bestRes[i] += max;
-						
-						Collections.reverse(cMarkers);
-						forwardFast1(cMarkers, Sc, startBin, endBin);
-						Collections.reverse(cMarkers);
-						
-						for (int b = 1; b <= endBin - startBin; ++b) { // make table non-decreasing
-							if (Scc[b] < Scc[b - 1])
-								Scc[b] = Scc[b - 1];
-						}
-						max = -1; 
-						for (int b = 0; b <= endBin - startBin; ++b) {
-							int s = Scc[b] + Sbb[b]; 
-							if (s > max)
-								max = s;
-						}
-						//System.out.println(max);
-						for (int i = old + 1; i <= numCis; ++i)  
-							bestRes2[i] += max;
-					}
-					old = numCis;
-				}
-			}
-		} else {
-			if (mapMarkers) // if there are no markers in c, then we can only consider nonMarkerScore after this...
-				oldScore = oldNonMarkerScore;
-			mapMarkers = false;
-		}
-		for (int ci = 0; ci <= cis.size(); ++ci) {
-			int mD = ci - cr;
-			if (ci > cr)
-				--mD;
-			bestRes[ci] += oldNonMarkerScore + nonMarkerScoreChange(cis, cr, cr, mD, false, 0); 
-			bestRes2[ci]+= oldNonMarkerScore + nonMarkerScoreChange(cis, cr, cr, mD, true, 0); 
-		}
-		//for (int ci = 0; ci <= cis.size(); ++ci) {
-		//	System.err.print(bestRes[ci] + " ");
-		//}
-		//System.err.println();
-
-		int max = 0;
-		for (int ci = 0; ci <= cis.size(); ++ci)
-			if (bestRes[ci] > bestRes[max]) 
-				max = ci;
-		
-		int max2 = 0;
-		for (int ci = 0; ci <= cis.size(); ++ci)
-			if (bestRes2[ci] > bestRes2[max2]) 
-				max2 = ci;
-		
-		if (bestRes[max] > oldScore || bestRes2[max2] > oldScore) {
-			int pos = max2;
-			if (bestRes[max] >= bestRes2[max2]) {
-				pos = max;
-				if (verbose)
-					System.err.println("MOVE\t" + c + "\t1\t" + bestRes[max]);
-			} else {
-				if (verbose)
-					System.err.println(((max2 == cr || max2 == cr + 1) ? "FLIP\t":"MOVE+FLIP\t") + c + "\t1\t" + bestRes2[max2]);
-				c.flipOrientation();
-			}
-			cis.remove(cr);
-			if (pos > cr)
-				cis.add(pos - 1, c);
-			else
-				cis.add(pos, c);
-		}
-		return Math.max(bestRes[max], bestRes2[max2]) - oldScore;
- 	}
-	
-	private ArrayList<ContigInterval> cloneContigs(ArrayList<ContigInterval> cis)
-	{
-		ArrayList<ContigInterval> ret = new ArrayList<ContigInterval>();
-		for (ContigInterval c : cis)
-			ret.add(new ContigInterval(c));
-		return ret;
-	}
-	
-	private void improveAnchoring()
-	{
-		improveAnchoring(intervalsInChr, true, true);
-	}
-	
-	//parallel implementation of calculateBest
-	private class CalculateBest implements Runnable{
-		private AtomicInteger index;
-		private AtomicBoolean stop;
-		private ArrayList<ContigInterval> cis;
-		private ArrayList<ContigInterval> cisOrig;
-		private ArrayList<Integer> perm;
-		private boolean verbose;
-		private boolean linked;
-		
-		private CalculateBest next;
-		private Thread thread; 
-		
-		private int score = 0;
-		private int scoreIndex = 0;
-		CalculateBest(ArrayList<ContigInterval> cis, ArrayList<Integer> perm, AtomicInteger index, AtomicBoolean stop, boolean verbose, boolean linked) {
-			this.index = index;
-			this.stop = stop;
-			//clone cis
-			this.cis = cloneContigs(cis);
-			this.cisOrig = new ArrayList<ContigInterval>();
-			cisOrig.addAll(this.cis);
-			this.perm = perm;
-			this.verbose = verbose;
-			this.linked = linked;
-		}
-		public void setNext(CalculateBest next)
-		{
-			this.next = next;
-		}
-		public void setScore(int score)
-		{
-			this.score = score;
-		}
-		@Override
-		public void run() {
-			long time = System.currentTimeMillis();
-			score = 0;
-			thread = null;
-			while (!stop.get()) { 
-				if (thread == null && next != null && System.currentTimeMillis() - time >= 1000) { // start a new thread every 1 secs
-					next.setCis(this.cis);
-					if (stop.get()) //it is worth breaking here
-						break; 
-					thread = new Thread(next);
-					if (stop.get()) //and maybe here as well even when we don't use thread...
-						break;
-					thread.start();
-				}
-				int i = index.getAndIncrement();
-				if (i >= perm.size())
-					break;
-				if (linked)
-					score = calculateBestLinkedContig_ts(cis, perm.get(i), verbose); // TODO: fix perm to cisOrig order
-				else
-					score = calculateBest(cis, cisOrig.get(perm.get(i)), verbose);
-				if (score > 0) {
-					scoreIndex = i;
-					stop.set(true);
-				}
-			}
-			if (thread != null && thread.isAlive())
-				try {
-					thread.join();
-				} catch (Exception e) {
-					e.printStackTrace();
-					System.exit(-1);
-				}
-		}
-		public void directRun(int i) {
-			if (linked)
-				score = calculateBestLinkedContig_ts(cis, perm.get(i), verbose);
-			else
-				score = calculateBest(cis, cisOrig.get(perm.get(i)), verbose);
-		}
-		public void setCis(ArrayList<ContigInterval> cis)
-		{
-			// avoid clone
-			//this.cis = cloneContigs(cis);
-			makeCisIdentical(this.cis, cis);
-		}
-		public int getScore()
-		{
-			return score;
-		}
-		public int getScoreIndex()
-		{
-			return scoreIndex;
-		}
-	}
-	// make two lists of ContigIntervals indentical by placement and orientation, source=>target
-	// lists must contain exactly the same contigs...
-	private void makeCisIdentical(ArrayList<ContigInterval> target, ArrayList<ContigInterval> source)
-	{
-		HashMap<ContigInterval, ContigInterval> map1to1 = new HashMap<ContigInterval, ContigInterval>();
-		for (ContigInterval c : target) {
-			if (map1to1.containsKey(c)) {
-				System.err.println("Error: same contig multiple times...");
-
-				for (ContigInterval c2 : target) {
-					System.err.println(c2);
-					
-				}
-				System.exit(-1);
-				
-			}
-			map1to1.put(c, c);
-		}
-		target.clear();
-		for (ContigInterval c : source) {
-			ContigInterval c2 = map1to1.get(c);
-			if (c2 == null) {
-				System.err.println("Error: some contig(s) not found...");
-				System.exit(-1);
-			}
-			target.add(c2);
-			c2.setOrientation(c.getOrientation());
-		}
-	}
-	
-	private void improveAnchoring(ArrayList<ContigInterval> cis, boolean finalRound, boolean verbose)
-	{
-		if (cis.size() == 0)
-			return;
-
-		if (finalRound)
-			System.out.print("#initial score " +  (calculateScore(cis, false) + calculateNonMarkerScore(cis)));
-		
-		
-		int numCis = cis.size(); 
-
-		ArrayList<Integer> perm = new ArrayList<Integer>();
-		for (int i = 0; i < numCis; ++i)
-			perm.add(i);
-
-		boolean foundBetter = false;
-
-		
-		int iteration = 0;
-		
-		int bestScore = -1;
-		ArrayList<ContigInterval> cis_best = new ArrayList<ContigInterval>();
-		ArrayList<Integer> cis_bestO = new ArrayList<Integer>();
-		
-		for (int run = 0; run < numRuns; ++run) {
-			if (run > 0) {
-				int n = cis.size();
-				for (ContigInterval ci : cis)
-					if (Math.random() < 0.05)
-						ci.flipOrientation();
-				if (n > 1)
-					for (int flips = 0; flips < n; ++flips) { 
-						int i = (int) (Math.random() * (n - 1));
-						ContigInterval tmp = cis.get(i);
-						cis.set(i, cis.get(i + 1));
-						cis.set(i + 1, tmp);
-					}
-			}
-			
-			do {
-				if (finalRound) {
-					System.err.println("iteration " + (++iteration) + " score=" +  (calculateScore(cis, false) + calculateNonMarkerScore(cis)));
-				}
-				foundBetter = false;
-				Collections.shuffle(perm); // random order
-	
-				if (numThreads <= 1) {
-					ArrayList<ContigInterval> cisOrig = new ArrayList<ContigInterval>();
-					cisOrig.addAll(cis);
-					for (int i = 0; i < numCis; ++i)
-						if (calculateBest(cis, cisOrig.get(perm.get(i)), verbose) > 0)
-							foundBetter = true;
-	
-					//try linked version...
-					if (!foundBetter)
-						for (int i = 0; i < numCis; ++i) {
-							//ArrayList<ContigInterval> cis_ = new ArrayList<ContigInterval>();
-							//cis_.addAll(cis);
-							//calculateBestLinkedContig_ts(cis_, perm.get(i), verbose);
-
-							if (calculateBestLinkedContig_ts(cis, perm.get(i), verbose) > 0)
-								foundBetter = true;
-						}
-				} else {
-					for (int linked = 0; linked < 2; ++linked) {
-						AtomicInteger index = new AtomicInteger();
-						AtomicBoolean stop = new AtomicBoolean();
-						
-						CalculateBest[] cbs = new CalculateBest[numThreads];
-						for (int t = 0; t < numThreads; ++t) {
-							cbs[t] = new CalculateBest(cis, perm, index, stop, verbose, linked == 1);
-							if (t > 0)
-								cbs[t - 1].setNext(cbs[t]);
-						}
-						while (true) {
-							cbs[0].run();
-							int best = 0;
-							for (int t = 1; t < numThreads; ++t) {
-								if (cbs[t].getScore() > cbs[best].getScore())
-									best = t;
-							}
-							if (cbs[best].getScore() > 0) {
-								if (best > 0) {
-									CalculateBest tmp = cbs[0]; //swap cbs[0] and cbs[best]
-									cbs[0] = cbs[best];
-									cbs[best] = tmp;
-									for (int t = 1; t < numThreads; ++t)
-										cbs[t - 1].setNext(cbs[t]);
-									cbs[numThreads - 1].setNext(null);
-								}
-								for (int t = 1; t < numThreads; ++t) { //run other contigs that improved the score...
-									if (cbs[t].getScore() > 0) {
-										cbs[0].directRun(cbs[t].getScoreIndex());
-									}
-								}
-								stop.set(false);
-								foundBetter = true;
-								for (int t = 0; t < numThreads; ++t)
-									cbs[t].setScore(0);
-							} else
-								break;
-						}
-						if (foundBetter) {
-							makeCisIdentical(cis, cbs[0].cis);
-							break; // linked only if !foundBetter
-						}
-					}
-					//if (!foundBetter) //calculateBestLinkedContig is not thread safe...
-					//	for (int i = 0; i < numCis; ++i)
-					//		if (calculateBestLinkedContig(cis, perm.get(i), verbose) > 0)
-					//			foundBetter = true;
-
-				}
-			} while (foundBetter);
-			int score = (calculateScore(cis, false) + calculateNonMarkerScore(cis));
-			if (score > bestScore) {
-				bestScore = score;
-				cis_best.clear();
-				cis_bestO.clear();
-				for (ContigInterval ci : cis) {
-					cis_best.add(ci);
-					cis_bestO.add(ci.getOrientation());
-				}
-			} else {
-				cis.clear();
-				int i = 0;
-				for (ContigInterval ci : cis_best) {
-					cis.add(ci);
-					ci.setOrientation(cis_bestO.get(i++));
-				}
-			}
-		}
-		
-		if (finalRound) {
-			ArrayList<Double> orderSupport = calculateSupport(cis);
-			System.out.println(" final score " +  (calculateScore(cis, false) + calculateNonMarkerScore(cis)));
-			printAnchoring(cis, orderSupport);
-			findLikelyAssemblyErrors(cis);
-		}
-	}
-
-	private void printAnchoring(ArrayList<ContigInterval> cis, ArrayList<Double> orderSupport) {
-		printAnchoring(System.out, cis, orderSupport);
-	}
-	private void printAnchoring(PrintStream stream, ArrayList<ContigInterval> cis, ArrayList<Double> orderSupport) {
-		stream.print("#contig\tstart\tend\torientation\tchr\torder_support\torig_start/alt_start\torig_end/alt_end\tlinked1\tvia_1\tlink_score1\tlinked2\tvia_2\tlink_score2\tpos_support");
-		for (int map = 0; map < numMaps; ++map)
-			stream.print("\tmap" + (map + 1));
-		stream.println();
-		
-		boolean knownOrientation[] = new boolean[cis.size()]; // calculate whether global orientation is known...
-
-		
-		//calculate map info and follow linked2 links (fill forwards in knownOrientation)
-		int prevC = 0;
-		for (int cii = 0; cii < cis.size(); ++cii) {
-			ContigInterval ci = cis.get(cii);
-			boolean linked2 = false; // from chain file...
-			if (cii + 1 < cis.size() && linkedIntervals(cis, cii, cii + 1))
-				linked2 = true;
-			if (!linked2) {
-				for (int  map = 0; map < numMaps; ++map) {
-					int max = Integer.MIN_VALUE;
-					int min = Integer.MAX_VALUE;
-					for (int c = prevC; c <= cii; ++c)
-						for (Marker m : cis.get(c).getMarkers(map)) {
-							max = Math.max(max, m.pPlus);
-							min = Math.min(min, m.pPlus);
-						}
-					if (max > min)
-						for (int c = prevC; c <= cii; ++c)
-							knownOrientation[c] = true;
-				}
-				prevC = cii + 1;
-			}
-		}
-
-		long  starts[] = new long[cis.size()]; // calculate start of each contig
-		long  ends[] = new long[cis.size()]; // calculate end of each contig
-
-		long  starts2[] = new long[cis.size()]; // calculate start of each contig
-		long  ends2[] = new long[cis.size()]; // calculate end of each contig
-
-		boolean prevSwapped = false; // fix for contigs cut out more than their length (a haplotype of two other contigs)
-		for (int cii = 0; cii < cis.size(); ++cii) {
-			ContigInterval ci = cis.get(cii);
-			
-			boolean linked1 = false; // from chain file...
-			boolean linked2 = false; // from chain file...
-			if (cii > 0 && linkedIntervals(cis, cii - 1, cii))
-				linked1 = true;
-			if (cii < cis.size() - 1 && linkedIntervals(cis, cii, cii + 1))
-				linked2 = true;
-
-			ContigInterval prev = ((linked1) ? cis.get(cii - 1): null);
-			ContigInterval next = ((linked2) ? cis.get(cii + 1): null);
-			
-			long start = ci.getStart();
-			long end = ci.getEnd();
-
-			long start2 = ci.getStart();
-			long end2 = ci.getEnd();
-
-			if (prev != null) {
-				String key = this.calculateKey(prev, ci);
-				if (chainLinkHash.containsKey(key)) {
-					if (ci.getOrientation() >= 0) {
-						start = chainLinkHashCut2.get(key);
-						start2 = chainLinkHashCut2a.get(key);
-						if (prevSwapped) {
-							long tmp = start;
-							start = start2;
-							start2 = tmp;
-						}
-					} else {
-						end = chainLinkHashCut2.get(key);
-						end2 = chainLinkHashCut2a.get(key);
-						if (prevSwapped) {
-							long tmp = end;
-							end = end2;
-							end2 = tmp;
-						}
-					}
-				}
-			}
-			if (next != null) {
-				String key = this.calculateKey(ci, next);
-				if (chainLinkHash.containsKey(key)) {
-					if (ci.getOrientation() >= 0) {
-						end = chainLinkHashCut1.get(key);
-						end2 = chainLinkHashCut1a.get(key);
-						if (end < start - 1 && end2 > end) { // more than full length aligned...
-							long tmp = end;
-							end = end2;
-							end2 = tmp;
-							prevSwapped = true;
-						} else
-							prevSwapped = false;
-					} else {
-						start = chainLinkHashCut1.get(key);
-						start2 = chainLinkHashCut1a.get(key);
-						if (end < start - 1 && start2 < start) { // more than full length aligned...
-							long tmp = start;
-							start = start2;
-							start2 = tmp;
-							prevSwapped = true;
-						} else
-							prevSwapped = false;
-					}
-				} else
-					prevSwapped = false;
-			}
-
-			starts[cii] = start;
-			starts2[cii] = start2;
-
-			ends[cii] = end;
-			ends2[cii] = end2;
-		}
-		
-		//finally try skipping negative length contigs and try to find new starts and ends... 
-		for (int cii = 2; cii < cis.size(); ++cii) {
-			if (ends[cii] >= starts[cii] - 1) { // non negative length
-				int prevNN = cii - 1;
-				while (prevNN >= 0 && ends[prevNN] < starts[prevNN] - 1) // negative length
-					--prevNN;
-				if (prevNN < cii - 1 && prevNN >= 0 && linkedIntervals(cis, prevNN, cii)) {
-					ContigInterval ci = cis.get(cii);
-					ContigInterval ci2 = cis.get(prevNN);
-					String key = calculateKey(ci2, ci);
-					if (chainLinkHash.containsKey(key)) {
-						System.err.println("skipping contig " + cis.get(cii - 1));
-						if (ci.getOrientation() >= 0) {
-							starts[cii] = chainLinkHashCut2.get(key);
-							starts2[cii] = chainLinkHashCut2a.get(key);
-						} else {
-							ends[cii] = chainLinkHashCut2.get(key);
-							ends2[cii] = chainLinkHashCut2a.get(key);
-						}
-						if (ci2.getOrientation() >= 0) {
-							ends[prevNN] = chainLinkHashCut1.get(key);
-							ends2[prevNN] = chainLinkHashCut1a.get(key);
-						} else {
-							starts[prevNN] = chainLinkHashCut1.get(key);
-							starts2[prevNN] = chainLinkHashCut1a.get(key);
-						}
-					}
-				}
-			}
-		}
-		
-		boolean toggleScaffolding = true;
-		for (int cii = 0; cii < cis.size(); ++cii) {
-			ContigInterval ci = cis.get(cii);
-			
-			boolean linked1 = false; // from chain file...
-			boolean linked2 = false; // from chain file...
-			if (cii > 0 && linkedIntervals(cis, cii - 1, cii))
-				linked1 = true;
-			if (cii < cis.size() - 1 && linkedIntervals(cis, cii, cii + 1))
-				linked2 = true;
-
-			ContigInterval prev = ((linked1) ? cis.get(cii - 1): null);
-			ContigInterval next = ((linked2) ? cis.get(cii + 1): null);
-			
-			String map_info = "";
-			String orientation = "?";
-			
-			int posSupport = 0;
-			
-			for (int  map = 0; map < numMaps; ++map) {
-				int max = Integer.MIN_VALUE;
-				int min = Integer.MAX_VALUE;
-				for (Marker m : ci.getMarkers(map)) {
-					max = Math.max(max, m.pPlus);
-					min = Math.min(min, m.pPlus);
-					posSupport += m.inside(m.pPlus); 
-				}
-				if (max >= min)
-					map_info = map_info + "\t" + min + "-" + max;
-				else
-					map_info = map_info + "\t-";
-			}
-			if (knownOrientation[cii]) 
-				orientation = ((ci.getOrientation() >= 0) ?  "+" : "-");
-			else if (linked1 || linked2) {
-				if (!linked1)
-					toggleScaffolding = !toggleScaffolding;
-				if (!toggleScaffolding)
-					orientation = ((ci.getOrientation() >= 0) ?  "++" : "--");
-				else
-					orientation = ((ci.getOrientation() >= 0) ?  "+++" : "---");
-			}
-			
-			int scorePrev = 0;
-			int scoreNext = 0;
-
-			String prevScaffoldInfo = "null";		
-			String nextScaffoldInfo = "null";		
-			
-			if (prev != null) {
-				String key = this.calculateKey(prev, ci);
-				if (chainLinkHash.containsKey(key)) {
-					scorePrev = chainLinkHash.get(key);
-					if (useChainAndPaf && scaffoldingLink.containsKey(key)) {
-						scorePrev += scaffoldingLink.get(key);
-						prevScaffoldInfo = "chain+" + scaffoldingLinkInfo.get(key);
-					} else
-						prevScaffoldInfo = "chain";
-				} else if (scaffoldingLink.containsKey(key)) {
-					scorePrev = scaffoldingLink.get(key);
-					prevScaffoldInfo = scaffoldingLinkInfo.get(key);
-				}
-				int sp = ((prox == null) ? 0 : prox.linkScore(cis, cii - 1, cii));
-				if (sp > 0) {
-					scorePrev +=sp ;
-					prevScaffoldInfo = prevScaffoldInfo + "+proximity";
-				}
-			}
-			if (next != null) {
-				String key = this.calculateKey(ci, next);
-				if (chainLinkHash.containsKey(key)) {
-					scoreNext = chainLinkHash.get(key);
-					if (useChainAndPaf && scaffoldingLink.containsKey(key)) {
-						scoreNext += scaffoldingLink.get(key);
-						nextScaffoldInfo = "chain+" + scaffoldingLinkInfo.get(key);
-					}
-					else
-						nextScaffoldInfo = "chain";
-				} else if (scaffoldingLink.containsKey(key)) {
-					scoreNext = scaffoldingLink.get(key);
-					nextScaffoldInfo = scaffoldingLinkInfo.get(key);
-				}
-				int sp = ((prox == null) ? 0 : prox.linkScore(cis, cii, cii + 1));
-				if (sp > 0) {
-					scoreNext += prox.linkScore(cis, cii, cii + 1);
-					nextScaffoldInfo = nextScaffoldInfo + "+proximity";
-				}
-			} // next != null
-
-			//just get the start and end from the previously computed arrays...
-			long start = starts[cii];
-			long end = ends[cii];
-			long start2 = starts2[cii];
-			long end2 = ends2[cii];
-
-			if (commentOutput)
-				stream.print("#");
-			stream.println(ci.getContig() + "\t" + start + "\t" + end + "\t" + orientation + "\t"
-			        + ci.getChromosome() + "\t" + orderSupport.get(cii) + "\t" + ci.getStart() + (start2==ci.getStart() ? "":"/" + start2) +  "\t" + ci.getEnd() + (end2==ci.getEnd() ? "":"/" + end2)
-					+ "\t" + (prev == null ? "null": prev.getContig()) + "\t" + prevScaffoldInfo + "\t" + scorePrev 
-					+ "\t" + (next == null ? "null": next.getContig()) + "\t" + nextScaffoldInfo + "\t" + scoreNext + "\t" + posSupport + map_info);
-		}
-	}
-	
-	
-	ArrayList<Double> logTable = new ArrayList<Double>();
-
-	private double myLog(int x) {
-		if (logTable.size() <= x) {
-			for (int i = logTable.size(); i <= x; ++i)
-				logTable.add(Math.log(i));
-		}
-		return logTable.get(x);
-	}
-
-	
-	
-	//markers is sorted within contig so no need to check orientation
-	private String getOneInterval(ArrayList<Marker> markers, int m1, int m2)
-	{
-		Marker mm1 = markers.get(m1);
-		Marker mm2 = markers.get(m2);
-		ContigInterval ci = mm1.getContigInterval(); 
-		long start = 0;
-		long end = 0;
-		
-		if (m1 == 0 || !ci.equals(markers.get(m1 - 1).getContigInterval()))
-				start = ci.getStart();
-		else
-				start = (mm1.getPosition() + markers.get(m1 - 1).getPosition()) / 2;
-
-		if (m2 + 1 == markers.size() || !ci.equals(markers.get(m2 + 1).getContigInterval()))
-				end = ci.getEnd();
-		else
-				end = (mm2.getPosition() + markers.get(m1 + 1).getPosition()) / 2;
-		
-		return ci.getContig() + "\t" + start + "\t" + end;  
-	}
-
-	//markers is sorted
-	private String getIntervals(ArrayList<Marker> markers, int m1, int m2)
-	{
-		String ret = "";
-		ContigInterval prev = null;
-		int start = -1;
-		int end = -1;
-		for (int i = m1; i <= m2; ++i) {
-			Marker m = markers.get(i);
-			ContigInterval c = m.getContigInterval();
-			if (c.equals(prev))
-				end = i;
-			else {
-				if (start >= 0)
-					ret += '\t' + getOneInterval(markers, start, end);
-				start = i;
-				end = i;
-			}
-			prev = c;
-		}
-		return ret + '\t' + getOneInterval(markers, start, end);
-	}
-	
-	private class PossibleError implements Comparable<PossibleError>{
-		private double ll;
-		private String info;
-		private int ci;
-		private long pos1[], pos2[];
-		public  PossibleError(double ll, int ci, String info) {
-			this.ll = ll;
-			this.info = info;
-			this.ci = ci;
-		}
-		public  PossibleError(double ll, int ci, String info, long pos1[], long pos2[]) {
-			this.ll = ll;
-			this.info = info;
-			this.ci = ci;
-			this.pos1 = pos1;
-			this.pos2 = pos2;
-		}
-		public String getInfo(){return info;}
-		@Override
-		public int compareTo(PossibleError other) {
-			if (ll < other.ll)
-				return 1;
-			if (ll > other.ll)
-				return -1;
-			return 0;
-		}
-		public int getCi() {
-			return ci;
-		}
-		public long[] getPos1() {
-			return pos1;
-		}
-		public long[] getPos2() {
-			return pos2;
-		}
-	}
-	
-	// log( (a/(a+b))^a * (b/(a+b))^b)
-	private double logLike(int a, int b)
-	{
-		double ret = 0;
-		if (a > 0)
-			ret += a * (myLog(a) - myLog(a + b));
-		if (b > 0)
-			ret += b * (myLog(b) - myLog(a + b));
-		return ret;
-	}
-
-	// log( (a/(a+b))^c * (b/(a+b))^d)
-	private double logLike(int a, int b, int c, int d)
-	{
-		double ret = 0;
-		if (c > 0)
-			ret += c * (myLog(a) - myLog(a + b));
-		if (d > 0)
-			ret += d * (myLog(b) - myLog(a + b));
-		return ret;
-	}
-
-	// find max maxNumErrors regions with more errors than expected, error rate is e0/(e0 + e1)
-	private void calculateErrors2(ArrayList<Marker> markers_, ArrayList<PossibleError> errors, int e0, int e1, int maxNumErrors)
-	{
-		boolean inside[] = new boolean[markers_.size()];
-		int cumulative[] = new int[markers_.size() + 1];
-		
-		int sum = 0;
-		for (int mi = 0; mi < markers_.size(); ++mi) {
-			Marker m = markers_.get(mi);
-			if (m.inside(m.pPlus) > 0)
-				inside[mi] = true;
-			else
-				++sum;
-			cumulative[mi + 1] = sum;
-		}
-		if (sum == 0) // all inside or no markers
-			return;
-		
-		ArrayList<Integer> markers = new ArrayList<Integer>();
-
-		for (int mi = 0; mi < markers_.size(); ++mi) { // take only first and last marker of multiple adjacent markers !inside
-			if ((mi == 0 || inside[mi - 1]) && !inside[mi])
-				markers.add(mi);
-			else
-				if ((mi + 1 == markers_.size() || inside[mi + 1]) && !inside[mi])
-					markers.add(mi);
-		}
-		//System.err.println(markers.size() + "\t" + markers_.size());
-
-		int numMarkers = markers.size();
-		
-		ArrayList<int[]> found = new ArrayList<int[]>(); 
-		for (int iteration = 0; iteration < maxNumErrors; ++iteration) {
-			double max = 0;
-			int max1 = -1;
-			int max2 = -1;
-			int maxo0 = 0;
-			int maxo1 = 0;
-out2:		for (int m1i = 0; m1i < numMarkers; ++m1i) {
-				int m1 = markers.get(m1i); 
-				for (int[] f : found)
-					if (f[1] >= m1 && f[0] <= m1) // found intervals contain m1
-						continue out2;
-				for (int m2i = m1i; m2i < numMarkers; ++m2i) {
-					int m2 = markers.get(m2i);
-					for (int[] f : found)
-						if (f[1] >= m2 && f[0] <= m2) // found intervals intersect m2 ([m1...m2])
-							continue out2;
-					int o0 = cumulative[m2 + 1] - cumulative[m1]; // number of markers outside interval
-					int o1 = (m2 - m1 + 1) - o0; // number of markers within interval 
-					//o0 * (e0 + e1) > e0 * (o0 + o1) (positive e and o) <=> o0 / (o0 + o1) > e0 / (e0 + e1)
-					if ( o0 * (long)(e0 + e1) > e0 * (long)(o0 + o1)) { //more errors than expected
-						double l = logLike(o0, o1) - logLike(e0, e1, o0, o1); //likelihood ratio
-						if (l > max) {
-							max = l;
-							max1 = m1; 
-							max2 = m2;
-							maxo0 = o0;
-							maxo1 = o1;
-						}
-					} else
-						continue out2; // no need to continue if we fall short
-				}
-			}
-			if (max > 0) {
-				found.add(new int[]{max1, max2});
-				ContigInterval ci = markers_.get(max1).getContigInterval();
-				long pos1 = markers_.get(max1).getPosition();
-				long pos1n = ((max1 > 0) ? markers_.get(max1 - 1).getPosition() + 1 : ci.getStart());
-				
-				long pos2 = markers_.get(max2).getPosition();
-				long pos2n = ((max2 + 1 < markers_.size()) ? markers_.get(max2 + 1).getPosition() - 1 : ci.getEnd());
-				
-				//if (pos1 < pos1n || pos2 > pos2n) {
-				//	System.exit(-1);
-				//}
-
-				String info = max + "\t" + maxo0 + "\t" + maxo1 + "\t" + ci.getContig() + "\t" + pos1n + "-" + pos1 + "\t" + pos2 + "-" + pos2n;
-				errors.add(new PossibleError(max, ci.getRank(), info , new long[]{pos1n, pos1}, new long[]{pos2, pos2n}));
-			}
-		}
-	}
-	
-	
-	
-	private ArrayList<Integer> calculateBinSum(ArrayList<Marker> markers, int endBin, boolean plusOrientation){
-		//calculate map position distribution
-		ArrayList<Integer> binSum = new ArrayList<Integer>();
-		for (int i = 0; i <= endBin; ++i)
-			binSum.add(0);
-
-		//int plus = 0;
-		//int minus = 0;
-		for (Marker m : markers) {
-			if (plusOrientation)
-				binSum.set(m.pPlus, binSum.get(m.pPlus) + 1);
-			else
-				binSum.set(m.pMinus, binSum.get(m.pMinus) + 1);
-		}
-		return binSum;
-	}
-
-	private class LongComparator0 implements Comparator<long[]>
-	{
-		@Override
-		public int compare(long[] l1, long[] l2){
-			return Long.compare(l1[0], l2[0]);
-		}
-	}
-
-	private class LongComparator1 implements Comparator<long[]>
-	{
-		@Override
-		public int compare(long[] l1, long[] l2){
-			return Long.compare(l1[1], l2[1]);
-		}
-	}
-	
-	//calculate how much score could be increasing if we split a contig...
-	//make a gap in map positions L..R, and see how many points we could add there
-	private ArrayList<Integer> increaseScore(ArrayList<Marker> markers, ArrayList<Integer> binSum){
-		
-		ArrayList<Integer> ret = new ArrayList<Integer>(); 
-
-		int endBin = getMaxBin(markers);
-		if (endBin < binSum.size() - 1)
-			endBin = binSum.size() - 1;
-		int startBin = getMinBin(markers);
-		if (startBin > 0)
-			startBin = 0;
-		
-		int numMarkers = markers.size();
-		
-		int S[][] = new int[numMarkers + 1][endBin - startBin + 1];
-
-		int Sp[] = new int[endBin - startBin + 1]; 
-	
-		int Sb[][] = new int[numMarkers + 1][endBin - startBin + 1];
-
-		//simple way to calculate (about correct) backward table...
-		Collections.reverse(markers);
-		forwardFast2(markers, Sb, startBin, endBin);
-		Collections.reverse(markers);
-		forwardFast1(markers, S, startBin, endBin);
-		//Should we make S and Sb monotonic (+/- 1) ?
-
-		for (int i = 0; i <= numMarkers; ++i) {
-			int max = 0;
-			//int maxL = 0;
-			//int maxR = 0;
-
-			//reuse P as PSp
-			for (int b = 0; b < endBin - startBin; ++b) { // add binSum to S
-				int bs = 0;
-				if (b + startBin < binSum.size())
-					bs = binSum.get(b + startBin);
-
-				//either we take score S[i][b]+bs or skip b and get bs + score Sp[b-1]
-				if (b == 0) {
-					Sp[b] = S[i][b] + bs;
-					//P[i][b] = b;
-				} else {
-					int s1 = S[i][b] + bs;
-					int s2 = Sp[b - 1] + bs;
-					if (s1 >= s2) {
-						Sp[b] = s1;
-						//P[i][b] = b;
-					} else {
-						Sp[b] = s2;
-						//P[i][b] = P[i][b - 1];
-					}
-				}
-			}
-			
-
-			for (int b = 0; b <= endBin - startBin; ++b) {
-				int s = Sp[b] + Sb[numMarkers - i][b];
-				if (s > max) {
-					max = s;
-					//maxR = P[i][b] + startBin;
-					//maxL = b + startBin;
-				}
-			}
-			ret.add(max);
-		}
-		return ret;
-	}
-	
-	
-	private ArrayList<PossibleError> findNonHaplotypeAssemblyErrors(ArrayList<ContigInterval> cis, boolean verbose)
-	{
-		ArrayList<PossibleError> ret = new ArrayList<PossibleError>(); 
-
-		ArrayList<PossibleError> errors = new ArrayList<PossibleError>(); 
-		int e0 = 0;
-		int e1 = 0;
-		for (int iteration = 0; iteration < 2; ++iteration) { //first iteration: calculate e0 and e1, second iteration find errors...
-			for (int cii = 0; cii < cis.size(); ++cii) {
-				ContigInterval ci = cis.get(cii);
-				
-				//Haplotypes are typical sources of errors, 
-  				//by adjusting start and end, one could reduce errors caused by them...
-				//best way would be to remove markers from one pair (with less markers) of haplotype and re-evaluate the maps...
-/*				
-				long start = ci.getStart();
-				long end = ci.getEnd();
-                int orientation = ci.getOrientation();
-				if (cii > 0) {
-					ContigInterval prev = cis.get(cii - 1);
-					String key = calculateKey(prev, ci);
-					Long cut = chainLinkHashCut2.get(key); //Cut2a
-					if (cut != null)
-						if (orientation >= 0)
-							start = cut;
-						else
-							end = cut;
-				}
-				if (cii + 1  < cis.size()) {
-					ContigInterval next = cis.get(cii + 1);
-					String key = calculateKeyInverse(ci, next);
-					Long cut = chainLinkHashCut2.get(key); //Cut2a
-					if (cut != null)
-						if (orientation >= 0)
-							end = cut;
-						else
-							start = cut;
-				}*/
-	
-				if (iteration == 0) {
-					for (int  map = 0; map < numMaps; ++map)
-						for (Marker m : ci.getMarkers(map))
-							//if (m.getPosition() >= start && m.getPosition() <= end)
-								if (m.inside(m.pPlus) > 0) // TODO: allow any scores, now 0 vs >0
-									++e1;
-								else
-									++e0;
-							
-				} else {
-					//System.err.println(e1 + "\t" + e0);
-					ArrayList<Marker> markersCi = new ArrayList<Marker>();			
-					for (int  map = 0; map < numMaps; ++map)
-						for (Marker m : ci.getMarkers(map))
-							markersCi.add(m);
-					Collections.sort(markersCi);
-					//calculateErrors(markersCi, errors, e0, e1);
-					calculateErrors2(markersCi, errors, e0, e1, numErrorsPerContig);
-				}
-			}
-		}
-
-		if (verbose) {
-			System.err.println("#*** possible errors ***");
-			System.err.println("#total outside/inside:\t" + e0 + "\t" + e1);
-			System.err.println("#X2\t0\t>0\tcontig\tstart\tend\tcontig2\tpos");
-		}
-
-		Collections.sort(errors);
-		if (errors != null)
-			for (int i = 0; i < numErrors && i < errors.size(); ++i) {
-				ret.add(errors.get(i));
-				PossibleError ff = findFix(cis, errors.get(i), false); 
-				ret.add(ff);
-				if (verbose) {
-					System.err.println(errors.get(i).getInfo() + ((ff == null) ? "" : "\t" + ff.getInfo()) + "\terror");
-				}
-			}
-		return ret;
-	}
-	
-	//TODO: Check that calculateChainScore is ok
-	//note: assumes that score has been evaluated for the markers in cis and in the corresponding order and orientation
-	private void findLikelyAssemblyErrors(ArrayList<ContigInterval> cis)
-	{
-		System.err.println("*** possible haplotypes ***");
-		System.err.println("score\tcontig\tstart\tend\tof_contig\tstart\tend\tcontig_aligment_start\tcontig_aligment_end");
-		
-		ArrayList<PossibleError> haplotypes = new ArrayList<PossibleError>(); 
-		
-		for (int cii = 0; cii < cis.size(); ++cii) {
-			ContigInterval ci = cis.get(cii);
-			int score = 0;
-			for (int  map = 0; map < numMaps; ++map)
-				for (Marker m : ci.getMarkers(map))
-					score += m.inside(m.pPlus);
-			if (cii > 0)
-				score += calculateChainScore(cis.get(cii - 1), ci);
-			if (cii + 1  < cis.size())
-				score += calculateChainScore(ci, cis.get(cii + 1));
-
-			//int scoreH = 0;
-			//ContigInterval haplotypeOf = null;
-			for (ContigInterval ci2 : cis) {
-				Integer s = calculateChainScoreHaplotype(ci2, ci);
-				if (s != null && s > score) {
-					long ha[] = calculateChainScoreHaplotypeCut(ci2, ci);
-					haplotypes.add(new PossibleError((s - score), 0, (s - score) + "\t" + ci + "\t" + ci2 + "\t" + ha[0] + "\t" + ha[1]));
-//					scoreH = s;
-//					haplotypeOf = ci2;
-				}
-			}
-//			if (scoreH > score) {
-//				haplotypes.add(new PossibleError((scoreH - score), (scoreH - score) + "\t" + ci + "\t" + haplotypeOf));
-//				//System.err.println((scoreH - score) + "\t" + ci + "\t" + haplotypeOf); 
-//			}
-
-		}
-		Collections.sort(haplotypes);
-		for (PossibleError pe: haplotypes)
-			System.err.println(pe.getInfo() + "\thaplotype");
-		
-		findNonHaplotypeAssemblyErrors(cis, true);
-		
-	}
-	void setMaxIntersect(int parseInt) {
-		maxIntersect = parseInt;
-	}
-
-	void setMinLinkAlignmentScore(int parseInt) {
-		minLinkAlignmentScore = parseInt;
-		
-	}
-
-	private void setMinHaplotypeAlignmentScore(int parseInt) {
-		minHaplotypeAlignmentScore = parseInt;		
-	}
-
-	//autogenerated stubs...
-	void setMaxBridge(int parseInt) {
-		maxBridge = parseInt;		
-	}
-
-	void setCutPenalty(double parseDouble) {
-		cutPenalty = parseDouble;
-	}
-
-	void setOrientationPenalty(double parseDouble) {
-		orientationPenalty = parseDouble;
-	}
-
-	void setScaleScore(double parseDouble) {
-		scaleScore = parseDouble;
-	}
-	void setNumThreads(int nt) {
-		numThreads = nt;
-	}
-
-	private ArrayList<ArrayList<String>> myLiftover(ArrayList<ArrayList<String>> markers, ArrayList<long[]> alignment, boolean sameOrientation, String newContig)
-	{
-		ArrayList<ArrayList<String>> ret = new ArrayList<ArrayList<String>>();
-		for (ArrayList<String> row: markers) {
-			//System.err.println(row);
-			long position = InputData.myParseLong(row.get(1));
-			long position_new = mapPosition12(alignment, position, sameOrientation);
-			//System.err.println(position + "->" + position_new);
-			if (position_new > 0) {
-				//System.err.println("HIPHEI");
-				ArrayList<String> nrow = new ArrayList<String>(); 
-				for (int i = 0; i < row.size(); ++i)
-					if (i == 0)
-						nrow.add(newContig);
-					else if (i == 1)
-						nrow.add("" + position_new);
-					else
-						nrow.add(row.get(i));
-				ret.add(nrow);
-			}
-		}
-		return ret;
-	}
-	
-	private void liftover__(ContigInterval hap, ContigInterval c2, ArrayList<long[]> alignment, boolean sameOrientation, long ascore, HashMap<ContigInterval, Long> bestScore, HashMap<ContigInterval, ContigInterval> bestScoreContig, HashMap<ContigInterval, ArrayList<ArrayList<String>>> map, HashMap<ContigInterval, ArrayList<ArrayList<String>>> liftoverMap) {
-		Long prevScore = bestScore.get(hap);
-		if (prevScore != null) {
-			ContigInterval c3 = bestScoreContig.get(hap);
-			if (c3.getContig().equals(c2.getContig()) && Misc.intersectIntervals(c2.getStart(), c2.getEnd(), c3.getStart(), c3.getEnd())) { // same alignment...
-				if (ascore > prevScore) {
-					liftoverMap.put(hap, myLiftover(map.get(hap), alignment, sameOrientation, c2.getContig())); // do liftover
-					bestScoreContig.put(hap, c2);
-					bestScore.put(hap, ascore);					
-				}
-			} else {
-				if (ascore > prevScore) {
-					bestScoreContig.put(hap, c2);
-					bestScore.put(hap, ascore);					
-				}
-				if (ascore > 2 * prevScore) {
-					liftoverMap.put(hap, myLiftover(map.get(hap), alignment, sameOrientation, c2.getContig())); // do liftover
-				} 
-				else if (ascore > liftoverScoreDiff * prevScore) {// too little score difference...
-					liftoverMap.get(hap).clear(); // remove markers...
-					//System.err.println("remove");
-				}
-			}
-			
-		} else {
-			//System.err.println("liftover");
-			liftoverMap.put(hap, myLiftover(map.get(hap), alignment, sameOrientation, c2.getContig())); // do liftover
-			bestScore.put(hap, ascore);
-			bestScoreContig.put(hap, c2);
-		}
-	}
-	
-	private void liftover_(String fn, HashMap<ContigInterval, ArrayList<ArrayList<String>>> map) {
-		System.err.println("loading alignment chain...");
-		
-		HashMap<ContigInterval, Long> bestScore = new HashMap<ContigInterval, Long>(); // score of used chain   
-		HashMap<ContigInterval, ContigInterval> bestScoreContig = new HashMap<ContigInterval, ContigInterval>(); // contigInterval of used chain   
-		
-		HashMap<ContigInterval, ArrayList<ArrayList<String>>> liftoverMap = new HashMap<ContigInterval, ArrayList<ArrayList<String>>>(); // store liftover markers...
-		
-		for (ContigInterval ci : map.keySet()) {
-			liftoverMap.put(ci, new ArrayList<ArrayList<String>>());
-			//System.err.println(ci);
-		}
-		
-		try {
-			BufferedReader br = null;
-			if (fn.equals("-"))
-				br = new BufferedReader(new InputStreamReader(System.in));
-			else
-				br = new BufferedReader(new FileReader(fn));
-			do {
-				ArrayList<String> row = Input.loadTableRow(br, "\t ");
-				if (row == null)
-					break;
-				boolean skip = true;
-				if (row.size() >= 12 && "chain".equals(row.get(0))) {
-					String contig1 = row.get(2);
-					String contig2 = row.get(7);
-					
-					boolean someMarkers1 = false;
-					if (haplotypeHash.containsKey(contig1))
-						for (ContigInterval hap : haplotypeHash.get(contig1))
-							if (map.containsKey(hap)) {
-								someMarkers1 = true;
-								break;
-							}
-					boolean someMarkers2 = false;
-					if (haplotypeHash.containsKey(contig2))
-						for (ContigInterval hap : haplotypeHash.get(contig2)) {
-							if (map.containsKey(hap)) {
-								someMarkers2 = true;
-								break;
-							}
-						}
-					if (!someMarkers1 && !someMarkers2) // no markers to do liftover...
-						continue;
-
-					skip = false;
-					long p1_[] = chain2OneBase(row.get(3), row.get(4), row.get(5), row.get(6));
-					long p2_[] = chain2OneBase(row.get(8), row.get(9), row.get(10), row.get(11));
-					if ("-".equals(row.get(4))) {
-						System.err.println("Error: only ++, and +- orientation allowed in the chain file");
-						continue;
-					}
-					
-					//System.err.println("running");
-					
-					boolean sameOrientation = row.get(4).equals(row.get(9));
-
-					// load alignment for liftover...
-					ArrayList<long[]> alignment_ = new ArrayList<long[]>();
-					ArrayList<String> row2 = null;
-					long v1 = p1_[0];
-					long v2 = ((sameOrientation) ? p2_[0] : p2_[1]);
-					int v3 = 0;
-					do {
-						row2 = Input.loadTableRow(br, "\t ");
-						
-						v3 = Integer.parseInt(row2.get(0));
-						alignment_.add(new long[]{v1, v2, v3});
-						v1 += v3;
-						v2 += ((sameOrientation) ? v3 : -v3);
-						if (row2.size() >= 3) {
-							v1 += Integer.parseInt(row2.get(1));
-							v2 += ((sameOrientation) ? Integer.parseInt(row2.get(2)) : -Integer.parseInt(row2.get(2)));
-						}
-					} while (row2 != null && row2.size() >= 3);
-					
-					long ascore_ = Long.parseLong(row.get(1));
-
-					if (someMarkers1) //  && haplotypeHash.containsKey(contig1)
-						for (ContigInterval hap : haplotypeHash.get(contig1)) 
-							if (map.containsKey(hap)) {
-								ContigInterval c2 = new ContigInterval(contig2, p2_[0], p2_[1]);
-								
-								ArrayList<long[]> alignment = new ArrayList<long[]>();
-								double t = trimChain(alignment_, sameOrientation, hap, c2, alignment);
-								if (t == 0.0) // all trimmed
-									continue;
-
-								if (t < 1.0) { // update c2 start and end
-									long p[] = getStartEnd2(alignment, sameOrientation);
-									c2 = new ContigInterval(contig2, p[0], p[1]);
-								} else {
-									alignment = alignment_;
-								}
-
-								long ascore = (long)(t * ascore_);
-								
-								boolean doLift = true;
-								if (haplotypeHash.containsKey(contig2))
-									for (ContigInterval hap2 : haplotypeHash.get(contig2)) // no liftover between haplotypes...
-										if (Misc.intersectIntervals(hap2.getStart(), hap2.getEnd(), c2.getStart(), c2.getEnd())) {
-											doLift = false;
-											break;
-										}
-								if (doLift)
-									liftover__(hap, c2, alignment, sameOrientation, ascore, bestScore, bestScoreContig, map, liftoverMap);
-							}
-					//otherway round...
-					if (someMarkers2) { //  && haplotypeHash.containsKey(contig2)
-						ArrayList<long[]> revAlignment_ = reverseAlignment(alignment_, sameOrientation);
-						for (ContigInterval hap : haplotypeHash.get(contig2))
-							if (map.containsKey(hap)) {
-								ContigInterval c2 = new ContigInterval(contig1, p1_[0], p1_[1]);
-								
-								ArrayList<long[]> alignment = new ArrayList<long[]>();
-								double t = trimChain(revAlignment_, sameOrientation, hap, c2, alignment);
-								if (t == 0.0) // all trimmed
-									continue;
-								if (t < 1.0) { // update c2 start and end
-									long p[] = getStartEnd2(alignment, sameOrientation);			 						
-									c2 = new ContigInterval(contig1, p[0], p[1]);
-								} else
-									alignment = revAlignment_; 
-								long ascore = (long)(t * ascore_);
-
-								boolean doLift = true;
-								if (haplotypeHash.containsKey(contig1))
-									for (ContigInterval hap2 : haplotypeHash.get(contig1)) // no liftover between haplotypes...
-										if (Misc.intersectIntervals(hap2.getStart(), hap2.getEnd(), c2.getStart(), c2.getEnd())) {
-											doLift = false;
-											break;
-										}
-								if (doLift)
-									liftover__(hap, c2, alignment, sameOrientation, ascore, bestScore, bestScoreContig, map, liftoverMap);
-							}
-					}
-				} else {
-					if (skip && (row.size() == 3 || row.size() == 1))
-						;
-					else
-						System.err.println("Warning: skipping " + row);
-				}
-			} while (true);
-			br.close();
-			int numLifoverMarkers = 0;
-			for (ContigInterval ci : liftoverMap.keySet()) {
-				ArrayList<ArrayList<String>> lom = liftoverMap.get(ci);
-				numLifoverMarkers += lom.size();
-				StringBuilder sb = new StringBuilder(); 
-				for (ArrayList<String> row : lom) {
-					sb.append(row.get(0));
-					for (int i = 1; i < row.size(); ++i) {
-						sb.append('\t');
-						sb.append(row.get(i));
-					}
-					sb.append('\n');
-				}
-				System.out.print(sb);
-			}
-			System.err.println("Lifting over " + numLifoverMarkers + " markers");
-		} catch (Exception e) {
-	     	e.printStackTrace();
-			System.err.println("Error in file " + fn);
-      	}
-	}
-
-	public void liftover(String haplotypeFile, String chainFile, String mapFile) {
-		ArrayList<ContigInterval> haplotypes = InputData.loadHaplotypes(haplotypeFile);
-		
-		for (ContigInterval hapci: haplotypes) {
-			String key = hapci.getContig(); 
-			ArrayList<ContigInterval> list = haplotypeHash.get(key);
-			if (list == null) {
-				list = new ArrayList<ContigInterval>(); 
-				haplotypeHash.put(key, list);
-			}
-			list.add(hapci);
-		}
-
-		HashMap<ContigInterval, ArrayList<ArrayList<String>>> map = InputData.loadRaw(mapFile, haplotypeHash);
-		//System.out.println(map);
-		
- 		liftover_(chainFile, map);
-		
-	}
-
-	private void loadCutSites(String fn) {
-		try {
-			HashMap<String, ArrayList<ContigInterval>> bedHash2 = new HashMap<String, ArrayList<ContigInterval>>();
-			for (ContigInterval ci : bed) {
-				if (ci.getStart() != ci.getMinStart() || ci.getEnd() != ci.getMaxEnd()) { // ContigInterval with uncertainty in its start or end
-					String contig = ci.getContig();
-					if (!bedHash2.containsKey(contig))
-						bedHash2.put(contig, new ArrayList<ContigInterval>());
-					bedHash2.get(contig).add(ci);
-				}
-			}
-			int numCutSites = 0;
-			BufferedReader	br = new BufferedReader(new FileReader(fn));
-			do {
-				ArrayList<String> row = Input.loadTableRow(br, "\t ");
-				if (row == null)
-					break;
-				if (row.size() >= 2) {
-					String contig = row.get(0);
-					long position = 0;
-					long position2 = 0;
-					if (bedHash2.containsKey(contig))
-						for (ContigInterval ci : bedHash2.get(contig)) {
-							if (position == 0) {
-								position = Long.parseLong(row.get(1));
-								if (row.size() >= 3) {
-									position2 = Long.parseLong(row.get(2));
-									--position; //N gap 
-									++position2;
-								} else
-									position2 = position + 1;
-							}
-							
-							
-							if (position2 >= ci.getMinStart() && position2 <= ci.getMaxStart()) {
-								++numCutSites;
-								ci.setStart(position2);
-								break;
-							}
-							if (position >= ci.getMinEnd() && position <= ci.getMaxEnd()) {
-								++numCutSites;
-								ci.setEnd(position);
-								break;
-							}
-						}
-				}
-			} while (true);
-			br.close();
-			System.err.println("Trimming " + numCutSites + " contig ends based on cutSites file");
-		} catch (Exception e) {
-	     	e.printStackTrace();
-			System.err.println("Error in file " + fn);
-      	}
-	}
-	
-	//find how to fix likely erroneous genomic interval (e)
-	//assumes solve has been called on the cis 
-	private PossibleError findFix(ArrayList<ContigInterval> cis, PossibleError e, boolean verbose){
-		//update rank and numContigIntervals
-		int numContigIntervals = 0; // update rank (might be corrupted)
-		for (ContigInterval c : cis)
-			c.setRank(numContigIntervals++);
-
-		//calculate full anchoring score
-		ArrayList<Integer> oldPos = new ArrayList<Integer>(); 
-		int oldFullScore = 0;
-		for (int map = 0; map < numMaps; ++map)
-			for (Marker m : getMarkers(cis, null, map)) {
-				oldFullScore += m.inside(m.pPlus);
-				oldPos.add(m.pPlus); // store mPlus, as this is changed...
-			}
-
-		//get error region (region inside one contigInterval)
-		ContigInterval errorContig = cis.get(e.getCi());
-		long pos1[] = e.getPos1();
-		long pos2[] = e.getPos2();
-	
-		int s0 = 0; // old score for region e
-		int s1 = 0; // score for e in + orient
-		int s2 = 0; // score for e in - orient
-		
-		ArrayList<ArrayList<Integer>> iss = new ArrayList<ArrayList<Integer>>(); //store increaseScores... 
-
-		for (int map = 0; map < numMaps; ++map) {
-			//get markers spanning error region for each map separately 
-
-			ArrayList<Marker> errorMarkers = new ArrayList<Marker>();
-			ArrayList<Marker> nonErrorMarkers = new ArrayList<Marker>();
-			
-			for (ContigInterval c : cis)
-				for (Marker m : c.getMarkers(map)) {
-					if ((c == errorContig) && m.getPosition() >= pos1[0] && m.getPosition() <= pos2[1]) 
-						errorMarkers.add(m);
-					else
-						nonErrorMarkers.add(m);
-				}
-
-			int numMarkers = errorMarkers.size();
-			//calculate old score
-			//int oldScore[] = new int[numMarkers];
-			for (int i = 0; i < numMarkers; ++i) {
-				Marker m = errorMarkers.get(i);
-				int s = m.inside(m.pPlus);
-				s0 += s;
-			}
-			s1 += solveForward(errorMarkers);
-			s2 += solveBackward(errorMarkers);
-
-			ArrayList<Marker> mm2 = new ArrayList<Marker>();
-			for (int i = 0; i < numMarkers; ++i) {
-				Marker m = errorMarkers.get(i);
-				if (m.inside(m.pPlus) > 0) // marker is now contributing to the score
-					mm2.add(m);
-			}
-			int maxBin = getMaxBin(errorContig.getMarkers(map));
-			
-			iss.add(increaseScore(nonErrorMarkers, calculateBinSum(mm2, maxBin, true))); // mm2 in + orientation
-			
-			mm2.clear();
-			for (int i = 0; i < numMarkers; ++i) {
-				Marker m = errorMarkers.get(i);
-				if (m.inside(m.pMinus) > 0) // marker is now contributing to the score
-					mm2.add(m);
-			}
-			
-			iss.add(increaseScore(nonErrorMarkers, calculateBinSum(mm2, maxBin, false))); // mm2 in - orientation
-			
-			//System.err.println("size=" + nonErrorMarkers.size());
-
-		}
-
-		int pi = 0;
-		for (int map = 0; map < numMaps; ++map)
-			for (Marker m : getMarkers(cis, null, map))
-				m.pPlus = oldPos.get(pi++); // restore mPlus, this is changed by increaseScore
-		
-		if ((s0 >= s1 && s0 >= s2))
-			return null; // no fix found...
-				
-		//System.err.println("max score delta = " + (s1 - s0) + " or " + (s2 - s0) + "\t" + s0 + "\t" + s1 + "\t" + s2 + "\t" + e.getInfo());
-		//merge results from each increaseScore
-
-		long maxScore = oldFullScore;
-		int maxC = 0;
-		long maxP1 = 0;
-		long maxP2 = 0;
-		
-		for (int orient = 0; orient < 2; ++orient) {
-			int startMarker[] = new int[numMaps];
-			for (ContigInterval c : cis) {
-				//store cut intervals
-				//if interval [a,b] is in cov, then prefix can be [1..a], [1..a+1],...,[1..b]
-				ArrayList<long []> cov = new ArrayList<long []>();
-			
-				for (int map = 0; map < numMaps; ++map) {
-					ArrayList<Integer> is = iss.get(map + map + orient);
-					
-					//System.err.println("size=" + is.size());
-					
-					ArrayList<Marker> markers = new ArrayList<Marker>(); 
-					for (Marker m : c.getMarkers(map))
-						if ((errorContig == c) && m.getPosition() >= pos1[0] && m.getPosition() <= pos2[1]) // errorMarker
-							;
-						else
-							markers.add(m);
-
-					//System.err.println("size=" + markers.size());
-					
-					int numMarkers = markers.size();
-					if (numMarkers > 0) {
-						long isi = is.get(startMarker[map]);
-						if (c.getOrientation() >= 0) { // + orientation
-							cov.add(new long[]{c.getStart() - 1, markers.get(0).getPosition() - 1, isi});
-							for (int mi = 1; mi < numMarkers; ++mi) {
-								//Marker m = markers.get(mi);
-								isi = is.get(startMarker[map] + mi);
-								cov.add(new long[]{markers.get(mi - 1).getPosition(), markers.get(mi).getPosition() - 1, isi});
-							}
-							isi = is.get(startMarker[map] + numMarkers);
-							cov.add(new long[]{markers.get(numMarkers - 1).getPosition(), c.getEnd(), isi});
-						} else {
-							cov.add(new long[]{markers.get(0).getPosition(), c.getEnd(), isi});
-							for (int mi = 1; mi < numMarkers; ++mi) {
-								//Marker m = markers.get(mi);
-								isi = is.get(startMarker[map] + mi);
-								cov.add(new long[]{markers.get(mi).getPosition(), markers.get(mi - 1).getPosition() - 1, isi});
-							}
-							isi = is.get(startMarker[map] + numMarkers);
-							cov.add(new long[]{c.getStart() - 1, markers.get(numMarkers - 1).getPosition() - 1, isi});
-						}
-					} else { // 0 markers
-						int isi = is.get(startMarker[map]);
-						cov.add(new long[]{c.getStart() - 1, c.getEnd(), isi});
-					}
-					startMarker[map] += numMarkers;
-				}
-				ArrayList<Long> cov_ret = Misc.cov(cov);
-				//System.err.println(cov_ret);
-				
-				for (int i = 0; i < cov_ret.size(); i+=2) {
-					long pos = cov_ret.get(i);
-					long cr = cov_ret.get(i + 1);
-					//System.err.println(pos + "\t" + cr);
-					if (cr > maxScore) {
-						maxScore = cr;
-						maxC = c.getRank();
-						maxP1 = pos;
-						maxP2 = ((i + 2 < cov_ret.size()) ? cov_ret.get(i + 2) - 1 : maxP1); 
-					}
-				}
-			}
-		}
-
-		if (verbose)
-			System.err.println(cis.get(maxC).getContig() + "\t" + maxP1 + "-" + maxP2 + "\t" + errorContig.getContig() + "\t" + pos1[0] + "-" + pos1[1] + "\t" + pos2[0] + "-" + pos2[1] + "\t" + (maxScore - oldFullScore) + "\tfix");
-		
-		String info = cis.get(maxC).getContig() + "\t" + maxP1 + "-" + maxP2;
-
-		if (maxScore <= oldFullScore) {
-			return null;
-		}
-		return new PossibleError((maxScore - oldFullScore), maxC, info , new long[]{maxP1, maxP2}, null);		
-	}
-
-	// find a region inside an error with even higher error rate 
-	private PossibleError splitError(ContigInterval c, PossibleError e)
-	{
-		//PossibleError ret = new PossibleError(max, ci.getRank(), info , new long[]{pos1n, pos1}, new long[]{pos2, pos2n}
-		long pos1[] = e.getPos1();
-		long pos2[] = e.getPos2();
-		ArrayList<Marker> markersC = new ArrayList<Marker>();
-		int e0 = 0;
-		int e1 = 0;
-		for (int  map = 0; map < numMaps; ++map)
-			for (Marker m : c.getMarkers(map))
-				if (m.getPosition() >= pos1[0] && m.getPosition() <= pos2[1]) {
-					if (m.inside(m.pPlus) > 0)
-						++e1;
-					else
-						++e0;
-					markersC.add(m);
-				}
-		Collections.sort(markersC);
-		//System.err.println("e0=" + e0 + "\te1=" + e1);
-		
-		//calculateErrors(markersCi, errors, e0, e1);
-		ArrayList<PossibleError> pes = new ArrayList<PossibleError>(); 
-		calculateErrors2(markersC, pes, e0, e1, 1);
-		if (pes.size() > 0) {
-			PossibleError ret = pes.get(0);
-			long p1[] = ret.getPos1(); // adjust region so that it is within the original error...
-			if (p1[0] < pos1[0])
-				p1[0] = pos1[0];
-			long p2[] = ret.getPos2();
-			if (p2[1] > pos2[1])
-				p2[1] = pos2[1];
-			ret.ci = e.ci; // rank might be corrupted so calculateErrors2 could fail to get this right
-			return ret;
-		}
-
-		return null;
-	}
-	//iterative version of findLikelyAssemblyErrors
-	private void findContigErrors(int minImprovement) {
-		System.err.println("Finding contig errors...");
-		ArrayList<ContigInterval> newcis = new ArrayList<ContigInterval>();
-		
-		int animation = 0;
-		boolean foundFix = true;
-		
-		HashMap<String, Double> missedErrors = new HashMap<String, Double>();
-		
-		while (foundFix) {
-			foundFix = false;
-			int scoreOld = calculateScore(intervalsInChr, false) + calculateNonMarkerScore(intervalsInChr);
-
-			int orientation[] = new int[intervalsInChr.size()]; // store orientaions
-			for (int ci = 0; ci < orientation.length; ++ci)
-				orientation[ci] = intervalsInChr.get(ci).getOrientation();
-			
-			//ArrayList<PossibleError> pe = findNonHaplotypeAssemblyErrors(intervalsInChr, false);
-			ArrayList<PossibleError> pe = findNonHaplotypeAssemblyErrors(intervalsInChr, false);
-			
-			System.err.println("score = " + scoreOld);
-
-		out:for (int e = 0; e + e < pe.size(); ++e) {
-				PossibleError pe1 = pe.get(e + e);
-				ContigInterval c1 = intervalsInChr.get(pe1.getCi());
-				
-				PossibleError pe2 = pe.get(e + e + 1);
-				String errorId = pe1.getInfo() + ((pe2 == null) ? "" : "\t" + pe2.getInfo());
-				
-				// see if we have already tried to fix this error, skip with decreasing prob
-				String errorId2 = errorId.substring(errorId.indexOf('\t'));
-				if (missedErrors.containsKey(errorId2)) {
-					double newValue = missedErrors.get(errorId2) * 0.5;
-					if (Math.random() >= newValue)
-						continue;
-					missedErrors.put(errorId2, newValue);
-				} else
-					missedErrors.put(errorId2, 2.0); // try twice, then with pr 1/2, 1/4, 1/8, ...
-				
-				System.err.println(errorId);
-				for (int fixIteration = 0; fixIteration < 2; ++fixIteration) { // try to split each region in fixIteration==1
-					if (fixIteration == 1) {
-						calculateScore(intervalsInChr, false); // update pPlus...
-						pe1 = splitError(c1, pe1);
-						if (pe1 == null) {
-							//System.err.println("no split");
-							break;
-						}
-						pe2 = findFix(intervalsInChr, pe1, false);
-						errorId = pe1.getInfo() + ((pe2 == null) ? "" : "\t" + pe2.getInfo());
-						System.err.println(errorId);
-					}
-					ContigInterval sp1[] = null;
-					ContigInterval sp2[] = null;
-					ContigInterval c2 = null;
-					
-					long p11[] = pe1.getPos1();
-					p11[0] -= 1; //-1
-					p11[1] -= 1; //-1
-					if (pe2 != null) {
-						c2 = intervalsInChr.get(pe2.getCi());
-						if (c1 == c2) {
-							sp1 = c1.splitContigInterval(p11, pe1.getPos2(), pe2.getPos1());
-						} else {
-							sp1 = c1.splitContigInterval(p11, pe1.getPos2());
-							sp2 = c2.splitContigInterval(pe2.getPos1());
-						}
-					} else {
-						sp1 = c1.splitContigInterval(p11, pe1.getPos2());
-					}
-		
-					newcis.clear();
-					for (ContigInterval ci : intervalsInChr) {
-						if (ci != c1 && ci != c2)
-							newcis.add(ci);
-						else if (ci == c1)
-							for (ContigInterval c : sp1)
-								newcis.add(c);
-						else
-							for (ContigInterval c : sp2)
-								newcis.add(c);
-					}
-					//System.err.println(newcis);
-					int splitSize1 = sp1.length;
-					int splitSize2 = ((sp2 == null) ? 1 : sp2.length);
-					if (splitSize1 == 1 && splitSize2 == 1) // no split...
-						continue;
-					
-	
-					//add scaffolding links
-					for (int ci = 1; ci < sp1.length; ++ci) {
-						String key1 = calculateKey(sp1[ci - 1], true, sp1[ci],     true);
-						String key2 = calculateKey(sp1[ci],    false, sp1[ci - 1], false);
-						scaffoldingLink.put(key1, 1);
-						scaffoldingLink.put(key2, 1);
-					}
-					if (sp2 != null)
-						for (int ci = 1; ci < sp2.length; ++ci) {
-							String key1 = calculateKey(sp2[ci - 1], true, sp2[ci],      true);
-							String key2 = calculateKey(sp2[ci],    false, sp2[ci - 1], false);
-							scaffoldingLink.put(key1, 1);
-							scaffoldingLink.put(key2, 1);
-						}
-					//keep old scaffoldingLinks
-					for (ContigInterval c : intervalsInChr) {
-						String k1 = calculateKey(c1, true, c, true);
-						if (scaffoldingLink.containsKey(k1)) {
-							scaffoldingLink.put(calculateKey(sp1[sp1.length - 1], true, c,true), 1);
-							scaffoldingLink.put(calculateKey(c, false, sp1[sp1.length - 1], false), 1);
-						}
-						String k2 = calculateKey(c, true, c1, true);
-						if (scaffoldingLink.containsKey(k2)) {
-							scaffoldingLink.put(calculateKey(c, true, sp1[0], true), 1);
-							scaffoldingLink.put(calculateKey(sp1[0], false, c, false), 1);
-						}
-						if (sp2 != null) {
-							k1 = calculateKey(c2, true, c, true);
-							if (scaffoldingLink.containsKey(k1)) {
-								scaffoldingLink.put(calculateKey(sp2[sp2.length - 1], true, c,true), 1);
-								scaffoldingLink.put(calculateKey(c, false, sp2[sp2.length - 1], false), 1);
-							}
-							k2 = calculateKey(c, true, c2, true);
-							if (scaffoldingLink.containsKey(k2)) {
-								scaffoldingLink.put(calculateKey(c, true, sp2[0], true), 1);
-								scaffoldingLink.put(calculateKey(sp2[0], false, c, false), 1);
-							}
-						}
-					}
-					//keep old chainLinks
-					for (ContigInterval c : intervalsInChr) {
-						for (int o = 0; o < 2; ++o)
-							for (int o1 = 0; o1 < 2; ++o1) {
-								String k1 = calculateKey(c, o == 0, c1, o1 == 0);
-								if (chainLinkHash.containsKey(k1)) {
-									String knew = calculateKey(c, o == 0, (o1==0) ? sp1[0] : sp1[sp1.length - 1], o1 == 0);
-									chainLinkHash.put(knew, chainLinkHash.get(k1));
-								}
-								String k2 = calculateKey(c1, o1 == 0, c, o == 0);
-								if (chainLinkHash.containsKey(k2)) {
-									String knew = calculateKey((o1==0) ? sp1[sp1.length - 1]: sp1[0], o1 == 0, c, o == 0);
-									chainLinkHash.put(knew, chainLinkHash.get(k2));
-								}
-								if (sp2 != null) {
-									String k3 = calculateKey(c, o == 0, c2, o1 == 0);
-									if (chainLinkHash.containsKey(k3)) {
-										String knew = calculateKey(c, o == 0, (o1==0) ? sp2[0] : sp2[sp2.length - 1], o1 == 0);
-										chainLinkHash.put(knew, chainLinkHash.get(k3));
-									}
-									String k4 = calculateKey(c2, o1 == 0, c, o == 0);
-									if (chainLinkHash.containsKey(k4)) {
-										String knew = calculateKey((o1==0) ? sp2[sp2.length - 1]: sp2[0], o1 == 0, c, o == 0);
-										chainLinkHash.put(knew, chainLinkHash.get(k4));
-									}
-									
-								}
-
-							}
-					}
-					if (sp2 != null) // keep chain links between c1 to c2
-						for (int o1 = 0; o1 < 2; ++o1)
-							for (int o2 = 0; o2 < 2; ++o2) {
-								String k1 = calculateKey(c1, o1 == 0, c2, o2 == 0); 
-								if (chainLinkHash.containsKey(k1)) {
-									String knew = calculateKey((o1==0) ? sp1[sp1.length - 1]: sp1[0], o1 == 0, (o2==0) ? sp2[0]: sp2[sp2.length - 1], o2 == 0);
-									chainLinkHash.put(knew, chainLinkHash.get(k1));
-								}
-								String k2 = calculateKey(c2, o2 == 0, c1, o1 == 0); 
-								if (chainLinkHash.containsKey(k2)) {
-									String knew = calculateKey((o2==0) ? sp2[sp2.length - 1]: sp2[0], o2 == 0, (o1==0) ? sp1[0]: sp1[sp1.length - 1], o1 == 0);
-									chainLinkHash.put(knew, chainLinkHash.get(k2));
-								}
-							}
-					
-					
-							
-					//improveAnchoring(newcis, false, false);
-	
-					//faster version of improveAnchoring 
-					{
-						int bestScore = -1;
-						ArrayList<ContigInterval> newcontigs = new ArrayList<ContigInterval>();
-						for (ContigInterval c : sp1) 
-							newcontigs.add(c);
-						if (sp2 != null)
-							for (ContigInterval c : sp2)
-								newcontigs.add(c);
-						ArrayList<ContigInterval> newcis2 = new ArrayList<ContigInterval>();
-						newcis2.addAll(newcis);
-						
-						ArrayList<Integer> bestOrientation = new ArrayList<Integer>(); 
-	
-						for (int run = 0; run < numRuns; ++run) {
-							Collections.shuffle(newcontigs);
-							for (ContigInterval c : newcontigs) {
-								c.setOrientation((int)(2.0 * Math.random()) - 1);
-							}
-							boolean foundBetter = true;
-							
-							while (foundBetter) {
-								foundBetter = false;
-								for (ContigInterval c : newcontigs) {
-									if (calculateBest(newcis2, c, false) > 0)
-										foundBetter = true;
-								}
-							}
-							int score = calculateScore(newcis2, false) + calculateNonMarkerScore(newcis2);
-							if (score > bestScore) {
-								bestScore = score;
-	
-								newcis.clear();
-								newcis.addAll(newcis2);
-								
-								bestOrientation.clear();
-								for (ContigInterval c : newcis)
-									bestOrientation.add(c.getOrientation());
-							}
-						}
-						int oi = 0;
-						for (ContigInterval c : newcis)
-							c.setOrientation(bestOrientation.get(oi++));
-					}
-	
-					int score = calculateScore(newcis, false) + calculateNonMarkerScore(newcis);
-					//System.err.println(score);
-					if (score >= minImprovement + scoreOld + 2 * (splitSize1 + splitSize2 - 2)) { // at least +minImprovement in score and +2 for each cut...
-						System.err.println("split into " + splitSize1 + (splitSize2 <= 1 ? "" : "+" + splitSize2));
-						System.err.print("number of markers");
-						for (ContigInterval c : sp1)
-							System.err.print("\t" + c.getNumMarkers());
-						if (sp2 != null) {
-							System.err.print("\t|");
-							for (ContigInterval c : sp2)
-								System.err.print("\t" + c.getNumMarkers());
-						}
-						System.err.println();
-						
-						if (!printAnimation.equals("")) {
-							if (animation == 0) { 
-								String fn = printAnimation + animation + ".la";
-								
-								ArrayList<Double> orderSupport = calculateSupport(intervalsInChr);
-								try {
-									PrintStream ps = new PrintStream(fn);
-									printAnchoring(ps, intervalsInChr, orderSupport);
-									ps.close();
-								}
-								catch (Exception ex){
-									ex.printStackTrace();
-								}
-							}
-							++animation;							
-							String fn = printAnimation + animation + ".la";
-							ArrayList<Double> orderSupport = calculateSupport(newcis);
-							try {
-								PrintStream ps = new PrintStream(fn);
-								printAnchoring(ps, newcis, orderSupport);
-								ps.close();
-							}
-							catch (Exception ex){
-								ex.printStackTrace();
-							}
-						}
-	
-						System.err.println("Score improvement = " + (score - scoreOld) + " score = " + score);
-						//System.err.println("score = " + score);
-						intervalsInChr.clear();
-						intervalsInChr.addAll(newcis);
-						foundFix = true;
-						
-						break out; // found fix...
-					}
-					// set orientations back to stored state
-					for (int ci = 0; ci < orientation.length; ++ci)
-						intervalsInChr.get(ci).setOrientation((orientation[ci]));
-				} // fixIteration
-			} // for (int inr e=0; ...
-		} // while foundFix
-		int score = calculateScore(intervalsInChr, false);
-		System.out.println("#final score with corrected contigs " +  score + " " + calculateNonMarkerScore(intervalsInChr));
-		ArrayList<Double> orderSupport = calculateSupport(intervalsInChr);
-
-		printAnchoring(intervalsInChr, orderSupport);
-
-		//print bed for another run of Lep-Anchor
-		ContigInterval start = null;
-		for (int ci = 0; ci < intervalsInChr.size(); ++ci) {
-			ContigInterval c = intervalsInChr.get(ci);
-			ContigInterval next = ((ci + 1 < intervalsInChr.size()) ? intervalsInChr.get(ci + 1) : null);
-			boolean linked = false;
-			if (next != null) { 						 
-				String key = calculateKey(c, next);
-				if (scaffoldingLink.containsKey(key) && scaffoldingLink.get(key) > 0)
-					linked = true;
-			}
-			if (start == null)
-				start = c;
-			
-			if (!linked) {
-				long pos1[] = c.getStartI();
-				long pos2[] = c.getEndI();
-				if (c != start) // more than one linked contigsIntervals...
-					if (c.getOrientation() >= 0) {
-						pos1 = start.getStartI();
-					} else {
-						pos2 = start.getEndI();
-					}
-				System.err.println(c.getContig() + "\t" + pos1[0] + "-" + pos1[1] + "\t" + pos2[0]+ "-" + pos2[1] + ((pos2.length==2) ? "" : "*") + "\t?\t" + c.getChromosome() + "\tbed");
-
-				start = null;
-			}
- 		}
-	}
-	
-	private static void usageInfo()
-	{
-        System.err.println("usage: java PlaceAndOrientContigs bed=bed.file map=map1.txt [map2 [map3 ...]] options");
-        System.err.println("       bed=file                    a file containing (contig start stop) intervals in 1-based coordinates");
-        System.err.println("       map=file1 [file2 [...]]     linkage map file(s)");
-        System.err.println("       columns contig, pos, chromosome, map_bin_start [map_bin_stop [map_bin_start2 map_bin_stop2] [...]]");
-        System.err.println("       orientation=+/- [+/- [...]] manual orientation for each map file (found automatically by default)");
-        System.err.println("       chain=file                  chain file ");
-        System.err.println("       noChromosome=1              input file does not have chromosome column ");
-        System.err.println("       noIntervals=1               input file does not have intervals but map positions");
-        System.err.println("       numRuns=NUM                 run this many runs to find better anchoring [5]");
-        System.err.println("       chromosome=NUM              take only chromosome NUM from the bed (chr=column 5) [not set]");
-        System.err.println("                                   and from the map(s)");
-        System.err.println("       numThreads=NUM              number of threads [1]");
-
-        System.err.println("       compressMap=0	           Do not compress map positions [1]");
-
-        System.err.println("       randomOrder=1               Start with a random anchoring [not set]");
-        
-        System.err.println("       keepEmptyIntervals=1        Keep (contig)intervals without any markers [not set]");
-        
-        System.err.println("       numErrors=NUM               List at most this many potential errors [40]");
-        System.err.println("       numErrorsPerContig=NUM      List at most this many potential errors from one contig [3]\n");
-        
-        System.err.println("       paf=file                    load alignment file in paf (minimap2) format");
-        System.err.println("       maxBridge=NUM               maximum scaffolding bridge length (for paf input) [50000]");
-        System.err.println("       scalePaf=NUM                multiply scaffolding links by NUM [1]");
-        System.err.println("       maxIntersect=NUM            maximum alignment intersection from paf [2000]");
-        System.err.println("       maxPafScore=NUM             maximum link score from the paf [not set]\n");
-
-        System.err.println("       scaleScore=NUM              scale aligment scores to markers [0.00001] (0.00001 = 1kb 100% identity = 1)");
-        System.err.println("       orientationPenalty=NUM      if an aligment is in wrong orientation, multiply score by this [0.5]");
-        System.err.println("       cutPenalty=NUM              alignment cut penalty [0.001] (0.001 = 1kb gap = -1");
-        
-        System.err.println("       useChainAndPaf=0            do not use both chain and paf score between contigs when available [not set]");
-        
-        System.err.println("       proximity=file NUM1 NUM2 NUM3  load proximity data, NUM1=bin size [10000]");
-        System.err.println("                                      NUM2=max distance in bins[25], NUM3=scale score [1.0]");
-
-
-        System.err.println("       minHaplotypeAlignmentScore=NUM   min alignment score required to consider haplotype [-10]");
-        System.err.println("       minLinkAlignmentScore=NUM   min alignment score required to consider contig link [-10]\n");
-
-        System.err.println("       evaluateAnchoring=FILE      load initial anchring from a FILE (experimental)");
-        System.err.println("       improveAnchoring=1          improve loaded initial anchring (experimental)");
-
-        System.err.println("       cutSites=FILE               list possible contig cut sites for contigs");
-        System.err.println("                                   the first cut site within each cut region is taken");
-        
-        System.err.println("       findContigErrors=1          Iteratively find possible contig errors based on the map only");
-        System.err.println("                                   paf, proximity and keepEmptyIntervals not allowed");
-
-        System.err.println("       minImprovement=NUM          minimum improvement for findContigErrors [1]");
-        System.err.println("                                   improvement of (NUM + 2*number_of_cuts) required");
-
-        System.err.println("       printAnimation=file	       print iterative solutions of findContigErrors to file0.la,...,fileN.la");
-
-        System.err.println("       alternativeJoins=1	       prints alternative scaffolding joins, does not consider map information (yet)");
-        System.err.println("       linksWithin=FILE	           only keep links between contig pairs listed in FILE");
-
-	}
-	
-	public static void main(String[] args)
-	{
-		
-        if (args.length == 0) {
-        	usageInfo();
-            System.exit(0);
-        }
-	    String extraParameters = "";
-	    for (int i = 0; i < args.length; ++i) {
-	            extraParameters +=  " " + args[i];
-	    }
-		ParameterParser pp = new ParameterParser();
-		if (!pp.init(extraParameters)) {
-        	usageInfo();
-            System.exit(0);
-		}
-		pp.warning(new String[]{"findContigErrors","maxPafScore", "map", "bed", "orientation", "chain", "noIntervals", "noChromosome", "randomOrder", "paf", "evaluateAnchoring", "numRuns", "numErrors", "numErrorsPerContig", "scaleScore", "orientationPenalty", "cutPenalty", "maxBridge", "scalePaf", "minLinkAlignmentScore","minHaplotypeAlignmentScore", "maxIntersect", "chromosome", "keepEmptyIntervals", "cutSites", "useChainAndPaf", "proximity", "printAnimation", "compressMap", "minImprovement", "improveAnchoring", "alternativeJoins", "numThreads", "linksWithin"});
-		
-//		ArrayList<Marker> m = InputData.loadMap(pp.getValueAsString("map", null));
-		//PlaceAndOrientContigs.solve(m);
-		
-		PlaceAndOrientContigs poc = new PlaceAndOrientContigs();
-		
-		System.out.println("#java PlaceAndOrientContigs" + extraParameters);
-		
-		boolean findContigErrors = pp.getValueAsString("findContigErrors", "0").equals("1");
-		
-		String chain = pp.getValueAsString("chain", null);
-		String paf = pp.getValueAsString("paf", null);
-		String prox = pp.getValueAsString("proximity", 0, null);
-
-		if (findContigErrors && (paf != null || prox != null || pp.getValueAsString("keepEmptyIntervals", "0").equals("1"))) {
-			System.err.println("parameters paf, proximity and keepEmptyIntervals not allowed with findContigErrors!");
-			System.exit(-1);
-		}
-
-		poc.setNumThreads(Integer.parseInt(pp.getValueAsString("numThreads", "1")));
-		poc.setScaleScore(Double.parseDouble(pp.getValueAsString("scaleScore", "0.00001")));
-
-		poc.setMaxIntersect(Integer.parseInt(pp.getValueAsString("maxIntersect", "2000")));
-
-		poc.setOrientationPenalty(Double.parseDouble(pp.getValueAsString("orientationPenalty", "0.5")));
-		poc.setCutPenalty(Double.parseDouble(pp.getValueAsString("cutPenalty", "0.001")));
-		poc.setMaxBridge(Integer.parseInt(pp.getValueAsString("maxBridge", "50000")));
-
-		int numMaps = pp.getNumberOfValues("map"); 
-
-		int chromosome = Integer.parseInt(pp.getValueAsString("chromosome", "-1"));
-		String bed = pp.getValueAsString("bed", null);
-		if (bed != null && numMaps > 0) 
-			poc.loadBed(bed, chromosome);
-		else {
-			System.err.println("You have to provide bed and one or more map file(s)!");
-			System.exit(-1);
-		}
-
-		String cutSites = pp.getValueAsString("cutSites", null);
-		if (cutSites != null) {
-			poc.loadCutSites(cutSites);
-		}
-		
-		boolean findOrientation = false;
-		for (int i = 0; i < pp.getNumberOfValues("map"); ++i) {
-			String o = pp.getValueAsString("orientation", i, "?");
-			if (!o.equals("+") && !o.equals("-"))
-				findOrientation = true;
-		}
-		if (pp.getNumberOfValues("map") != pp.getNumberOfValues("orientation") && pp.getNumberOfValues("orientation") > 0) {
-			System.err.println("You have to provide orientation for all maps or none!");
-			System.exit(-1);
-		}
-
-		poc.setCompressMap(pp.getValueAsString("compressMap", "1").equals("1"));
-		
-		for (int i = 0; i < pp.getNumberOfValues("map"); ++i) {
-			String o = pp.getValueAsString("orientation", i, "?");
-			poc.addMap(pp.getValueAsString("map", i, null), !findOrientation && o.equals("-"), pp.getValueAsString("noChromosome", "0").equals("1"), pp.getValueAsString("noIntervals", "0").equals("1"), chromosome);
-		}
-
-		if (chain != null) {
-			poc.loadChain(chain);
-		}
-		
-		int maxPafScore = Integer.parseInt(pp.getValueAsString("maxPafScore", "" + Integer.MAX_VALUE));
-		
-		if (paf != null)
-			poc.loadPaf(paf, maxPafScore, Double.parseDouble(pp.getValueAsString("scalePaf", "1")));
-
-		if (prox != null) {
-			int bin = Integer.parseInt(pp.getValueAsString("proximity", 1, "10000"));
-			int maxD = Integer.parseInt(pp.getValueAsString("proximity", 2, "25"));
-			double scale = Double.parseDouble(pp.getValueAsString("proximity", 3, "1.0"));
-			poc.loadProximity(prox, bin, maxD, scale);
-		}
-		
-		poc.setNumRuns(Integer.parseInt(pp.getValueAsString("numRuns", "5")));
-
-		poc.setNumErrors(Integer.parseInt(pp.getValueAsString("numErrors", "40")));
-		poc.setNumErrorsPerContig(Integer.parseInt(pp.getValueAsString("numErrorsPerContig", "3")));
-
-		poc.setMinHaplotypeAlignmentScore(Integer.parseInt(pp.getValueAsString("minHaplotypeAlignmentScore", "-10")));
-		poc.setMinLinkAlignmentScore(Integer.parseInt(pp.getValueAsString("minLinkAlignmentScore", "-10")));
-		
-		poc.setKeepEmptyIntervals(pp.getValueAsString("keepEmptyIntervals", "0").equals("1"));
-		poc.setUseChainAndPaf(pp.getValueAsString("useChainAndPaf", "1").equals("1"));
-		poc.setPrintAnimation(pp.getValueAsString("printAnimation", ""));
-		
-		String lwf = pp.getValueAsString("linksWithin", null);
-		if (lwf != null)
-			poc.linksWithin(lwf);
-		
-		poc.setCommentOutput(findContigErrors);
-		
-		String eval = pp.getValueAsString("evaluateAnchoring", null);
-		if (eval != null) {
-  			 poc.combineMaps(findOrientation, false, false);
-			 ArrayList<ContigInterval> eval_result = InputData.loadLa(eval);
-			 poc.evaluateScore(eval_result, pp.getValueAsString("improveAnchoring", "0").equals("1"));
-		} else {
-			poc.combineMaps(findOrientation, pp.getValueAsString("randomOrder", "0").equals("1"), true);
-		}
-
-		if (findContigErrors) {
-			poc.setCommentOutput(false);
-			poc.findContigErrors(Integer.parseInt(pp.getValueAsString("minImprovement", "1")));
-		}
-		
-		if (pp.getValueAsString("alternativeJoins", "0").equals("1")) {
-			poc.printAlternativeJoins();
-		}
-		
-		
-		//System.out.println(m);
-	}
-	
-	private String[] contigs(String key)
-	{
-		String split[] = key.split("\t");
-		int ip = split[2].indexOf('+');
-		int im = split[2].indexOf('-');
-		int p = Math.max(ip, im);
-		if (ip > 0 && im > 0)
-			p = Math.min(ip, im);
-		return new String[]{split[0], split[3].substring(p + 1)};
-		
-	}
-	
-	private void linksWithin(String lwf) {
-		// TODO Clear proximity as well...
-		HashMap<String, Integer> pairs = new HashMap<String, Integer>();
-		ArrayList<ArrayList<String>> table = Input.loadTable(lwf, "\t ");
-		for (ArrayList<String> row : table) {
-			if (row.size() >= 2)
-				pairs.put(row.get(0) + "\t" + row.get(1), 1);
-		}
-		
-		for (String key : chainLinkHash.keySet()) {
-			String cs[] = contigs(key);
-			String p1 = cs[0] + "\t" + cs[1];
-			if (!pairs.containsKey(p1)) {
-				String p2 = cs[1] + "\t" + cs[0];
-				if (!pairs.containsKey(p2))
-					chainLinkHash.put(key, 0);
-			}
-		}
-		for (String key : scaffoldingLink.keySet()) {
-			String cs[] = contigs(key);
-			String p1 = cs[0] + "\t" + cs[1];
-			if (!pairs.containsKey(p1)) {
-				String p2 = cs[1] + "\t" + cs[0];
-				if (!pairs.containsKey(p2))
-					scaffoldingLink.put(key, 0);
-			}
-		}
-	}
-	private int findLastIndex(ArrayList<ContigInterval> cis, int start, int maxDistance, boolean right) {
-		if (prox == null)
-			return start;
-		int n = cis.size();
-		int end = start;
-		int d = prox.binLength(cis.get(start));
-		if (right)
-			while (end + 1 < n && d < maxDistance) {
-				++end;
-				d += prox.binLength(cis.get(end));
-			}
-		else
-			while (end > 0 && d < maxDistance) {
-				--end;
-				d += prox.binLength(cis.get(end));
-			}
-		
-		return end;
-	}
-	
-	//score between c and c + 1, c in 0,1,...,cis.size() - 2
-	private int linkScore(ArrayList<ContigInterval> cis, int c) {
-		int ret = calculateChainScore(cis.get(c), cis.get(c + 1));
-		if (prox != null)
-			ret += prox.linkScore(cis, c, c + 1);
-		return ret;
-	}
-	
-	//score of [start,end] => [start2,end2] in all orientations (++, -+, +-, --)
-	private int[] scores(ArrayList<ContigInterval> cis, int start, int end, int start2, int end2){
-		ArrayList<ContigInterval> tmp1 = new ArrayList<ContigInterval>();
-		for (int i = start; i <= end; ++i)
-			tmp1.add(cis.get(i));
-
-		ArrayList<ContigInterval> tmp2 = new ArrayList<ContigInterval>();
-		for (int i = start2; i <= end2; ++i)
-			tmp2.add(cis.get(i));
-		
-		int s[] = new int[4];
-		for (int o2 = 0; o2 < 2; ++o2) { 
-			for (int o1 = 0; o1 < 2; ++o1) { 
-				ArrayList<ContigInterval> tmp = new ArrayList<ContigInterval>();
-				tmp.addAll(tmp1);
-				tmp.addAll(tmp2);
-				s[o1 + 2 * o2] = linkScore(tmp, end - start);
-
-				Collections.reverse(tmp1);
-				for (ContigInterval c : tmp1)
-					c.flipOrientation();
-			}
-			Collections.reverse(tmp2);
-			for (ContigInterval c : tmp2)
-				c.flipOrientation();
-		}
-		return s;
-	}
-	
-	private void printAlternativeJoins() {
-		int maxD = 0;
-		if (prox != null)
-				maxD = prox.getMaxDistance();
-		int n = intervalsInChr.size();
-		if (n <= 1)
-			return;
-		
-		int jTable[][] = new int[2 * n][2 * n];
-		int start = 0;
-		while (start < n) {
-			int end_ = findLastIndex(intervalsInChr, start, maxD, true); // this could be faster...
-			for (int end = ((start == 0) ? 0 : end_); end <= end_; ++end)
-				for (int start2 = end + 1; start2 < n; ++start2) {
-					int end2 = findLastIndex(intervalsInChr, start2, maxD, true); // and this
-					int s[] = scores(intervalsInChr, start, end, start2, end2);
-
-					//end2 is always maximal
-					boolean endMaximal = (end == end_);
-					boolean startMaximal = (findLastIndex(intervalsInChr, end, maxD, false) == start);
-					boolean start2Maximal = (findLastIndex(intervalsInChr, end2, maxD, false) == start2);
-					//remove non-maximal scores, otherwise you count each score multiple times for same endpoint with other end not maximal...
-
-					if (startMaximal)
-						jTable[2 * end]      [2 * start2]   += s[0]; // += is not needed, = is enough
-					if (endMaximal)
-						jTable[2 * start + 1][2 * start2]   += s[1];
-					if (startMaximal && start2Maximal)
-						jTable[2 * end]      [2 * end2 + 1] += s[2];
-					if (endMaximal && start2Maximal)
-						jTable[2 * start + 1][2 * end2 + 1] += s[3];
-							
-					int s2[] = scores(intervalsInChr, start2, end2, start, end);
-
-					if (start2Maximal && endMaximal)
-						jTable[2 * end2]      [2 * start]   += s2[0];
-					if (endMaximal)
-						jTable[2 * start2 + 1][2 * start]   += s2[1];
-					if (start2Maximal && startMaximal)
-						jTable[2 * end2]      [2 * end + 1] += s2[2];
-					if (startMaximal)
-						jTable[2 * start2 + 1][2 * end + 1] += s2[3];
-				}
-			++start;
-		}
-/*		for (int i = 0; i < n + n; ++i) {
-			StringBuilder sb = new StringBuilder();
-			for (int j = 0; j < n + n; ++j) {
-				if (j != 0) 
-					sb.append('\t');
-				if (i == j)
-					sb.append('X');
-				else
-				sb.append(jTable[i][j]);
-			}
-			System.err.println(sb);
-		}*/
-		System.err.println("*** alternativeJoins ***");
-		for (int ci = 0; ci < n; ++ci) {
-			//ArrayList<Integer> list = new ArrayList<Integer>();
-			for (int i = 0; i < n + n; ++i) {
-				int ip2 = i >> 1;
-				if (jTable[2 * ci][i] > 0) {
-					System.err.println(intervalsInChr.get(ci) + "\t+\t" + intervalsInChr.get(ip2) + "\t" + ("+-".substring(i & 1, (i & 1) + 1)) + "\t" + jTable[2 * ci][i] + "\t" + ci + "\t" + ip2);
-				}
-				if (jTable[2 * ci + 1][i] > 0) {
-					System.err.println(intervalsInChr.get(ci) + "\t-\t" + intervalsInChr.get(ip2) + "\t" + ("+-".substring(i & 1, (i & 1) + 1)) + "\t" + jTable[2 * ci + 1][i] + "\t" + ci + "\t" + ip2);
-				}
-			}
-			
-		}
-	}
-}
diff --git a/software/LepAnchor/src/Proximity.java b/software/LepAnchor/src/Proximity.java
deleted file mode 100644
index f1fa1e0..0000000
--- a/software/LepAnchor/src/Proximity.java
+++ /dev/null
@@ -1,657 +0,0 @@
-import java.io.BufferedReader;
-import java.io.FileReader;
-import java.io.InputStreamReader;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collections;
-import java.util.HashMap;
-
-
-public class Proximity {
-	private int binSize;
-	private int maxDistance;
-	private double scale;
-	//eg. binSize=10000 and maxDistance=25 =>10kb bins and max of 250kb
-	
-	//TODO: find possible assembly errors...
-
-	public Proximity(int binSize, int maxDistance, double scale){
-		this.binSize = binSize;
-		this.maxDistance = maxDistance;
-		this.scale = scale;
-	}
-	HashMap<String, int[]> distanceHash = new HashMap<String, int[]>();
-	
-	public int getMaxDistance(){
-		return maxDistance;
-	}
-	
-	public boolean loadData(String fn, HashMap<String, ArrayList<ContigInterval>> bedHash)
-	{
-		boolean nonEmpty = false;
-		System.err.println("loading proximity data...");
-		HashMap<String, String> symmetryHash = new HashMap<String, String>();
-		try {
-			HashMap<String, double[]> distanceHash_tmp = new HashMap<String, double[]>();
-			
-			BufferedReader br = null;
-			if (fn.equals("-"))
-				br = new BufferedReader(new InputStreamReader(System.in));
-			else
-				br = new BufferedReader(new FileReader(fn));
-			do {
-				ArrayList<String> row = Input.loadTableRow(br, "\t ");
-				if (row == null)
-					break;
-				String contig1 = row.get(0);
-				long pos1 = Long.parseLong(row.get(1));
-			if (bedHash.containsKey(contig1))
-				for (ContigInterval ci1 : bedHash.get(contig1))
-					if (ci1.inside(pos1)) {
-						
-						int p1 = bin(pos1);
-						
-						int de1 = bin(ci1.getEnd()) - p1;
-						int ds1 = p1 - bin(ci1.getStart());
-						
-						if (de1 >= maxDistance && ds1 >= maxDistance)
-							continue;
-
-						String contig2 = row.get(2);
-						long pos2 = Long.parseLong(row.get(3));
-					if (bedHash.containsKey(contig2))
-						for (ContigInterval ci2 : bedHash.get(contig2))
-							if (ci1 != ci2 && ci2.inside(pos2)) {
-								//DO MAGIC HERE
-								
-								int p2 = bin(pos2);
-								int de2 = bin(ci2.getEnd()) - p2;
-								int ds2 = p2 - bin(ci2.getStart()); 
-							
-								if (de2 >= maxDistance && ds2 >= maxDistance || Math.min(de1, ds1) + Math.min(de2, ds2) >= maxDistance)
-									continue;
-								
-								nonEmpty = true;
-								
-								double value = Double.parseDouble(row.get(4)) * scale;
-								
-								if (de1 + ds2 < maxDistance) { // ++
-									String key = calculateKey(ci1, true, ci2, true);
-									symmetryHash.put(key, calculateKey(ci2, false, ci1, false));
-									
-									double list[] = distanceHash_tmp.get(key);
-									if (list == null) {
-										list = new double[maxDistance];
-										distanceHash_tmp.put(key, list);
-									}
-									list[de1 + ds2] += value;  
-								}
-								if (de1 + de2 < maxDistance) { // +-
-									String key = calculateKey(ci1, true, ci2, false);
-									symmetryHash.put(key, calculateKey(ci2, true, ci1, false));
-									
-									double list[] = distanceHash_tmp.get(key);
-									if (list == null) {
-										list = new double[maxDistance];
-										distanceHash_tmp.put(key, list);
-									}
-									list[de1 + de2] += value;  
-								}
-								if (ds1 + ds2 < maxDistance) { // -+
-									String key = calculateKey(ci1, false, ci2, true);
-									symmetryHash.put(key, calculateKey(ci2, false, ci1, true));
-
-									double list[] = distanceHash_tmp.get(key);
-									if (list == null) {
-										list = new double[maxDistance];
-										distanceHash_tmp.put(key, list);
-									}
-									list[ds1 + ds2] += value;  
-								}
-								if (ds1 + de2 < maxDistance) { // --
-									String key = calculateKey(ci1, false, ci2, false);
-									symmetryHash.put(key, calculateKey(ci2, true, ci1, true));
-									
-									double list[] = distanceHash_tmp.get(key);
-									if (list == null) {
-										list = new double[maxDistance];
-										distanceHash_tmp.put(key, list);
-									}
-									list[ds1 + de2] += value;  
-								}
-							}
-					}
-			} while (true);
-			br.close();
-			
-			//transfer and truncate data from distanceHash_tmp (double) to distanceHash (int)
-			//make scores symmetric and do rounding
-			ArrayList<String> missingKeys = new ArrayList<String>(); 
-			for (String key : distanceHash_tmp.keySet()) {
-				String sk = symmetryHash.get(key);
-				if (!distanceHash_tmp.containsKey(sk))
-					missingKeys.add(key);
-			}
-			for (String key : missingKeys) { // put missing symmetric keys to the hashes
-				String sk = symmetryHash.get(key);
-				distanceHash_tmp.put(sk, distanceHash_tmp.get(key));
-				symmetryHash.put(sk, key);
-			}
-			
-			for (String key : distanceHash_tmp.keySet()) {
-				double list[] = distanceHash_tmp.get(key);
-				double list2[] = distanceHash_tmp.get(symmetryHash.get(key)); // symmetric key
-
-				int new_list[] = new int[maxDistance];
-				
-				double sum = 0.0;
-				for (int i = 0; i < maxDistance; ++i) {
-					sum += list[i] + list2[i];
-					new_list[maxDistance - i - 1] = (int)(0.5 * sum + 0.5);  
-				}
-				int maxLength = maxDistance;
-				while (maxLength > 0 && new_list[maxLength - 1] == 0)
-					--maxLength;
-				if (maxLength > 0)
-					distanceHash.put(key, Arrays.copyOf(new_list, maxLength));
-				
-/*				int maxIndex = maxDistance - 1;
-				double sum = 0.0;
-				while (maxIndex >= 0 && sum + list[maxIndex] + list2[maxIndex] < 1.0) {
-					sum += list[maxIndex] + list2[maxIndex];
-					--maxIndex;
-				}
-				if (maxIndex >= 0) {
-					int new_list[] = new int[maxIndex + 1];
-					while (maxIndex >= 0) {
-						sum += list[maxIndex] + list2[maxIndex];
-						new_list[maxIndex] = (int)(0.5 * sum + 0.5); 
-						--maxIndex;
-					}
-					distanceHash.put(key, new_list);
-				}*/
-			}
-
-		} catch (Exception e) {
-	     	e.printStackTrace();
-			System.err.println("Error in file " + fn);
-      	}
-		
-		System.err.println("Proximity links:"); 
-		for (String key: distanceHash.keySet())
-			System.err.println(key + "\t" +  distanceHash.get(key)[0]);
-		return nonEmpty;
-	}
-	
-	
-	
-	//"bin" a contig position
-	private int bin(long position)
-	{
-		return (int) ((position - 1) / binSize); 
-	}
-	
-	//how many bins a contig spans...
-	public int binLength(ContigInterval ci)
-	{
-		int s = bin(ci.getStart()); 
-		int e = bin(ci.getEnd());
-		return (e - s + 1); 
-	}
-
-	private String calculateKey(ContigInterval c1, ContigInterval c2)
-	{
-		return calculateKey(c1, c1.getOrientation() >= 0, c2, c2.getOrientation() >= 0);
-	}
-	
-	private String calculateKey(ContigInterval c1, boolean orientation1, ContigInterval c2, boolean orientation2)
-	{
-		return c1.toString() + (orientation1 ? '+':'-') + c2.toString() + (orientation2 ? '+':'-');
-	}
-
-	// calculate a list of contigs that should be evaluate against cis.get(ci)
-	private ArrayList<Integer> next(ArrayList<ContigInterval> cis, int ci, int last) {
-		ArrayList<Integer> ret = new ArrayList<Integer>();
-		//int n = cis.size();
-		int i = ci + 1;
-		int d = 0;
-		while (i <= last && d < maxDistance) {
-			ContigInterval c = cis.get(i);
-			ret.add(i);
-			d += binLength(c);
-			++i;
-		}
-		return ret;
-	}
-
-	// calculate a list of contigs that should be evaluate against cis.get(ci)
-	private ArrayList<Integer> prev(ArrayList<ContigInterval> cis, int ci, int first) {
-		ArrayList<Integer> ret = new ArrayList<Integer>();
-		int i = ci - 1;
-		int d = 0;
-		while (i >= first && d < maxDistance) {
-			ContigInterval c = cis.get(i);
-			ret.add(i);
-			d += binLength(c);
-			--i;
-		}
-		return ret;
-	}
-
-	private int borderScore(ArrayList<ContigInterval> cis, ArrayList<Integer> prev, ArrayList<Integer> next){
-		int ret = 0;
-		int dp = 0;
-		for (int pci : prev) {
-			ContigInterval pc = ((pci < 0) ? cis.get(-pci - 1) : cis.get(pci)); 
-			int dnp = dp;
-			dp += binLength(pc);
-			for (int nci : next) {
-				if (dnp >= maxDistance)
-					break;
-				ContigInterval nc = ((nci < 0) ? cis.get(-nci - 1) : cis.get(nci)); 
-				
-				ret += score(pc, pci < 0, nc, nci < 0, dnp);
-				dnp += binLength(nc); 
-			}
-		}
-		return ret;
-	}
-	// difference in score if cis[start...end] are moved to new_position and possibly flipped
-	public int scoreChange_slow(ArrayList<ContigInterval> cis, int start, int end, int moveDirection, boolean flip)
-	{
-		int scoreOld = score(cis);
-		PlaceAndOrientContigs.changeOrder(cis, start, end, moveDirection, flip);
-		int scoreNew = score(cis); 
-		PlaceAndOrientContigs.changeOrderReverse(cis, start, end, moveDirection, flip);
-		//System.err.println(scoreNew - scoreOld);
-		return scoreNew - scoreOld;
-	}
-	
-	// difference in score if cis[start...end] are moved to new_position and possibly flipped
-	public int scoreChange(ArrayList<ContigInterval> cis, int start, int end, int moveDirection, boolean flip)
-	{
-		int ret = 0;
-		int n = cis.size();
-		if (moveDirection == 0) { // flip 
-			if (flip) {
-				//first part
-				ArrayList<Integer> next = next(cis, start - 1, end); // start, start+1, ..., end
-				ArrayList<Integer> prev = prev(cis, start, 0); // start-1, start-2, ..., 0
-				
-				ArrayList<Integer> new_next = new ArrayList<Integer>();
-				int d = 0;
-				for (int i = end; d < maxDistance && i >= start; --i) {
-					ContigInterval nc = cis.get(i); 
-					new_next.add(-i - 1);
-					d += binLength(nc);
-				}
-				//subtract old score for start-1 -> start boundary, 
-				ret -= borderScore(cis, prev, next);
-				//...and add new score for this boundary
-				ret += borderScore(cis, prev, new_next);
-				
-				//second part
-				
-				next = next(cis, end, n - 1); // end+1, end+2, ..., n-1
-				prev = prev(cis, end + 1, start); // end, end-1, ..., start
-				
-				ArrayList<Integer> new_prev = new ArrayList<Integer>();
-				d = 0;
-				for (int i = start; d < maxDistance && i <= end; ++i) {
-					ContigInterval nc = cis.get(i); 
-					new_prev.add(-i - 1);
-					d += binLength(nc);
-				}
-				//subtract old score for end -> end+1 boundary,
-				ret -= borderScore(cis, prev, next);
-				//..and add new score for this boundary
-				ret += borderScore(cis, new_prev, next);
-
-			} // else nothing to do...
-		} else { // move one or multiple contigs...
-			if (moveDirection >= 0) { // actually moveDirection > 0
-				//int first = start 
-				//int second = end; 
-				//int third = end + moveDirection;
-				//first part
-				ArrayList<Integer> next = next(cis, start - 1, n - 1); // start, start+1, ..., n-1
-				ArrayList<Integer> prev = prev(cis, start, 0); // start-1, start-2, ..., 0
-				ret -= borderScore(cis, prev, next);
-				
-				ArrayList<Integer> new_next = new ArrayList<Integer>();
-				int d = 0;
-
-				for (int i = end + 1; d < maxDistance && i <= end + moveDirection; ++i) {
-					ContigInterval nc = cis.get(i); 
-					new_next.add(i);
-					d += binLength(nc);
-				}
-				
-				if (flip)
-					for (int i = end; d < maxDistance && i >= start; --i) {
-						ContigInterval nc = cis.get(i); 
-						new_next.add(-i - 1);
-						d += binLength(nc);
-					}
-				else
-					for (int i = start; d < maxDistance && i <= end; ++i) {
-						ContigInterval nc = cis.get(i); 
-						new_next.add(i);
-						d += binLength(nc);
-					}
-
-				for (int i = end + moveDirection + 1; d < maxDistance && i < n; ++i) {
-					ContigInterval nc = cis.get(i); 
-					new_next.add(i);
-					d += binLength(nc);
-				}
-				//flip:  new_next = end + 1, ..., end + moveDirection,end...start, end + moveDirection + 1 ... n - 1
-				//!flip: new_next = end + 1, ..., end + moveDirection,start...end, end + moveDirection + 1 ... n - 1
-				//prev = start - 1, start - 2, ..., 0
-
-				ret += borderScore(cis, prev, new_next);
-				
-				//second part
-				next = next(cis, end, n - 1); // second, second+1, ..., n-1
-				prev = prev(cis, end + 1, start); // second-1, second-2, ..., first
-
-				ret -= borderScore(cis, prev, next);
-				
-				new_next = new ArrayList<Integer>();
-				d = 0;
-				if (flip)
-					for (int i = end; d < maxDistance && i >= start; --i) {
-						ContigInterval nc = cis.get(i); 
-						new_next.add(-i - 1);
-						d += binLength(nc);
-					}
-				else
-					for (int i = start; d < maxDistance && i <= end; ++i) {
-						ContigInterval nc = cis.get(i); 
-						new_next.add(i);
-						d += binLength(nc);
-					}
-				for (int i = end + moveDirection + 1; d < maxDistance && i < n; ++i) {
-					ContigInterval nc = cis.get(i); 
-					new_next.add(i);
-					d += binLength(nc);
-				}
-				//flip:  new_next = end...start, end + moveDirection + 1 ... n - 1
-				//!flip: new_next = start..end, ..., end + moveDirection + 1 ... n - 1
-
-				ArrayList<Integer> new_prev = new ArrayList<Integer>();
-				d = 0;
-
-				for (int i = end + moveDirection; d < maxDistance && i > end; --i) { //TODO: check if (>= end or) > is proper
-					ContigInterval nc = cis.get(i); 
-					new_prev.add(i);
-					d += binLength(nc);
-				}
-				//new_prev = end + moveDirection...end
-				ret += borderScore(cis, new_prev, new_next);
-
-				//third part
-				next = next(cis, end + moveDirection, n - 1); // third, third+1, ..., n-1
-				prev = prev(cis, end + moveDirection + 1, end); // third-1, third-2, ..., second
-
-				ret -= borderScore(cis, prev, next);
-				new_prev = new ArrayList<Integer>();
-				
-				//TODO: calculate new_prev
-				d = 0;
-				if (flip)
-					for (int i = start; d < maxDistance && i <= end; ++i) {
-						ContigInterval nc = cis.get(i); 
-						new_prev.add(-i - 1);
-						d += binLength(nc);
-					}
-				else
-					for (int i = end; d < maxDistance && i >= start; --i) {
-						ContigInterval nc = cis.get(i); 
-						new_prev.add(i);
-						d += binLength(nc);
-					}
-				ret += borderScore(cis, new_prev, next);
-				//System.err.println(borderScore(cis, prev, next));
-				//System.err.println(prev);
-				//System.err.println(next);
-				
-			} else { //moveDirection < 0
-				//int first = start + moveDirection; 
-				//int second = start; 
-				//int third = end;
-				//first part
-				ArrayList<Integer> next = next(cis, start + moveDirection - 1, n - 1); // first, first+1, ..., n-1
-				ArrayList<Integer> prev = prev(cis, start + moveDirection, 0); // first-1, first-2, ..., 0
-				ret -= borderScore(cis, prev, next);
-				
-				ArrayList<Integer> new_next = new ArrayList<Integer>();
-				int d = 0;
-				if (flip)
-					for (int i = end; d < maxDistance && i >= start; --i) {
-						ContigInterval nc = cis.get(i); 
-						new_next.add(-i - 1);
-						d += binLength(nc);
-					}
-				else
-					for (int i = start; d < maxDistance && i <= end; ++i) {
-						ContigInterval nc = cis.get(i); 
-						new_next.add(i);
-						d += binLength(nc);
-					}
-				
-				for (int i = start + moveDirection; d < maxDistance && i < start; ++i) {
-					ContigInterval nc = cis.get(i); 
-					new_next.add(i);
-					d += binLength(nc);
-				}
-
-				for (int i = end + 1; d < maxDistance && i < n; ++i) {
-					ContigInterval nc = cis.get(i); 
-					new_next.add(i);
-					d += binLength(nc);
-				}
-
-				ret += borderScore(cis, prev, new_next);
-				//System.err.println("");
-				//System.err.println(prev);
-				//System.err.println(next);
-				//System.err.println("->");
-				//System.err.println(prev);
-				//System.err.println(new_next);
-				
-				//second part
-				next = next(cis, start - 1, n - 1); // second, second+1, ..., n-1
-				prev = prev(cis, start, start + moveDirection); // second-1, second-2, ..., first
-
-				ret -= borderScore(cis, prev, next);
-				
-				new_next = new ArrayList<Integer>();
-
-				d = 0;
-				for (int i = start + moveDirection; d < maxDistance && i < start; ++i) {
-					ContigInterval nc = cis.get(i); 
-					new_next.add(i);
-					d += binLength(nc);
-				}
-
-				for (int i = end + 1; d < maxDistance && i < n; ++i) {
-					ContigInterval nc = cis.get(i); 
-					new_next.add(i);
-					d += binLength(nc);
-				}
-
-				ArrayList<Integer> new_prev = new ArrayList<Integer>();
-
-				d = 0;
-				if (flip)
-					for (int i = start; d < maxDistance && i <= end; ++i) {
-						ContigInterval nc = cis.get(i); 
-						new_prev.add(-i - 1);
-						d += binLength(nc);
-					}
-				else
-					for (int i = end; d < maxDistance && i >= start; --i) {
-						ContigInterval nc = cis.get(i); 
-						new_prev.add(i);
-						d += binLength(nc);
-					}
-				
-				ret += borderScore(cis, new_prev, new_next);
-				//System.err.println("");
-				//System.err.println(prev);
-				//System.err.println(next);
-				//System.err.println("->");
-				//System.err.println(new_prev);
-				//System.err.println(new_next);
-
-				//third part
-				next = next(cis, end, n - 1); // third, third+1, ..., n-1
-				prev = prev(cis, end + 1, start); // third-1, third-2, ..., second
-
-				ret -= borderScore(cis, prev, next);
-				new_prev = new ArrayList<Integer>();
-				//TODO: calculate new_prev
-				d = 0;
-				for (int i = start - 1; d < maxDistance && i >= start + moveDirection; --i) {
-					ContigInterval nc = cis.get(i); 
-					new_prev.add(i);
-					d += binLength(nc);
-				}
-				ret += borderScore(cis, new_prev, next);
-				//System.err.println("");
-				//System.err.println(prev);
-				//System.err.println(next);
-				//System.err.println("->");
-				//System.err.println(new_prev);
-				//System.err.println(next);
-			}
-
-		}
-		//if (true) {
-		//	int value = scoreChange_slow(cis, start, end, moveDirection, flip);
-		//	if (value != ret)
-		//		System.err.println(ret + "!=" + value + " " + start + " " + end + " " + moveDirection + " " + flip);
-		//	return value;
-		//}
-
-		return ret;
-	}
-	
-	public int score(ArrayList<ContigInterval> cis)
-	{
-		int ret = 0;
-		for (int i = 1; i < cis.size(); ++i) {
-			int j = i - 1;
-			int d = 0;
-			while (j >= 0 && d < maxDistance) {
-				ret += score(cis.get(j), cis.get(i), d);
-				d += binLength(cis.get(j));
-				--j;
-			}
-		}
-		return ret;
-	}
-	
-	private int score(ContigInterval c1, ContigInterval c2, int distance)
-	{
-		int d[] = distanceHash.get(calculateKey(c1, c2));
-		if (d != null && d.length > distance) 
-			return d[distance];
-		return 0;
-	}
-
-	public int score(String key, int distance)
-	{
-		int d[] = distanceHash.get(key);
-		if (d != null && d.length > distance) 
-			return d[distance];
-		return 0;
-	}
-
-	private int score(ContigInterval c1, boolean flip1, ContigInterval c2, boolean flip2, int distance)
-	{
-		int d[] = distanceHash.get(calculateKey(c1, (c1.getOrientation() >= 0) ^ flip1, c2, (c2.getOrientation() >= 0) ^ flip2));
-		if (d != null && d.length > distance) 
-			return d[distance];
-		return 0;
-	}
-	
-	public static void main(String args[])
-	{
-		//Test Proximity class
-		ArrayList<ContigInterval> bed = InputData.loadBed("proximity.bed");
-		
-		HashMap<String, ArrayList<ContigInterval>> bedHash2 = new HashMap<String, ArrayList<ContigInterval>>();
-		for (ContigInterval ci : bed) {
-			String contig = ci.getContig();
-			if (!bedHash2.containsKey(contig))
-				bedHash2.put(contig, new ArrayList<ContigInterval>());
-			bedHash2.get(contig).add(ci);
-		}
-		Proximity p = new Proximity(10000, 2000, 0.01);
-		p.loadData("ld.txt", bedHash2);
-		ContigInterval c1 = bedHash2.get("000604F|quiver|pilon").get(0);
-		ContigInterval c2 = bedHash2.get("000000F|quiver|pilon").get(0);
-		ContigInterval c3 = bedHash2.get("000310F|quiver|pilon").get(0);
-		ArrayList<ContigInterval> cis = new ArrayList<ContigInterval>();
-		cis.add(c1);
-		cis.add(c2);
-		cis.add(c3);
-		Collections.reverse(cis);
-		for (int orient = 0; orient < 8; ++orient) {			
-			c1.setOrientation((orient & 4) - 1);
-			c2.setOrientation((orient & 2) - 1);
-			c3.setOrientation((orient & 1) - 1);
-			System.err.println(Integer.toBinaryString(orient + 8).substring(1) + ":\t" + p.score(cis));
-		}
-		System.err.println();
-		Collections.reverse(cis);
-		for (int orient = 0; orient < 8; ++orient) {			
-			c1.setOrientation((orient & 4) - 1);
-			c2.setOrientation((orient & 2) - 1);
-			c3.setOrientation((orient & 1) - 1);
-			System.err.println(Integer.toBinaryString(orient + 8).substring(1) + ":\t" + p.score(cis));
-		}
-
-		c1.setOrientation(1);
-		c2.setOrientation(-1);
-		c3.setOrientation(1);
-		System.err.println(p.score(cis));
-		System.err.println();
-		for (int i = 0; i < 3; ++i) {
-			System.err.println(p.scoreChange(cis, i, i, 0, true));
-			System.err.println(p.scoreChange_slow(cis, i, i, 0, true));
-			System.err.println();
-		}
-
-		for (int i = 0; i < 2; ++i) {
-			System.err.println(p.scoreChange(cis, i, i, 1, true));
-			System.err.println(p.scoreChange_slow(cis, i, i, 1, true));
-			System.err.println();
-		}
-		System.err.println(p.scoreChange(cis, 0, 0, 2, true));
-		System.err.println(p.scoreChange_slow(cis, 0, 0, 2, true));
-		System.err.println();
-
-		System.err.println(p.scoreChange(cis, 1, 2, -1, true));
-		System.err.println(p.scoreChange_slow(cis, 1, 2, -1, true));
-		System.err.println();
-
-		
-		System.err.println(p.scoreChange(cis, 0, 1, 1, true));
-		System.err.println(p.scoreChange_slow(cis, 0, 1, 1, true));
-		System.err.println();
-		
-	}
-	// linkScore between ... ,prevC-1, prevC and nextC, nextC + 1, ...
-	public int linkScore(ArrayList<ContigInterval> cis, int prevC, int nextC) {
-		ArrayList<Integer> next = next(cis, nextC - 1, cis.size() - 1);
-		ArrayList<Integer> prev = prev(cis, prevC + 1, 0);
-		return borderScore(cis, prev, next);
-	}
-
-	public boolean linkedIntervals(ArrayList<ContigInterval> cis, int c1, int c2) {
-		return (linkScore(cis, c1, c2) > 0);
-	}
-}
diff --git a/software/LepMap3/scripts/affx2post.awk b/software/LepMap3/scripts/affx2post.awk
deleted file mode 100644
index 9ca5d4a..0000000
--- a/software/LepMap3/scripts/affx2post.awk
+++ /dev/null
@@ -1,83 +0,0 @@
-#converts a genotype file (SNP_name + AA/AB/BB for each individual) to posterior
-#awk [-verror=0.001] -f affx2post.awk genotypes.txt >genotypes.post
-function alleles2Index(a, b)
-{
-	if (b == 1)
-		return a
-	if (b == 2)
-		return 3 + a
-	if (b == 3)
-		return 5 + a
-	return 10
-}
-function allele1(code)
-{
-	if (code <= 4)
-		return 1
-	if (code <= 7)
-		return 2
-	if (code <= 9)
-		return 3
-	return 4
-}
-function allele2(code)
-{
-	if (code <= 4)
-		return code
-	if (code <= 7)
-		return code - 3
-	if (code <= 9)
-		return code - 5
-	return 4
-}
-
-function distance(code1, code2       ,a1,a2,b1,b2)
-{
-	if (code1 == code2)
-		return 0
-	a1 = allele1(code1)
-	a2 = allele2(code1)
-
-	b1 = allele1(code2)
-	b2 = allele2(code2)
-
-	if (a1 == b1 || a1 == b2 || a2 == b1 || a2 == b2)
-		return 1
-	return 2
-}
-
-
-
-BEGIN{
-	FS="\t"
-	OFS="\t"
-	if (error == "")
-		error = 0.001
-
-	code = 1
-	for (i = 1; i <= 4; ++i)
-		for (j = i; j <= 4; ++j) {
-			s = ""
-			for (k = 1; k <= 10; ++k)
-				s = s " " error ^ distance(code, k)
-			map[i " " j] = substr(s, 2)
-			map[j " " i] = map[i " " j]
-			++code
-		}
-
-	map["0 0"] = "1 1 1 1 1 1 1 1 1 1"
-	map2["AA"]="1 1"
-	map2["AB"]="1 2"
-	map2["BB"]="2 2"
-	map2["NoCall"]="0 0"
-}
-
-($1 !~ /^#/) {
-	$1=$1"\t"$1
-	if (++line > 1)
-		for (i = 2; i <= NF; ++i)
-			$i = map[map2[$i]]
-	print
-} 
-
-
diff --git a/software/LepMap3/scripts/allPaternal.awk b/software/LepMap3/scripts/allPaternal.awk
deleted file mode 100644
index 5226eaf..0000000
--- a/software/LepMap3/scripts/allPaternal.awk
+++ /dev/null
@@ -1,45 +0,0 @@
-#flips maternally informative markers to paternally inf
-BEGIN{
-	FS="\t"
-	OFS="\t"
-	inf["0 1.0 0 0 0 0 0 0 0 0"]=1
-	inf["0 0 1.0 0 0 0 0 0 0 0"]=1
-	inf["0 0 0 1.0 0 0 0 0 0 0"]=1
-	inf["0 0 0 0 0 1.0 0 0 0 0"]=1
-	inf["0 0 0 0 0 0 1.0 0 0 0"]=1
-	inf["0 0 0 0 0 0 0 0 1.0 0"]=1
-
-	inf["0 1 0 0 0 0 0 0 0 0"]=1
-	inf["0 0 1 0 0 0 0 0 0 0"]=1
-	inf["0 0 0 1 0 0 0 0 0 0"]=1
-	inf["0 0 0 0 0 1 0 0 0 0"]=1
-	inf["0 0 0 0 0 0 1 0 0 0"]=1
-	inf["0 0 0 0 0 0 0 0 1 0"]=1
-
-}
-
-(NR<=7){print}
-
-(NR==2){for (i = 3; i<=NF; ++i) {if (!($i in d)) d[$i] = ++p; f[i]=d[$i]}}
-
-(NR==4){for (i = 3; i<=NF; ++i) if ($i==0) pa[f[i], ++count[f[i]]]=i}
-
-(NR==6){for (i = 3; i<=NF; ++i) sex[i]=$i}
-
-#(NR==7){print "#"}
-
-(NR>7){
-	for (j = 1; j <= p; ++j) {
-		i = 0
-		if (inf[$(pa[j, 1])]==1)
-			i += sex[pa[j, 1]]
-		if (inf[$(pa[j, 2])]==1)
-			i += sex[pa[j, 2]]
-		if (i == 2) {
-			tmp = $(pa[j, 1])
-			$(pa[j, 1]) = $(pa[j, 2])
-			$(pa[j, 2]) = tmp
-		}
- 	}
-	print
-}
diff --git a/software/LepMap3/scripts/genotypes2post.awk b/software/LepMap3/scripts/genotypes2post.awk
deleted file mode 100644
index e0baf69..0000000
--- a/software/LepMap3/scripts/genotypes2post.awk
+++ /dev/null
@@ -1,81 +0,0 @@
-#converts a genotype file (transpose of linkage file with marker names) to posterior
-#awk [-verror=0.001] -f genotypes2post.awk genotypes >genotypes.post
-function alleles2Index(a, b)
-{
-	if (b == 1)
-		return a
-	if (b == 2)
-		return 3 + a
-	if (b == 3)
-		return 5 + a
-	return 10
-}
-function allele1(code)
-{
-	if (code <= 4)
-		return 1
-	if (code <= 7)
-		return 2
-	if (code <= 9)
-		return 3
-	return 4
-}
-function allele2(code)
-{
-	if (code <= 4)
-		return code
-	if (code <= 7)
-		return code - 3
-	if (code <= 9)
-		return code - 5
-	return 4
-}
-
-function distance(code1, code2       ,a1,a2,b1,b2)
-{
-	if (code1 == code2)
-		return 0
-	a1 = allele1(code1)
-	a2 = allele2(code1)
-
-	b1 = allele1(code2)
-	b2 = allele2(code2)
-
-	if (a1 == b1 || a1 == b2 || a2 == b1 || a2 == b2)
-		return 1
-	return 2
-}
-
-
-
-BEGIN{
-	FS="\t"
-	OFS="\t"
-	if (error == "")
-		error = 0.001
-
-	code = 1
-	for (i = 1; i <= 4; ++i)
-		for (j = i; j <= 4; ++j) {
-			s = ""
-			for (k = 1; k <= 10; ++k)
-				s = s " " error ^ distance(code, k)
-			map[i " " j] = substr(s, 2)
-			map[j " " i] = map[i " " j]
-			map[j "  " i] = map[i " " j]
-			map[i "  " j] = map[i " " j]
-			++code
-		}
-
-	map["0 0"] = "1 1 1 1 1 1 1 1 1 1"
-	map["0  0"] = "1 1 1 1 1 1 1 1 1 1"
-}
-
-($1 !~ /^#/) {
-	if (++line > 6)
-		for (i = 3; i <= NF; ++i)
-			$i = map[$i]
-	print
-} 
-
-
diff --git a/software/LepMap3/scripts/loc2genotypes.awk b/software/LepMap3/scripts/loc2genotypes.awk
deleted file mode 100644
index feca503..0000000
--- a/software/LepMap3/scripts/loc2genotypes.awk
+++ /dev/null
@@ -1,102 +0,0 @@
-#converts a loc file (JoinMap) to genotypes, that can be converted back post file
-#should handle windows end-of-line characters as well
-#awk -f locsingle.awk file.loc|awk -f loc2genotypes.awk|awk -f genotypes2post.awk |java -cp Lep-MAP3/bin ... data=- ...
-BEGIN{
-	map2["-"] = 0
-	#<lmxll>
-	map2["l"] = 1
-	map2["m"] = 2
-	#<nnxnp>
-	map2["n"] = 1
-	map2["p"] = 2
-	#<hkxhk>
-	map2["h"] = 1
-	map2["k"] = 2
-	#<efxeg>
-	map2["e"] = 1
-	map2["f"] = 2
-	map2["g"] = 3
-	#<abxcd>
-	map2["a"] = 1
-	map2["b"] = 2
-	map2["c"] = 3
-	map2["d"] = 4
-	for (i in map2) {
-		map[i] = map2[i]
-		map[toupper(i)] = map2[i]
-	}
-	delete map2
-	markers["<lmxll>"]
-	markers["<nnxnp>"]
-	markers["<hkxhk>"]
-	markers["<efxeg>"]
-	markers["<abxcd>"]
-	markers["<abxab>"]
-	markers["<abxaa>"]
-	markers["<aaxab>"]
-}
-($2 in markers) {
-	if ($NF == "\r")	#windows end of line
-		--NF
-	++line
-	start = 3
-	if ($3 ~ /{.*}/ || $3 ~ /\(.*\)/)
-		start = 4
-#	if (start == 3 && !($3 ~ /{.*}/) {
-#		print "Error: missing phase on data" >/dev/stderr
-#		exit(-1)
-#	}
-
-	if (line == 1) { ## print pedigree
-		s = "CHR\tPOS"
-		for (i = start; i <= NF + 4; ++i)
-			s = s "\tF" 
-		print s
-		s = "CHR\tPOS\tGP1\tGP2\tP1\tP2"
-		for (i = start; i <= NF; ++i)
-			s = s "\t"  (i - start + 1)
-		print s
-		s = "CHR\tPOS\t0\t0\tGP1\tGP2"
-		for (i = start; i <= NF; ++i)
-			s = s "\tP1"
-		print s
-		s = "CHR\tPOS\t0\t0\t0\t0"
-		for (i = start; i <= NF; ++i)
-			s = s "\tP2"
-		print s
-		s = "CHR\tPOS\t1\t1\t1\t2"
-		for (i = start; i <= NF; ++i)
-			s = s "\t0"
-		print s
-		s = "CHR\tPOS"
-		for (i = start; i <= NF + 4; ++i)
-			s = s "\t0" 
-		print s
-	}
-	s = $1 "\t" line
-	if (start == 4) {
-		if ($3 ~ /{0/)
-			s = s "\t" map[substr($2, 2, 1)] " " map[substr($2, 2, 1)]
-		else  if ($3 ~ /{1/)
-			s = s "\t" map[substr($2, 3, 1)] " " map[substr($2, 3, 1)]
-		else 	
-			s = s "\t0 0"
-
-		if ($3 ~ /{.0/)
-			s = s "\t" map[substr($2, 5, 1)] " " map[substr($2, 5, 1)]
-		else  if ($3 ~ /{.1/)
-			s = s "\t" map[substr($2, 6, 1)] " " map[substr($2, 6, 1)]
-		else 	
-			s = s "\t0 0"
-
-	} else
-		s = s "\t0 0\t0 0"
-	s = s "\t" map[substr($2, 2, 1)] " " map[substr($2, 3, 1)] "\t" map[substr($2, 5, 1)] " " map[substr($2, 6, 1)]
-
-	for (i = start; i <= NF; ++i)
-		s = s "\t" map[substr($i, 1, 1)] " " map[substr($i, 2, 1)]
-	print s
-}
-END{
-	
-}
diff --git a/software/LepMap3/scripts/locsingle.awk b/software/LepMap3/scripts/locsingle.awk
deleted file mode 100644
index ac87d4f..0000000
--- a/software/LepMap3/scripts/locsingle.awk
+++ /dev/null
@@ -1,8 +0,0 @@
-#puts loc files on single line
-{
-	i = index($0, ";")
-	if (i > 0)
-		printf(substr($0, 1, i-1))
-	else
-		print
-}
diff --git a/software/LepMap3/scripts/map2genotypes.awk b/software/LepMap3/scripts/map2genotypes.awk
deleted file mode 100644
index a587300..0000000
--- a/software/LepMap3/scripts/map2genotypes.awk
+++ /dev/null
@@ -1,66 +0,0 @@
-#converts phased data to "genotypes"
-#usage: 
-#java ... OrderMarkers2 ... outputPhasedData=1 > order_with_phase_LM3.txt
-#awk [-vchr=X] [-vfullData=1] -f map2genotypes.awk order_with_phase_LM3.txt
-#output columns marker name, chr, male postion, female postion, genotypes coded as "1 1", "1 2", "2 2" and 0 as missing
-#providing fullData ouputs parents and pedigree...
-BEGIN{
-	map["00"]="1 1"
-	map["01"]="1 2"
-	map["10"]="2 1"
-	map["11"]="2 2"
-	map["0-"]="1 0"
-	map["-0"]="0 1"
-	map["-1"]="0 2"
-	map["1-"]="2 0"
-        map["--"]="0 0"
-	if (chr == "")
-		chr = 0
-}
-(/^[^#]/){
-	if (!notFirst && fullData){
-		notFirst = 1
-		s1 =  "MARKER\tCHR\tMALE_POS\tFEMALE_POS"
-		s2 =  "MARKER\tCHR\tMALE_POS\tFEMALE_POS"
-		s3 =  "MARKER\tCHR\tMALE_POS\tFEMALE_POS"
-		s4 =  "MARKER\tCHR\tMALE_POS\tFEMALE_POS"
-		s5 =  "MARKER\tCHR\tMALE_POS\tFEMALE_POS"
-		s6 =  "MARKER\tCHR\tMALE_POS\tFEMALE_POS"
-		for (i = 7; i<=NF; i+=3) {
-			n = length($i) / 2
-			p1 = "P" (++numParents)
-			p2 = "P" (++numParents)
-			s1 = s1 "\t" p1 "x" p2 "\t" p1 "x" p2
-			s2 = s2 "\t" p1 "\t" p2
-			s3 = s3 "\t" 0 "\t" 0
-			s4 = s4 "\t" 0 "\t" 0
-			s5 = s5 "\t" 1 "\t" 2
-			s6 = s6 "\t" 0 "\t" 0
-			for (j = 1; j <= n; ++j) {
-				s1 = s1 "\t" p1 "x" p2
-				s2 = s2 "\tC" (++numOffspring)
-				s3 = s3 "\t" p1
-				s4 = s4 "\t" p2
-				s5 = s5 "\t0" 
-				s6 = s6 "\t0" 
-			}
-		}
-		print s1
-		print s2
-		print s3
-		print s4
-		print s5
-		print s6
-	}
-	s = $1 "\t" chr "\t" $2 "\t" $3
-	for (i = 7; i<=NF; i+=3) {
-		if (fullData) #parental data
-			s = s "\t1 2\t1 2"
-		n = length($i) / 2
-		p1 = substr($i,1,n)
-		p2 = substr($i,n+1)
-		for (j = 1; j <= n; ++j)
-			s = s "\t" map[substr(p1, j, 1) substr(p2, j, 1)]		
-	}
-	print s
-}
diff --git a/software/LepMap3/scripts/order2data.awk b/software/LepMap3/scripts/order2data.awk
deleted file mode 100644
index 19e9e0f..0000000
--- a/software/LepMap3/scripts/order2data.awk
+++ /dev/null
@@ -1,65 +0,0 @@
-#script for marker binning...
-BEGIN{
-#ACxAG=AA,AC,AG,CG
-	map["AA"] = "1 0 0 0 0 0 0"#00
-	map["AC"] = "0 1 0 0 0 0 0"#01
-	map["AG"] = "0 0 1 0 0 0 0"#10
-	map["CG"] = "0 0 0 0 0 1 0"#11
-
-	if (chr == "")
-		 chr = 1
-}
-/^[^#]/{
-	for (j = 7; j <= NF; ++j)
-		if ($j ~ /#$/) {
-			$j = substr($j, 1, length($j) - 1)
-			oldNF = j
-			break
-		}
-	if (oldNF == NF)
-		next
-	if (prev == "" && pedigree) {
-		s1 = "CHR\tPOS"
-		s2 = "CHR\tPOS"
-		s3 = "CHR\tPOS"
-		s4 = "CHR\tPOS"
-		s5 = "CHR\tPOS"
-		s6 = "CHR\tPOS"
-		f = 1
-		nt = 0
-		for (j = 7; j <= oldNF; j+=3) {
-			n = length($j) / 2
-			s1 = s1 "\tF" f "\tF" f
-			s2 = s2 "\t" (nt + 1) "\t" (nt + 2)
-			s3 = s3 "\t0\t0"
-			s4 = s4 "\t0\t0"
-			s5 = s5 "\t1\t2"
-			s6 = s6 "\t0\t0"
-			for (i = 1; i <= n; ++i) {
-				s1 = s1 "\tF" f
-				s2 = s2 "\t" (nt + i + 2)
-				s3 = s3 "\t" (nt + 1)
-				s4 = s4 "\t" (nt + 2)
-				s5 = s5 "\t0"
-				s6 = s6 "\t0"
-			}
-			nt += n + 2
-			++f
-		}
-		print s1 "\n" s2 "\n" s3 "\n" s4 "\n" s5 "\n" s6 
-	}
-
-	s = ""
-	nt = 0
-	for (j = 7; j <= oldNF; j+=3) {
-		s = s "\t" map["AC"] "\t" map["AG"]
-		n = length($j) / 2
-		for (i = oldNF + nt + 1; i <= oldNF + nt + 4 *n; i+=4)
-			s = s "\t" $i " " $(i+1) " " $(i+2) " 0 0 " $(i+3) " 0"
-		nt += 4 * n
-	}
-	if (prev != s || FILENAME != prevFN)
-		print $1 "\t" chr s
-	prev = s
-	prevFN = FILENAME
-}
diff --git a/software/LepMap3/scripts/phasematch.awk b/software/LepMap3/scripts/phasematch.awk
deleted file mode 100644
index 100935a..0000000
--- a/software/LepMap3/scripts/phasematch.awk
+++ /dev/null
@@ -1,133 +0,0 @@
-#awk -f phasematch.awk order_reference.txt order_mapped.txt >order_mapped_in_reference_phase.txt
-#
-BEGIN{
-}
-(NR==FNR && /^[^#]/){
-	for (f = 7; f < NF; f+=3)
-		refdata[$1, f] = $f	
-	if (numF != "" && numF != NF) {
-		print "Error: different number of columns in the input orders" > "/dev/stderr"
-		exit 1
-	}
-	numF = NF
-}
-
-(NR!=FNR){
-	if (/^[#]/)
-		;
-	else {
-		if (numF != NF) {
-			print "Error: different number of columns in the input orders" > "/dev/stderr"
-			exit 1
-		}
-	}
-	data[FNR]=$0
-}
-
-END{
-	for (i = 1; i <= FNR; ++i) {
-		$0 = data[i]
-		if (/^[#]/)
-			;
-		else {
-			for (f = 7; f < NF; f+=3) {
-				if (($1 SUBSEP f) in refdata) {
-					ham1[f] += hamming1($f, refdata[$1, f])
-					maxham1[f] += maxh
-					ham2[f] += hamming2($f, refdata[$1, f])
-					maxham2[f] += maxh
-				}
-			}
-		}
-		
-	}
-for (f = 7; f < NF; f+=3) {
-		print "***" > "/dev/stderr"
-		print "hamming distance1 is " ham1[f] " of " maxham1[f] " (" abs(ham1[f])/(maxham1[f]+0.000000000000000001) ") for family " ++family > "/dev/stderr"
-		print "hamming distance2 is " ham2[f] " of " maxham2[f] " (" abs(ham2[f])/(maxham2[f]+0.000000000000000001) ") for family " family > "/dev/stderr"
-	}
-
-	for (i = 1; i <= FNR; ++i) {
-		$0 = data[i]
-		if (/^[#]/)
-			print
-		else {
-			for (f = 7; f < NF; f+=3) {
-				n = length($f) / 2
-				p1 = substr($f, 1, n)
-				p2 = substr($f, n + 1)
-				if (ham1[f] < 0) 
-					p1 = flip(p1)
-				if (ham2[f] < 0) 
-					p2 = flip(p2)
-				$f = p1 p2
-			}
-			
-
-			s = $1 "\t" $2 "\t" $3 "\t" $4 " " $5 " " $6
-			for (f = 7; f < NF; f+=3)
-				s = s "\t" $f " " $(f+1) " " $(f+2)
-			print s
-		}
-		
-	}
-}
-function abs(x) {
-	if (x < 0)
-		return -x
-	return x
-}
-
-function flip(x) {
-	gsub(/0/, "x", x)
-	gsub(/1/, "0", x)
-	gsub(/x/, "1", x)
-	return x
-}
-
-function hamming1(x, y  ,i,xi,yi,ret, n)
-{
-	n = length(y)
-	if (length(x) < n)
-		n = length(x)
-#	print x " " y
-	ret = 0
-	maxh = 0
-	n = n / 2
-	for (i = 1; i <= n; ++i) {
-		xi = substr(x, i, 1)
-		yi = substr(y, i, 1)
-		if (yi != "-" && xi != "-") {
-			++maxh
-			if (xi == yi) {
-				++ret
-			}
-			else
-				--ret
-		}
-	}
-	return ret
-}
-function hamming2(x, y  ,i,xi,yi,ret, n)
-{
-	n = length(y)
-	if (length(x) < n)
-		n = length(x)
-#	print x " " y
-	ret = 0
-	maxh = 0
-	for (i = n / 2 + 1; i <= n; ++i) {
-		xi = substr(x, i, 1)
-		yi = substr(y, i, 1)
-		if (yi != "-" && xi != "-") {
-			++maxh
-			if (xi == yi) {
-				++ret
-			}
-			else
-				--ret
-		}
-	}
-	return ret
-}
-
diff --git a/software/LepMap3/scripts/pileup2posterior.awk b/software/LepMap3/scripts/pileup2posterior.awk
deleted file mode 100644
index 84c6873..0000000
--- a/software/LepMap3/scripts/pileup2posterior.awk
+++ /dev/null
@@ -1,156 +0,0 @@
-#samtools mpileup -q 10 -Q 10 -s `cat sorted_bams`|awk -f pileupParser2.awk|awk -f pileup2posterior.awk
-#needs mapping.txt
-#Part of Lep-MAP3
-BEGIN{
-	if (limit7 == "") # maximum quality of a read base
-		limit7 = 0.001
-
-	map["a"]=1
-	map["A"]=1
-
-	map["c"]=2
-	map["C"]=2
-
-	map["g"]=3
-	map["G"]=3
-
-	map["t"]=4
-	map["T"]=4
-
-	"cat mapping.txt"|getline
-	if (NF == 0) {
-		print "Error: file mapping.txt not found!"  > "/dev/stderr"
-		exit
-	}
-	s = "CHR\tPOS"
-
-	numIndividuals = 0
-	for (i = 1; i <= NF; ++i) {
-		mapping[i] = $i
-		if (!($i in imapping))
-			listOrder[++numIndividuals] = $i
-		++imapping[$i]
-	}
-	print "Number of bams = "  NF > "/dev/stderr"
-	print "Number of individuals = "  numIndividuals > "/dev/stderr"
-	close("cat mapping.txt")
-
-
-	for (mi = 1; mi <= numIndividuals; ++mi) {
-		s = s "\t" listOrder[mi]
-	}
-	print s
-	FS="\t"
-
-	#ascii characters mapping to their quality
-	for (i = 33; i <= 127; ++i) {
-		if (i == 33) # q == 0
-			q = 0.75 # all bases equal probable
-		else if (i == 34) # q == 1
-			q = 0.5 * (0.75 + 10 ^ (-0.15))  # One base must be more probable than others, e.g. p \in ]10^-0.15, 0.75[
-		else
-			q = 10 ^ (-0.1 * (i - 33))
-	 	quality[sprintf("%c", i)] = q
-	}
-
-	for (i = 33; i <= 127; ++i)
-		for (j = 33; j <= 127; ++j) {
-			qs1 = sprintf("%c", i)
-			qs2 = sprintf("%c", j) 
-			p = combineQ(qs1, qs2)
-			if (p < limit7)
-				p = limit7
-
-			logP[qs1 qs2] = log(p / 3)
-			logNP[qs1 qs2] = log(1 - p) 
-			logNP2[qs1 qs2] = log(p / 3 + (1 - p)) + log(0.5)
-		}
-
-
-	logHalf = log(0.5)
-	logTwo = log(2.0)
-}
-
-#function phred2p(q    , p)
-#{
-#	p = ord[q] - 33
-#	if (p == 0)
-#		return 0.75;
-#	if (p == 1)
-#		return 0.725;
-#	else
-#		return 10^(-0.1 * p)
-#}
-
-
-function combineQ(q1, q2     ,ret,p1,p2)
-{
-	p1 = quality[q1]
-	p2 = quality[q2]
-	ret = p1 + p2 - p1 * p2
-	if (ret > 0.75)
-		ret = 0.75
-	return ret
-}
-
-function myexp(x)
-{
-	if (x < -100)
-		return 0
-	else
-		return exp(x)
-}
-
-{
-	delete prob
-	for (i = 5; i <= NF; i+=4)
-		for (j = 1; j <= length($i); ++j) {
-			a = substr($i, j, 1)
-			if (a in map) {
-				am = map[a]
-				individual = mapping[int(i / 4)] 
-
-				#p = combineQ(substr($(i+1), j, 1), substr($(i+2), j, 1))
-				#if (p < limit7)
-				#	p = limit7
-				#logP = log(p / 3)
-				#logNP = log(1 - p) 
-				#logNP2 = log(p / 3 + (1 - p)) + logHalf
-				#faster by using a table...
-				qs = substr($(i+1), j, 1) substr($(i+2), j, 1)
-
-				for (k = 1; k <= 4; ++k)
-					if (k == am)
-						prob[individual, k, k] += logNP[qs]
-					else
-						prob[individual, k, k] += logP[qs]
-
-				for (k = 1; k < 4; ++k)
-					for (l = k + 1; l <= 4; ++l)
-						if (k == am || l == am)
-							prob[individual, k, l] += logNP2[qs]
-						else
-							prob[individual, k, l] += logP[qs]
-			}
-		}
-	s = $1 "\t" $2
-	for (mi = 1; mi <= numIndividuals; ++mi) {
-		m = listOrder[mi]
-
-		maxp = prob[m,1,1] + 0
-		for (k = 1; k <= 4; ++k)
-			for (l = k; l <= 4; ++l)
-				if (prob[m, k, l] + 0 > maxp)
-					maxp = prob[m, k, l] + 0
-
-		for (k = 1; k <= 4; ++k)
-			for (l = k; l <= 4; ++l) {
-				if (k == 1 && l == 1)
-					s = s "\t"
-				else
-					s = s " "
-				s = s myexp(prob[m, k, l] - maxp)
-			}
-	}
-	print s
-}
diff --git a/software/LepMap3/scripts/pileupParser2.awk b/software/LepMap3/scripts/pileupParser2.awk
deleted file mode 100644
index 4f382c0..0000000
--- a/software/LepMap3/scripts/pileupParser2.awk
+++ /dev/null
@@ -1,90 +0,0 @@
-#samtools mpileup -q 10 -Q 10 -s `cat sorted_bams`|awk -f pileupParser2.awk|awk -f pileup2posterior.awk
-#needs mapping.txt
-#Part of Lep-MAP3
-BEGIN{
-        "cat mapping.txt"|getline
-        if (NF == 0) {
-                print "Error: file mapping.txt not found!" > "/dev/stderr"
-                exit
-        }
-	numIndividuals = 0
-        for (i = 1; i <= NF; ++i) {
-                mapping[i] = $i
-		if (!($i in ind))
-			++numIndividuals
-		ind[$i]
-	}
-        close("cat mapping.txt")
-
-
-	if (limit1 == "")
-		limit1 = 3 # coverage per individual
-	if (limit2 == "")
-		limit2 = 0.3 * numIndividuals # number of allowed individuals with lower coverage
-	if (limit3 == "")
-		limit3 = 0.1 * numIndividuals # minimum allele coverage
-	if (limit4 == "")
-		limit4 = limit1 * (numIndividuals - limit2)  # minimum total counts
-
-	print "PileupParser2 parameters: limit1=" limit1 " limit2=" limit2 " limit3=" limit3 " limit4="  limit4 > "/dev/stderr"
-
-	FS="\t"
-	OFS="\t"
-}
-
-function abs(a)
-{
-	if (a < 0)
-		return -a
-	else
-		return a
-}
-
-{
-	sum = 0
-	for (i = 4; i <= NF; i+=4)
-		sum += $i;
-
-	if (sum < limit4)
-		next
-
-	delete count
-	for (i = 4; i <= NF; i+=4)
-		count[mapping[int(i / 4)]]+=$i
-
-	missing = 0
-	for (ci in count)
-		if (count[ci] < limit1)
-			++missing
-
-	if (missing > limit2)
-		next
-
-	delete c
-	for (i = 5; i <= NF; i+=4) {
-		if ($(i-1) == 0)
-			$i = ""
-		gsub(/\$/,"",$i)  #remove end of reads
-		gsub(/\^./,"",$i) #remove quality
-		while (match($i, /[+-][1-9][0-9]*/) > 0) { #remove indels
-			$i = substr($i, 1, RSTART - 1) substr($i, RSTART + RLENGTH + substr($i, RSTART + 1, RLENGTH - 1))
-		}
-		tmp = $i
-		c[0] += gsub(/[Aa]/, "", tmp)
-		c[1] += gsub(/[Cc]/, "", tmp)
-		c[2] += gsub(/[Gg]/, "", tmp)
-		c[3] += gsub(/[Tt]/, "", tmp)
-	}
-	alleles = 0
-	if (c[0] >= limit3)
-		++alleles;
-	if (c[1] >= limit3)
-		++alleles;
-	if (c[2] >= limit3)
-		++alleles;
-	if (c[3] >= limit3)
-		++alleles;
-
-	if (alleles >= 2)
-		print
-}
diff --git a/software/LepMap3/scripts/somePaternal.awk b/software/LepMap3/scripts/somePaternal.awk
deleted file mode 100644
index 51234b1..0000000
--- a/software/LepMap3/scripts/somePaternal.awk
+++ /dev/null
@@ -1,26 +0,0 @@
-#flips informative markers based on a map
-#awk -f somePaternal map.txt data.call
-BEGIN{
-	FS="\t"
-	OFS="\t"
-}
-
-(NR==FNR && /^[^#]/) {
-	map[++markers] = $1
-}
-
-(NR!=FNR && FNR<=7){print}
-
-(NR!=FNR && FNR==2){for (i = 3; i<=NF; ++i) {if (!($i in d)) d[$i] = ++p; f[i]=d[$i]}}
-(NR!=FNR && FNR==4){for (i = 3; i<=NF; ++i) if ($i==0) pa[f[i], ++count[f[i]]]=i}
-
-(NR!=FNR && FNR>7){
-	for (j = 1; j <= p; ++j) {
-		if (map[FNR-7]>0) {
-			tmp = $(pa[j, 1])
-			$(pa[j, 1]) = $(pa[j, 2])
-			$(pa[j, 2]) = tmp
-		}
- 	}
-	print
-}

From f4f081ad3c2633ad9caccce2a3c3f222bcd1be06 Mon Sep 17 00:00:00 2001
From: Pavel Dimens <pdimens@live.com>
Date: Wed, 2 Feb 2022 16:50:24 -0500
Subject: [PATCH 03/46] update place/orient propogation

---
 rules/LepAnchor/LepAnchor.smk                 |  6 +-
 .../{place_orient.smk => place_orient1.smk}   | 23 +++--
 rules/LepAnchor/place_orient2.smk             | 87 +++++++++++++++++++
 rules/LepAnchor/place_orient3.smk             | 50 +++++++++++
 rules/LepAnchor/place_orient_ii.smk           | 60 -------------
 rules/LepAnchor/place_orient_iii.smk          | 74 ----------------
 6 files changed, 158 insertions(+), 142 deletions(-)
 rename rules/LepAnchor/{place_orient.smk => place_orient1.smk} (63%)
 create mode 100644 rules/LepAnchor/place_orient2.smk
 create mode 100644 rules/LepAnchor/place_orient3.smk
 delete mode 100644 rules/LepAnchor/place_orient_ii.smk
 delete mode 100644 rules/LepAnchor/place_orient_iii.smk

diff --git a/rules/LepAnchor/LepAnchor.smk b/rules/LepAnchor/LepAnchor.smk
index a746cef..62502be 100644
--- a/rules/LepAnchor/LepAnchor.smk
+++ b/rules/LepAnchor/LepAnchor.smk
@@ -21,9 +21,9 @@ lg_range = list(range(1,lg+1))
 
 include: "generate_inputs.smk"
 include: "mask_and_chain.smk"
-include: "place_orient.smk"
-include: "place_orient_ii.smk"
-include: "place_orient_iii.smk"
+include: "place_orient1.smk"
+include: "place_orient2.smk"
+include: "place_orient3.smk"
 include: "build_agp.smk"
 include: "build_fasta.smk"
 include: "mareymaps_untrimmed.smk"
diff --git a/rules/LepAnchor/place_orient.smk b/rules/LepAnchor/place_orient1.smk
similarity index 63%
rename from rules/LepAnchor/place_orient.smk
rename to rules/LepAnchor/place_orient1.smk
index dd3546c..ccf2ffe 100644
--- a/rules/LepAnchor/place_orient.smk
+++ b/rules/LepAnchor/place_orient1.smk
@@ -7,11 +7,11 @@ rule place_orient:
     lift = "10_PlaceAndOrientContigs/liftover.la"
   output:
     chrom = "10_PlaceAndOrientContigs/orient_1/chr.{lg_range}.la",
-    haplos = "10_PlaceAndOrientContigs/orient_1/haplotypes/chr.{lg_range}.haplo.suspected"
+    haplos = "10_PlaceAndOrientContigs/orient_1/haplotypes/chr.{lg_range}.haplo.suspected",
+    chromerr = report("10_PlaceAndOrientContigs/orient_1/logs/chr.{lg_range}.la.log", category = "Anchoring I Logs")
   log:
-    chrom = report("10_PlaceAndOrientContigs/orient_1/logs/chr.{lg_range}.la.log", category = "Anchoring I Logs"),
-    haplos = "10_PlaceAndOrientContigs/orient_1/haplotypes/chr.{lg_range}.haplo.all",
-    errors = "10_PlaceAndOrientContigs/orient_1/errors/chr.{lg_range}.errors"
+    errors = "10_PlaceAndOrientContigs/orient_1/errors/chr.{lg_range}.errors",
+    haplos = "10_PlaceAndOrientContigs/orient_1/haplotypes/chr.{lg_range}.haplo.all"
   params:
     chrom = "{lg_range}",
     extras = place_orient_extra,
@@ -21,12 +21,25 @@ rule place_orient:
   message: "Running the 1st round of PlaceAndOrientContigs for linkage group {params.chrom}"
   shell:
     """
-    gunzip -fc {input.chain} | java -cp software/LepAnchor PlaceAndOrientContigs numThreads={threads} bed={input.bedfile} chromosome={params.chrom} map={input.lift} chain=- paf={input.paf} proximity={input.prox} {params.datatype} {params.extras} > {output.chrom} 2> {log.chrom}
+    gunzip -fc {input.chain} | java -cp software/LepAnchor PlaceAndOrientContigs numThreads={threads} bed={input.bedfile} chromosome={params.chrom} map={input.lift} chain=- paf={input.paf} proximity={input.prox} {params.datatype} {params.extras} > {output.chrom} 2> {output.chromerr}
     sort -n -r {log.chrom} | awk '($NF=="haplotype" && (!(($5 SUBSEP $6 SUBSEP $7) in h))){{h[$2,$3,$4]; print}}' > {log.haplos}
     sort -n -r {log.chrom} | awk -vlimit={params.haplo} '($NF=="haplotype" && ($1>=($4-$3+1-limit)/limit) && (!(($5 SUBSEP $6 SUBSEP $7) in h))){{h[$2,$3,$4]; print}}'  > {output.haplos}  
     grep "error$" {log.chrom} > {log.errors}
     """
 
+rule propogate1:
+  input: 
+    placed = expand("10_PlaceAndOrientContigs/orient_1/chr.{lgs}.la", lgs = lg_range),
+    errors = expand("10_PlaceAndOrientContigs/orient_1/logs/chr.{lgs}.la.log", lgs = lg_range),
+    bedfile = "10_PlaceAndOrientContigs/map_extra.bed"
+  output:
+    propogated = "10_PlaceAndOrientContigs/map.propogated.bed",
+  message: "First round of propogation with propogate4.awk"
+  shell:
+    """
+    awk -f software/LepAnchor/scripts/propagate4.awk pass=1 {input.placed} pass=2 {input.errors} | awk -f software/LepAnchor/scripts/pickbed.awk - {input.bedfile} > {output.propogated}
+    #awk -f propagate4.awk pass=1 chr*[0-9].la pass=2 chr*[0-9].la.err|awk -f pickbed.awk - map_extra.bed >map_extra_prop.bed
+    """
 
 rule mergehaplos:
   input: expand("10_PlaceAndOrientContigs/orient_1/haplotypes/chr.{lg}.haplo.suspected", lg = lg_range)
diff --git a/rules/LepAnchor/place_orient2.smk b/rules/LepAnchor/place_orient2.smk
new file mode 100644
index 0000000..3dc38ec
--- /dev/null
+++ b/rules/LepAnchor/place_orient2.smk
@@ -0,0 +1,87 @@
+#rule liftover2:
+#  input:
+#    chain = "9_Chain/chainfile.gz",
+#    intervals = "10_PlaceAndOrientContigs/lepanchor.input",
+#    haplos = "10_PlaceAndOrientContigs/suspected.haplotypes.before",
+#    haplos2 = "10_PlaceAndOrientContigs/suspected.haplotypes.after",
+#    lengths = "10_PlaceAndOrientContigs/contigs.length"
+#  output:
+#    haplos = "10_PlaceAndOrientContigs/suspected.haplotypes.all",
+#    lift = report("10_PlaceAndOrientContigs/liftover.nohaplotypes.la", category = "Lifted Intervals"),
+#    sortedlift = report("10_PlaceAndOrientContigs/liftover.sorted.nohaplotypes.la", category = "Lifted Intervals"),
+#    mapfile = "10_PlaceAndOrientContigs/map.nohaplotypes.clean",
+#    bedfile = "10_PlaceAndOrientContigs/map.nohaplotypes.bed",
+#    unused = "10_PlaceAndOrientContigs/not_used.nohaplotypes.txt",
+#    chr0 = "10_PlaceAndOrientContigs/chr0.nohaplotypes.bed",
+#    mapextra = "10_PlaceAndOrientContigs/map.nohaplotypes.extra.bed"
+#  message: "Recreating bedfile omitting haplotypes discovered from PlaceAndOrientContigs"
+#  params:
+#    chrom = lg
+#  shell:
+#    """
+#    cat {input.haplos} {input.haplos2} > {output.haplos}
+#    gunzip -fc {input.chain} | java -cp software/LepAnchor LiftoverHaplotypes map={input.intervals} haplotypes={output.haplos} chain=- > {output.lift}
+#    cat {output.lift} | sort -V -k 1,1 -k 2,2n > {output.sortedlift}
+#    java -cp software/LepAnchor CleanMap map={output.sortedlift} > {output.mapfile}
+#    java -cp software/LepAnchor Map2Bed map={output.mapfile} contigLength={input.lengths} > {output.bedfile}
+#    cut -f 1 {input.lengths} | grep -v -w -F -f <(cut -f 2 {output.haplos}; cut -f 1 {output.bedfile}) > {output.unused}
+#    grep -w -F -f {output.unused} {input.lengths} | awk -vn={params.chrom} '{{s=$1"\t1\t"$2"\t?\t"; for (i=1;i<=n;++i) print s i}}' > {output.chr0}
+#    cat {output.bedfile} {output.chr0} > {output.mapextra}
+#    """
+
+
+rule place_orient2:
+  input:
+    chain = "9_Chain/chainfile.gz",
+    bedfile = "10_PlaceAndOrientContigs/map.propogated.bed",
+    paf = paf,
+    prox = proximity,
+    lift = "10_PlaceAndOrientContigs/liftover.la",
+    chrom = "10_PlaceAndOrientContigs/orient_1/chr.{lg_range}.la"
+  output:
+    chrom = "10_PlaceAndOrientContigs/orient_2/chr.{lg_range}.la",
+    haplos = "10_PlaceAndOrientContigs/orient_2/haplotypes/chr.{lg_range}.haplo.suspected",
+    chromerr = report("10_PlaceAndOrientContigs/orient_2/logs/chr.{lg_range}.la.log", category = "Anchoring II Logs")
+  log:
+    haplos = "10_PlaceAndOrientContigs/orient_2/haplotypes/chr.{lg_range}.haplo.all",
+    errors = "10_PlaceAndOrientContigs/orient_2/errors/chr.{lg_range}.errors"
+  params:
+    chrom = "{lg_range}",
+    extras = place_orient_extra,
+    datatype = data_type,
+    haplo = haplo_limit
+  threads: 3
+  message: "Running 2nd round of PlaceAndOrientContigs for linkage group {params.chrom}"
+  shell:
+    """
+    gunzip -fc {input.chain} | java -cp software/LepAnchor PlaceAndOrientContigs numThreads={threads} $(awk -f software/LepAnchor/scripts/pickorientation.awk {input.chrom}) bed={input.bedfile} chromosome={params.chrom} map={input.lift} chain=- paf={input.paf} proximity={input.prox} {params.datatype} {params.extras} > {output.chrom} 2> {output.chromerr}
+    sort -n -r {output.chromrr} | awk '($NF=="haplotype" && (!(($5 SUBSEP $6 SUBSEP $7) in h))){{h[$2,$3,$4]; print}}' > {log.haplos}
+    sort -n -r {output.chromerr} | awk -vlimit={params.haplo} '($NF=="haplotype" && ($1>=($4-$3+1-limit)/limit) && (!(($5 SUBSEP $6 SUBSEP $7) in h))){{h[$2,$3,$4]; print}}'  > {output.haplos}  
+    grep "error$" {log.chromerr} > {log.errors}
+    """
+
+  rule propogate2:
+    input:
+      placed = expand("10_PlaceAndOrientContigs/orient_2/logs/chr.{lgs}.la.log", lgs = lg_range),
+      bedfile = "10_PlaceAndOrientContigs/map.propogated.bed"
+    output:
+      prop = expand("10_PlaceAndOrientContigs/propogate/propogated.{lgs}.la", lgs = range(lg + 1)),
+      propogated = "10_PlaceAndOrientContigs/map.propogated2.bed",
+      iter1 = temp("10_PlaceAndOrientContigs/tmp1.la"),
+      iter2 = temp("10_PlaceAndOrientContigs/tmp2.la")
+    message: "Second round of propogation"
+    shell:
+      """
+      awk -f software/LepAnchor/scripts/propagate.awk {input.placed} > 10_PlaceAndOrientContigs/tmp1.la
+      awk -f software/LepAnchor/scripts/propagate.awk 10_PlaceAndOrientContigs/tmp1.la > 10_PlaceAndOrientContigs/tmp2.la
+      i=2
+
+      while ! cmp -s "10_PlaceAndOrientContigs/tmp$i.la" "10_PlaceAndOrientContigs/tmp$(( $i-1 )).la" ;do
+        awk -f software/LepAnchor/scripts/propagate.awk 10_PlaceAndOrientContigs/tmp$i.la > 10_PlaceAndOrientContigs/tmp$[$i+1].la
+        i=$[$i+1]
+      done
+
+      #create prop*.la
+      awk -f software/LepAnchor/scripts/propagate2.awk tmp$i.la | awk '(/^[^#]/ && NF>=8){{++d[$1"\t"($7+0)"\t"($8+0)]; data[++line]=$0}}END{{for (i=1; i<=line; ++i) {{$0=data[i];if (d[$1"\t"($7+0)"\t"($8+0)] == 1) {{fn="10_PlaceAndOrientContigs/propogate/propogated."$5".la";print $0>fn}}}}}}'
+      awk '{{print $1"\t"($7+0)"\t"($8+0)"\t?\t"$5}}' {output.prop} | awk -f software/LepAnchor/scripts/pickbed.awk - {input.bedfile} > {output.propogated}
+      """
\ No newline at end of file
diff --git a/rules/LepAnchor/place_orient3.smk b/rules/LepAnchor/place_orient3.smk
new file mode 100644
index 0000000..2b05cfd
--- /dev/null
+++ b/rules/LepAnchor/place_orient3.smk
@@ -0,0 +1,50 @@
+rule place_orient3:
+  input:
+    chain = "9_Chain/chainfile.gz",
+    bedfile = "10_PlaceAndOrientContigs/map.propogated2.bed",
+    paf = paf,
+    prox = proximity,
+    lift = "10_PlaceAndOrientContigs/liftover.nohaplotypes.la",
+    chrom = "10_PlaceAndOrientContigs/orient_1/chr.{lg_range}.la",
+    propogated = "10_PlaceAndOrientContigs/propogate/propogated.{lg_range}.la"
+  output:
+    chrom = "10_PlaceAndOrientContigs/orient_3/chr.{lg_range}.la",
+    haplos = "10_PlaceAndOrientContigs/orient_3/haplotypes/chr.{lg_range}.haplo.suspected"
+  log:
+    chrom = report("10_PlaceAndOrientContigs/orient_3/logs/chr.{lg_range}.la.log", category = "Anchoring III Logs"),
+    haplos = "10_PlaceAndOrientContigs/orient_3/haplotypes/chr.{lg_range}.haplo.all",
+    errors = "10_PlaceAndOrientContigs/orient_3/errors/chr.{lg_range}.errors"
+  params:
+    chrom = "{lg_range}",
+    extras = place_orient_extra,
+    datatype = data_type,
+    haplo = haplo_limit
+  message: "Running 3rd round of PlaceAndOrientContigs for linkage group {params.chrom}"
+  threads: 3
+  shell:
+    """
+    gunzip -fc {input.chain} | java -cp software/LepAnchor PlaceAndOrientContigs numThreads={threads} $(awk -f software/LepAnchor/scripts/pickorientation.awk {input.chrom}) bed={input.bedfile} chromosome={params.chrom} map={input.lift} chain=- paf={input.paf} proximity={input.prox} evaluateAnchoring={input.propogated} improveAnchoring=1 {params.datatype} {params.extras} > {output.chrom} 2> {log.chrom}
+    sort -n -r {log.chrom} | awk '($NF=="haplotype" && (!(($5 SUBSEP $6 SUBSEP $7) in h))){{h[$2,$3,$4]; print}}' > {log.haplos}
+    sort -n -r {log.chrom} | awk -vlimit={params.haplo} '($NF=="haplotype" && ($1>=($4-$3+1-limit)/limit) && (!(($5 SUBSEP $6 SUBSEP $7) in h))){{h[$2,$3,$4]; print}}'  > {output.haplos}  
+    grep "error$" {log.chrom} > {log.errors}
+    """
+
+
+rule prune:
+  input: 
+    oriented = expand("10_PlaceAndOrientContigs/orient_3/chr.{lgs}.la", lgs = lg_range),
+    bedfile = "10_PlaceAndOrientContigs/map.propogated2.bed"
+  output: 
+    pruned = report("10_PlaceAndOrientContigs/orient_3/pruned.la", category = "Logs"),
+    cleaned = report("10_PlaceAndOrientContigs/overlaps_rm.la", category = "Logs")
+  message: "Pruning contig blocks without map support and removing overlaps"
+  params:
+    chrom = lg
+  shell:
+    """
+    for i in $(seq {params.chrom})
+    do
+      awk -f software/LepAnchor/scripts/prune.awk 10_PlaceAndOrientContigs/orient_3/ichr.$i.la > 10_PlaceAndOrientContigs/orient_3/ichr.${{i}}.pruned.la
+    done 2> {output.pruned}
+    awk -f software/LepAnchor/scripts/removeOverlaps.awk {input.bedfile} 10_PlaceAndOrientContigs/orient_3/ichr.*.pruned.la > {output.cleaned}
+    """
\ No newline at end of file
diff --git a/rules/LepAnchor/place_orient_ii.smk b/rules/LepAnchor/place_orient_ii.smk
deleted file mode 100644
index 4bbb5f6..0000000
--- a/rules/LepAnchor/place_orient_ii.smk
+++ /dev/null
@@ -1,60 +0,0 @@
-rule liftover2:
-  input:
-    chain = "9_Chain/chainfile.gz",
-    intervals = "10_PlaceAndOrientContigs/lepanchor.input",
-    haplos = "10_PlaceAndOrientContigs/suspected.haplotypes.before",
-    haplos2 = "10_PlaceAndOrientContigs/suspected.haplotypes.after",
-    lengths = "10_PlaceAndOrientContigs/contigs.length"
-  output:
-    haplos = "10_PlaceAndOrientContigs/suspected.haplotypes.all",
-    lift = report("10_PlaceAndOrientContigs/liftover.nohaplotypes.la", category = "Lifted Intervals"),
-    sortedlift = report("10_PlaceAndOrientContigs/liftover.sorted.nohaplotypes.la", category = "Lifted Intervals"),
-    mapfile = "10_PlaceAndOrientContigs/map.nohaplotypes.clean",
-    bedfile = "10_PlaceAndOrientContigs/map.nohaplotypes.bed",
-    unused = "10_PlaceAndOrientContigs/not_used.nohaplotypes.txt",
-    chr0 = "10_PlaceAndOrientContigs/chr0.nohaplotypes.bed",
-    mapextra = "10_PlaceAndOrientContigs/map.nohaplotypes.extra.bed"
-  message: "Recreating bedfile omitting haplotypes discovered from PlaceAndOrientContigs"
-  params:
-    chrom = lg
-  shell:
-    """
-    cat {input.haplos} {input.haplos2} > {output.haplos}
-    gunzip -fc {input.chain} | java -cp software/LepAnchor LiftoverHaplotypes map={input.intervals} haplotypes={output.haplos} chain=- > {output.lift}
-    cat {output.lift} | sort -V -k 1,1 -k 2,2n > {output.sortedlift}
-    java -cp software/LepAnchor CleanMap map={output.sortedlift} > {output.mapfile}
-    java -cp software/LepAnchor Map2Bed map={output.mapfile} contigLength={input.lengths} > {output.bedfile}
-    cut -f 1 {input.lengths} | grep -v -w -F -f <(cut -f 2 {output.haplos}; cut -f 1 {output.bedfile}) > {output.unused}
-    grep -w -F -f {output.unused} {input.lengths} | awk -vn={params.chrom} '{{s=$1"\t1\t"$2"\t?\t"; for (i=1;i<=n;++i) print s i}}' > {output.chr0}
-    cat {output.bedfile} {output.chr0} > {output.mapextra}
-    """
-
-
-rule place_orient2:
-  input:
-    chain = "9_Chain/chainfile.gz",
-    bedfile = "10_PlaceAndOrientContigs/map.nohaplotypes.extra.bed",
-    paf = paf,
-    prox = proximity,
-    lift = "10_PlaceAndOrientContigs/liftover.nohaplotypes.la"
-  output:
-    chrom = "10_PlaceAndOrientContigs/orient_2/chr.{lg_range}.la",
-    haplos = "10_PlaceAndOrientContigs/orient_2/haplotypes/chr.{lg_range}.haplo.suspected"
-  log:
-    chrom = report("10_PlaceAndOrientContigs/orient_2/logs/chr.{lg_range}.la.log", category = "Anchoring II Logs"),
-    haplos = "10_PlaceAndOrientContigs/orient_2/haplotypes/chr.{lg_range}.haplo.all",
-    errors = "10_PlaceAndOrientContigs/orient_2/errors/chr.{lg_range}.errors"
-  params:
-    chrom = "{lg_range}",
-    extras = place_orient_extra,
-    datatype = data_type,
-    haplo = haplo_limit
-  threads: 3
-  message: "Running 2nd round of PlaceAndOrientContigs for linkage group {params.chrom}"
-  shell:
-    """
-    gunzip -fc {input.chain} | java -cp software/LepAnchor PlaceAndOrientContigs numThreads={threads} bed={input.bedfile} chromosome={params.chrom} map={input.lift} chain=- paf={input.paf} proximity={input.prox} {params.datatype} {params.extras} > {output.chrom} 2> {log.chrom}
-    sort -n -r {log.chrom} | awk '($NF=="haplotype" && (!(($5 SUBSEP $6 SUBSEP $7) in h))){{h[$2,$3,$4]; print}}' > {log.haplos}
-    sort -n -r {log.chrom} | awk -vlimit={params.haplo} '($NF=="haplotype" && ($1>=($4-$3+1-limit)/limit) && (!(($5 SUBSEP $6 SUBSEP $7) in h))){{h[$2,$3,$4]; print}}'  > {output.haplos}  
-    grep "error$" {log.chrom} > {log.errors}
-    """
\ No newline at end of file
diff --git a/rules/LepAnchor/place_orient_iii.smk b/rules/LepAnchor/place_orient_iii.smk
deleted file mode 100644
index 5938a5e..0000000
--- a/rules/LepAnchor/place_orient_iii.smk
+++ /dev/null
@@ -1,74 +0,0 @@
-rule propogate:
-  input: 
-    placed = expand("10_PlaceAndOrientContigs/orient_2/chr.{lgs}.la", lgs = lg_range),
-    bedfile = "10_PlaceAndOrientContigs/map.nohaplotypes.bed"
-  output:
-    propogated = "10_PlaceAndOrientContigs/map.propogated.bed",
-    tmp_prop = temp(expand("10_PlaceAndOrientContigs/propogate/propogated.{lgs}.la", lgs = range(lg + 1))),
-  message: "Propogating ...something"
-  shell:
-    """
-    awk -f software/LepAnchor/scripts/propagate.awk {input.placed} > 10_PlaceAndOrientContigs/tmp1.la
-    awk -f software/LepAnchor/scripts/propagate.awk 10_PlaceAndOrientContigs/tmp1.la > 10_PlaceAndOrientContigs/tmp2.la
-    i=2
-
-    while ! cmp -s "10_PlaceAndOrientContigs/tmp$i.la" "10_PlaceAndOrientContigs/tmp$(( $i-1 )).la" ;do
-	    awk -f software/LepAnchor/scripts/propagate.awk 10_PlaceAndOrientContigs/tmp$i.la > 10_PlaceAndOrientContigs/tmp$[$i+1].la
-	    i=$[$i+1]
-    done
-    #create prop*.la
-    awk '/^[^#]/{{++d[$1 "\t" $7+0 "\t" $8+0]; data[++line]=$0}}END{{for (i = 1; i <= line; ++i) {{$0=data[i];if (d[$1 "\t" $7+0 "\t" $8+0] == 1) fn="10_PlaceAndOrientContigs/propogate/propogated."$5".la"; else if ($5==1) fn="10_PlaceAndOrientContigs/propogate/propogated.0.la"; else fn=""; if (fn != "") print $0>fn}}}}' 10_PlaceAndOrientContigs/tmp$i.la
-
-    #create a new bed by combining propogated.[1-9]*.la and map.nohaplotypes.bed
-    awk '(NR==FNR){{print;c[$1]}}(NR!=FNR && !($1 in c)){{print $1 "\t" $7+0 "\t" $8+0"\t?\t"$5}}' {input.bedfile} {output.tmp_prop} > {output.propogated}
-    rm 10_PlaceAndOrientContigs/tmp*.la
-    """
-
-
-rule place_orient3:
-  input:
-    chain = "9_Chain/chainfile.gz",
-    bedfile = "10_PlaceAndOrientContigs/map.propogated.bed",
-    paf = paf,
-    prox = proximity,
-    lift = "10_PlaceAndOrientContigs/liftover.nohaplotypes.la"
-  output:
-    chrom = "10_PlaceAndOrientContigs/orient_3/ichr.{lg_range}.la",
-    haplos = "10_PlaceAndOrientContigs/orient_3/haplotypes/chr.{lg_range}.haplo.suspected"
-  log:
-    chrom = report("10_PlaceAndOrientContigs/orient_3/logs/ichr.{lg_range}.la.log", category = "Anchoring III Logs"),
-    haplos = "10_PlaceAndOrientContigs/orient_3/haplotypes/chr.{lg_range}.haplo.all",
-    errors = "10_PlaceAndOrientContigs/orient_3/errors/chr.{lg_range}.errors"
-  params:
-    chrom = "{lg_range}",
-    extras = place_orient_extra,
-    datatype = data_type,
-    haplo = haplo_limit
-  message: "Running 3rd round of PlaceAndOrientContigs for linkage group {params.chrom}"
-  shell:
-    """
-    gunzip -fc {input.chain} | java -cp software/LepAnchor PlaceAndOrientContigs bed={input.bedfile} chromosome={params.chrom} map={input.lift} chain=- paf={input.paf} proximity={input.prox} {params.datatype} {params.extras} > {output.chrom} 2> {log.chrom}
-    sort -n -r {log.chrom} | awk '($NF=="haplotype" && (!(($5 SUBSEP $6 SUBSEP $7) in h))){{h[$2,$3,$4]; print}}' > {log.haplos}
-    sort -n -r {log.chrom} | awk -vlimit={params.haplo} '($NF=="haplotype" && ($1>=($4-$3+1-limit)/limit) && (!(($5 SUBSEP $6 SUBSEP $7) in h))){{h[$2,$3,$4]; print}}'  > {output.haplos}  
-    grep "error$" {log.chrom} > {log.errors}
-    """
-
-
-rule prune:
-  input: 
-    oriented = expand("10_PlaceAndOrientContigs/orient_3/ichr.{lgs}.la", lgs = lg_range),
-    bedfile = "10_PlaceAndOrientContigs/map.propogated.bed"
-  output: 
-    pruned = report("10_PlaceAndOrientContigs/orient_3/pruned.la", category = "Logs"),
-    cleaned = report("10_PlaceAndOrientContigs/overlaps_rm.la", category = "Logs")
-  message: "Pruning contig blocks without map support and removing overlaps"
-  params:
-    chrom = lg
-  shell:
-    """
-    for i in $(seq {params.chrom})
-    do
-      awk -f software/LepAnchor/scripts/prune.awk 10_PlaceAndOrientContigs/orient_3/ichr.$i.la > 10_PlaceAndOrientContigs/orient_3/ichr.${{i}}.pruned.la
-    done 2> {output.pruned}
-    awk -f software/LepAnchor/scripts/removeOverlaps.awk {input.bedfile} 10_PlaceAndOrientContigs/orient_3/ichr.*.pruned.la > {output.cleaned}
-    """
\ No newline at end of file

From 9b76a78b41288a9f290c5a1f9e6a38d318824603 Mon Sep 17 00:00:00 2001
From: Pavel Dimens <pdimens@live.com>
Date: Wed, 2 Feb 2022 16:58:44 -0500
Subject: [PATCH 04/46] finish updaing placeorient

---
 rules/LepAnchor/build_agp.smk     |  6 +++---
 rules/LepAnchor/place_orient2.smk | 32 -------------------------------
 rules/LepAnchor/place_orient3.smk |  2 +-
 3 files changed, 4 insertions(+), 36 deletions(-)

diff --git a/rules/LepAnchor/build_agp.smk b/rules/LepAnchor/build_agp.smk
index a3f19bc..a277777 100644
--- a/rules/LepAnchor/build_agp.smk
+++ b/rules/LepAnchor/build_agp.smk
@@ -1,6 +1,6 @@
 rule construct_agp:
   input:
-    cleaned = "10_PlaceAndOrientContigs/overlaps_rm.la"
+    cleaned = "10_PlaceAndOrientContigs/overlaps.removed.la"
   output:
     agp = report("11_AGP/contigs/chr.{lg_range}.agp", category = "Contig AGP Files"),
     scaff_agp = report("11_AGP/scaffolds/chr.{lg_range}.scaffolds.agp", category = "Scaffold AGP Files")
@@ -18,14 +18,14 @@ rule unused:
   input:
     lengths = "10_PlaceAndOrientContigs/contigs.length",
     haplos = "10_PlaceAndOrientContigs/suspected.haplotypes.before",
-    agp = expand("11_AGP/contigs/chr.{lgs}.agp", lgs = lg_range),
+    cleaned = "10_PlaceAndOrientContigs/overlaps.removed.la",
   output: 
     txt = "11_AGP/not_used_final.txt",
     agp = "11_AGP/not_used.agp"
   message: "Finding unused contigs"
   shell:
     """
-    cut -f 1 {input.lengths} | grep -v -w -F -f <(cut -f 2 {input.haplos};awk '($5!="U"){{print $6}}' {input.agp}) > {output.txt}
+    cut -f 1 {input.lengths} | grep -v -w -F -f <(cut -f2 {input.haplos}; cut -f1 {input.cleaned}) > {output.txt}
     grep -F -w -f {output.txt} {input.lengths} | awk '{{print $1,1,$2,1,"W",$1,1,$2,"+"}}' > {output.agp}
     """
 
diff --git a/rules/LepAnchor/place_orient2.smk b/rules/LepAnchor/place_orient2.smk
index 3dc38ec..6137323 100644
--- a/rules/LepAnchor/place_orient2.smk
+++ b/rules/LepAnchor/place_orient2.smk
@@ -1,35 +1,3 @@
-#rule liftover2:
-#  input:
-#    chain = "9_Chain/chainfile.gz",
-#    intervals = "10_PlaceAndOrientContigs/lepanchor.input",
-#    haplos = "10_PlaceAndOrientContigs/suspected.haplotypes.before",
-#    haplos2 = "10_PlaceAndOrientContigs/suspected.haplotypes.after",
-#    lengths = "10_PlaceAndOrientContigs/contigs.length"
-#  output:
-#    haplos = "10_PlaceAndOrientContigs/suspected.haplotypes.all",
-#    lift = report("10_PlaceAndOrientContigs/liftover.nohaplotypes.la", category = "Lifted Intervals"),
-#    sortedlift = report("10_PlaceAndOrientContigs/liftover.sorted.nohaplotypes.la", category = "Lifted Intervals"),
-#    mapfile = "10_PlaceAndOrientContigs/map.nohaplotypes.clean",
-#    bedfile = "10_PlaceAndOrientContigs/map.nohaplotypes.bed",
-#    unused = "10_PlaceAndOrientContigs/not_used.nohaplotypes.txt",
-#    chr0 = "10_PlaceAndOrientContigs/chr0.nohaplotypes.bed",
-#    mapextra = "10_PlaceAndOrientContigs/map.nohaplotypes.extra.bed"
-#  message: "Recreating bedfile omitting haplotypes discovered from PlaceAndOrientContigs"
-#  params:
-#    chrom = lg
-#  shell:
-#    """
-#    cat {input.haplos} {input.haplos2} > {output.haplos}
-#    gunzip -fc {input.chain} | java -cp software/LepAnchor LiftoverHaplotypes map={input.intervals} haplotypes={output.haplos} chain=- > {output.lift}
-#    cat {output.lift} | sort -V -k 1,1 -k 2,2n > {output.sortedlift}
-#    java -cp software/LepAnchor CleanMap map={output.sortedlift} > {output.mapfile}
-#    java -cp software/LepAnchor Map2Bed map={output.mapfile} contigLength={input.lengths} > {output.bedfile}
-#    cut -f 1 {input.lengths} | grep -v -w -F -f <(cut -f 2 {output.haplos}; cut -f 1 {output.bedfile}) > {output.unused}
-#    grep -w -F -f {output.unused} {input.lengths} | awk -vn={params.chrom} '{{s=$1"\t1\t"$2"\t?\t"; for (i=1;i<=n;++i) print s i}}' > {output.chr0}
-#    cat {output.bedfile} {output.chr0} > {output.mapextra}
-#    """
-
-
 rule place_orient2:
   input:
     chain = "9_Chain/chainfile.gz",
diff --git a/rules/LepAnchor/place_orient3.smk b/rules/LepAnchor/place_orient3.smk
index 2b05cfd..a8776f8 100644
--- a/rules/LepAnchor/place_orient3.smk
+++ b/rules/LepAnchor/place_orient3.smk
@@ -36,7 +36,7 @@ rule prune:
     bedfile = "10_PlaceAndOrientContigs/map.propogated2.bed"
   output: 
     pruned = report("10_PlaceAndOrientContigs/orient_3/pruned.la", category = "Logs"),
-    cleaned = report("10_PlaceAndOrientContigs/overlaps_rm.la", category = "Logs")
+    cleaned = report("10_PlaceAndOrientContigs/overlaps.removed.la", category = "Logs")
   message: "Pruning contig blocks without map support and removing overlaps"
   params:
     chrom = lg

From 5c2c92c417e135f1fdc5b38e5f1a84f8bd687110 Mon Sep 17 00:00:00 2001
From: "Pavel V. Dimens" <pdimens@live.com>
Date: Wed, 2 Feb 2022 19:08:25 -0500
Subject: [PATCH 05/46] Update LepWrap

---
 LepWrap | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/LepWrap b/LepWrap
index 4561ff7..8443514 100755
--- a/LepWrap
+++ b/LepWrap
@@ -1,4 +1,4 @@
-LepWrap#! /usr/bin/env bash
+#! /usr/bin/env bash
 
 if which snakemake &>/dev/null; then
   foo=1
@@ -227,4 +227,4 @@ if [ $LA == "true" ]; then
   lepanchor $1 $CONF
 else
   echo "Skipping LepAnchor"
-fi
\ No newline at end of file
+fi

From caa87ffda4673b2175d0ed5d211f649d468e7d9e Mon Sep 17 00:00:00 2001
From: Pavel Dimens <pdimens@live.com>
Date: Thu, 3 Feb 2022 20:02:16 -0500
Subject: [PATCH 06/46] updates to fit LA updates

---
 rules/LepAnchor/LepAnchor.smk     |  1 +
 rules/LepAnchor/build_agp.smk     |  2 +-
 rules/LepAnchor/place_orient2.smk | 57 ++++++++++++--------------
 rules/LepAnchor/place_orient3.smk | 68 ++++++++++++++++++-------------
 rules/LepAnchor/place_orient4.smk | 49 ++++++++++++++++++++++
 5 files changed, 115 insertions(+), 62 deletions(-)
 create mode 100644 rules/LepAnchor/place_orient4.smk

diff --git a/rules/LepAnchor/LepAnchor.smk b/rules/LepAnchor/LepAnchor.smk
index 62502be..e15c3fe 100644
--- a/rules/LepAnchor/LepAnchor.smk
+++ b/rules/LepAnchor/LepAnchor.smk
@@ -24,6 +24,7 @@ include: "mask_and_chain.smk"
 include: "place_orient1.smk"
 include: "place_orient2.smk"
 include: "place_orient3.smk"
+include: "place_orient4.smk"
 include: "build_agp.smk"
 include: "build_fasta.smk"
 include: "mareymaps_untrimmed.smk"
diff --git a/rules/LepAnchor/build_agp.smk b/rules/LepAnchor/build_agp.smk
index a277777..125850f 100644
--- a/rules/LepAnchor/build_agp.smk
+++ b/rules/LepAnchor/build_agp.smk
@@ -17,7 +17,7 @@ rule construct_agp:
 rule unused:
   input:
     lengths = "10_PlaceAndOrientContigs/contigs.length",
-    haplos = "10_PlaceAndOrientContigs/suspected.haplotypes.before",
+    haplos = "10_PlaceAndOrientContigs/fullHaplotypes50.txt",
     cleaned = "10_PlaceAndOrientContigs/overlaps.removed.la",
   output: 
     txt = "11_AGP/not_used_final.txt",
diff --git a/rules/LepAnchor/place_orient2.smk b/rules/LepAnchor/place_orient2.smk
index 6137323..44cd219 100644
--- a/rules/LepAnchor/place_orient2.smk
+++ b/rules/LepAnchor/place_orient2.smk
@@ -8,48 +8,41 @@ rule place_orient2:
     chrom = "10_PlaceAndOrientContigs/orient_1/chr.{lg_range}.la"
   output:
     chrom = "10_PlaceAndOrientContigs/orient_2/chr.{lg_range}.la",
-    haplos = "10_PlaceAndOrientContigs/orient_2/haplotypes/chr.{lg_range}.haplo.suspected",
-    chromerr = report("10_PlaceAndOrientContigs/orient_2/logs/chr.{lg_range}.la.log", category = "Anchoring II Logs")
-  log:
-    haplos = "10_PlaceAndOrientContigs/orient_2/haplotypes/chr.{lg_range}.haplo.all",
-    errors = "10_PlaceAndOrientContigs/orient_2/errors/chr.{lg_range}.errors"
+    chromerr = "10_PlaceAndOrientContigs/orient_2/logs/chr.{lg_range}.err"
   params:
     chrom = "{lg_range}",
     extras = place_orient_extra,
     datatype = data_type,
     haplo = haplo_limit
-  threads: 3
+  threads: 5
   message: "Running 2nd round of PlaceAndOrientContigs for linkage group {params.chrom}"
   shell:
     """
     gunzip -fc {input.chain} | java -cp software/LepAnchor PlaceAndOrientContigs numThreads={threads} $(awk -f software/LepAnchor/scripts/pickorientation.awk {input.chrom}) bed={input.bedfile} chromosome={params.chrom} map={input.lift} chain=- paf={input.paf} proximity={input.prox} {params.datatype} {params.extras} > {output.chrom} 2> {output.chromerr}
-    sort -n -r {output.chromrr} | awk '($NF=="haplotype" && (!(($5 SUBSEP $6 SUBSEP $7) in h))){{h[$2,$3,$4]; print}}' > {log.haplos}
-    sort -n -r {output.chromerr} | awk -vlimit={params.haplo} '($NF=="haplotype" && ($1>=($4-$3+1-limit)/limit) && (!(($5 SUBSEP $6 SUBSEP $7) in h))){{h[$2,$3,$4]; print}}'  > {output.haplos}  
-    grep "error$" {log.chromerr} > {log.errors}
     """
 
-  rule propogate2:
-    input:
-      placed = expand("10_PlaceAndOrientContigs/orient_2/logs/chr.{lgs}.la.log", lgs = lg_range),
-      bedfile = "10_PlaceAndOrientContigs/map.propogated.bed"
-    output:
-      prop = expand("10_PlaceAndOrientContigs/propogate/propogated.{lgs}.la", lgs = range(lg + 1)),
-      propogated = "10_PlaceAndOrientContigs/map.propogated2.bed",
-      iter1 = temp("10_PlaceAndOrientContigs/tmp1.la"),
-      iter2 = temp("10_PlaceAndOrientContigs/tmp2.la")
-    message: "Second round of propogation"
-    shell:
-      """
-      awk -f software/LepAnchor/scripts/propagate.awk {input.placed} > 10_PlaceAndOrientContigs/tmp1.la
-      awk -f software/LepAnchor/scripts/propagate.awk 10_PlaceAndOrientContigs/tmp1.la > 10_PlaceAndOrientContigs/tmp2.la
-      i=2
+rule propogate2:
+  input:
+    placed = expand("10_PlaceAndOrientContigs/orient_2/logs/chr.{lgs}.err", lgs = lg_range),
+    bedfile = "10_PlaceAndOrientContigs/map.propogated.bed"
+  output:
+    prop = expand("10_PlaceAndOrientContigs/propogate/propogated.{lgs}.la", lgs = range(lg + 1)),
+    propogated = "10_PlaceAndOrientContigs/map.propogated2.bed",
+    iter1 = temp("10_PlaceAndOrientContigs/tmp1.la"),
+    iter2 = temp("10_PlaceAndOrientContigs/tmp2.la")
+  message: "Second round of propogation"
+  shell:
+    """
+    awk -f software/LepAnchor/scripts/propagate.awk {input.placed} > 10_PlaceAndOrientContigs/tmp1.la
+    awk -f software/LepAnchor/scripts/propagate.awk 10_PlaceAndOrientContigs/tmp1.la > 10_PlaceAndOrientContigs/tmp2.la
+    i=2
 
-      while ! cmp -s "10_PlaceAndOrientContigs/tmp$i.la" "10_PlaceAndOrientContigs/tmp$(( $i-1 )).la" ;do
-        awk -f software/LepAnchor/scripts/propagate.awk 10_PlaceAndOrientContigs/tmp$i.la > 10_PlaceAndOrientContigs/tmp$[$i+1].la
-        i=$[$i+1]
-      done
+    while ! cmp -s "10_PlaceAndOrientContigs/tmp$i.la" "10_PlaceAndOrientContigs/tmp$(( $i-1 )).la" ;do
+      awk -f software/LepAnchor/scripts/propagate.awk 10_PlaceAndOrientContigs/tmp$i.la > 10_PlaceAndOrientContigs/tmp$[$i+1].la
+      i=$[$i+1]
+    done
 
-      #create prop*.la
-      awk -f software/LepAnchor/scripts/propagate2.awk tmp$i.la | awk '(/^[^#]/ && NF>=8){{++d[$1"\t"($7+0)"\t"($8+0)]; data[++line]=$0}}END{{for (i=1; i<=line; ++i) {{$0=data[i];if (d[$1"\t"($7+0)"\t"($8+0)] == 1) {{fn="10_PlaceAndOrientContigs/propogate/propogated."$5".la";print $0>fn}}}}}}'
-      awk '{{print $1"\t"($7+0)"\t"($8+0)"\t?\t"$5}}' {output.prop} | awk -f software/LepAnchor/scripts/pickbed.awk - {input.bedfile} > {output.propogated}
-      """
\ No newline at end of file
+    #create prop*.la
+    awk -f software/LepAnchor/scripts/propagate2.awk tmp$i.la | awk '(/^[^#]/ && NF>=8){{++d[$1"\t"($7+0)"\t"($8+0)]; data[++line]=$0}}END{{for (i=1; i<=line; ++i) {{$0=data[i];if (d[$1"\t"($7+0)"\t"($8+0)] == 1) {{fn="10_PlaceAndOrientContigs/propogate/propogated."$5".la";print $0>fn}}}}}}'
+    awk '{{print $1"\t"($7+0)"\t"($8+0)"\t?\t"$5}}' {output.prop} | awk -f software/LepAnchor/scripts/pickbed.awk - {input.bedfile} > {output.propogated}
+    """
\ No newline at end of file
diff --git a/rules/LepAnchor/place_orient3.smk b/rules/LepAnchor/place_orient3.smk
index a8776f8..26bf843 100644
--- a/rules/LepAnchor/place_orient3.smk
+++ b/rules/LepAnchor/place_orient3.smk
@@ -4,47 +4,57 @@ rule place_orient3:
     bedfile = "10_PlaceAndOrientContigs/map.propogated2.bed",
     paf = paf,
     prox = proximity,
-    lift = "10_PlaceAndOrientContigs/liftover.nohaplotypes.la",
+    lift = "10_PlaceAndOrientContigs/liftover.la",
     chrom = "10_PlaceAndOrientContigs/orient_1/chr.{lg_range}.la",
     propogated = "10_PlaceAndOrientContigs/propogate/propogated.{lg_range}.la"
   output:
     chrom = "10_PlaceAndOrientContigs/orient_3/chr.{lg_range}.la",
-    haplos = "10_PlaceAndOrientContigs/orient_3/haplotypes/chr.{lg_range}.haplo.suspected"
-  log:
-    chrom = report("10_PlaceAndOrientContigs/orient_3/logs/chr.{lg_range}.la.log", category = "Anchoring III Logs"),
-    haplos = "10_PlaceAndOrientContigs/orient_3/haplotypes/chr.{lg_range}.haplo.all",
-    errors = "10_PlaceAndOrientContigs/orient_3/errors/chr.{lg_range}.errors"
+    errors = "10_PlaceAndOrientContigs/orient_3/errors/chr.{lg_range}.err"
   params:
     chrom = "{lg_range}",
     extras = place_orient_extra,
     datatype = data_type,
-    haplo = haplo_limit
   message: "Running 3rd round of PlaceAndOrientContigs for linkage group {params.chrom}"
-  threads: 3
+  threads: 5
   shell:
     """
-    gunzip -fc {input.chain} | java -cp software/LepAnchor PlaceAndOrientContigs numThreads={threads} $(awk -f software/LepAnchor/scripts/pickorientation.awk {input.chrom}) bed={input.bedfile} chromosome={params.chrom} map={input.lift} chain=- paf={input.paf} proximity={input.prox} evaluateAnchoring={input.propogated} improveAnchoring=1 {params.datatype} {params.extras} > {output.chrom} 2> {log.chrom}
-    sort -n -r {log.chrom} | awk '($NF=="haplotype" && (!(($5 SUBSEP $6 SUBSEP $7) in h))){{h[$2,$3,$4]; print}}' > {log.haplos}
-    sort -n -r {log.chrom} | awk -vlimit={params.haplo} '($NF=="haplotype" && ($1>=($4-$3+1-limit)/limit) && (!(($5 SUBSEP $6 SUBSEP $7) in h))){{h[$2,$3,$4]; print}}'  > {output.haplos}  
-    grep "error$" {log.chrom} > {log.errors}
+    gunzip -fc {input.chain} | java -cp software/LepAnchor PlaceAndOrientContigs numThreads={threads} $(awk -f software/LepAnchor/scripts/pickorientation.awk {input.chrom}) bed={input.bedfile} chromosome={params.chrom} map={input.lift} chain=- paf={input.paf} proximity={input.prox} evaluateAnchoring={input.propogated} improveAnchoring=1 {params.datatype} {params.extras} > {output.chrom} 2> {output.errors}
     """
-
-
-rule prune:
-  input: 
-    oriented = expand("10_PlaceAndOrientContigs/orient_3/chr.{lgs}.la", lgs = lg_range),
-    bedfile = "10_PlaceAndOrientContigs/map.propogated2.bed"
-  output: 
-    pruned = report("10_PlaceAndOrientContigs/orient_3/pruned.la", category = "Logs"),
-    cleaned = report("10_PlaceAndOrientContigs/overlaps.removed.la", category = "Logs")
-  message: "Pruning contig blocks without map support and removing overlaps"
+    
+rule findhaplotypes:
+  input:
+    errors = expand("10_PlaceAndOrientContigs/orient_3/errors/chr.{lgs}.err", lgs = lg_range)
+  output:
+    haplos = "10_PlaceAndOrientContigs/fullHaplotypes50.txt"
+  message: "Finding full haplotypes"
   params:
-    chrom = lg
+    haplo = haplo_limit
   shell:
     """
-    for i in $(seq {params.chrom})
-    do
-      awk -f software/LepAnchor/scripts/prune.awk 10_PlaceAndOrientContigs/orient_3/ichr.$i.la > 10_PlaceAndOrientContigs/orient_3/ichr.${{i}}.pruned.la
-    done 2> {output.pruned}
-    awk -f software/LepAnchor/scripts/removeOverlaps.awk {input.bedfile} 10_PlaceAndOrientContigs/orient_3/ichr.*.pruned.la > {output.cleaned}
-    """
\ No newline at end of file
+    awk '($NF=="haplotype")' {input.errors} | 
+      sort -n -r | 
+      awk -vlimit={params.haplo} '($NF=="haplotype" && ($1>=($4-$3+1-limit)/limit) && (!(($5 SUBSEP $6 SUBSEP $7) in h))){{h[$2,$3,$4]; print}}' > {output.haplos}
+    """
+
+rule liftoverHaplotypes:
+  input:
+    chain = "9_Chain/chainfile.gz",
+    chrom = "10_PlaceAndOrientContigs/orient_1/chr.{lg_range}.la",
+    haplos = "10_PlaceAndOrientContigs/fullHaplotypes50.txt"
+  output: "10_PlaceAndOrientContigs/liftover/chr.{lg_range}.liftover"
+  message: "Running liftoverHaplotypes for {input.chrom}"
+  threads: 1
+  shell:
+    """
+    gunzip -fc {input.chain} | java -cp software/LepAnchor LiftoverHaplotypes map={input.chrom} haplotypes={input.haplos} chain=- > $i.liftover
+    """
+
+rule removehaplotypes:
+  input:
+    mapfile = "10_PlaceAndOrientContigs/map.propogated2.bed", 
+    haplos = "10_PlaceAndOrientContigs/fullHaplotypes50.txt"
+  output:
+    bedfile = "10_PlaceAndOrientContigs/map.propogated2.nohaplo.bed"
+  message: "Removing haplotypes from the map"
+  threads: 1
+  shell: "awk -f software/LepAnchor/scripts/removeHaplotypes.awk {input} > {output}"
diff --git a/rules/LepAnchor/place_orient4.smk b/rules/LepAnchor/place_orient4.smk
new file mode 100644
index 0000000..6c46ec1
--- /dev/null
+++ b/rules/LepAnchor/place_orient4.smk
@@ -0,0 +1,49 @@
+rule place_orient4:
+    input:
+        chain = "9_Chain/chainfile.gz",
+        bedfile = "10_PlaceAndOrientContigs/map.propogated2.nohaplo.bed",
+        paf = paf,
+        prox = proximity,
+        lift = "10_PlaceAndOrientContigs/liftover.la",
+        chrom = "10_PlaceAndOrientContigs/orient_1/chr.{lg_range}.la",
+        chromlast = "10_PlaceAndOrientContigs/orient_3/chr.{lg_range}.la",
+        liftover = expand("10_PlaceAndOrientContigs/liftover/chr.{lgs}.liftover", lgs = lg_range)
+    output:
+        chrom = "10_PlaceAndOrientContigs/orient_4/chr.{lg_range}.la",
+        err = "10_PlaceAndOrientContigs/orient_4/errors/chr.{lg_range}.errors"
+    message: "Running 4th round of PlaceAndOrientContigs for linkage group {params.chrom}"
+    params:
+        chrom = "{lg_range}",
+        extras = place_orient_extra,
+        datatype = data_type,
+    threads: 5
+    shell:
+        """
+        gunzip -fc {input.chain} | java -cp software/LepAnchor PlaceAndOrientContigs numThreads={threads} $(awk -f software/LepAnchor/scripts/pickorientation.awk {input.chrom}) bed={input.bedfile} chromosome={params.chrom} map=$MAPL chain=- paf={input.paf} proximity={input.prox} {params.datatype} {params.extras} keepEmptyIntervals=1 evaluateAnchoring={input.chromlast} improveAnchoring=1 > {output.chrom} 2> {output.err}
+        """
+
+rule prune_contigblocks:
+    input: "10_PlaceAndOrientContigs/orient_4/chr.{lg_range}.la"
+    output: 
+        chrom = "10_PlaceAndOrientContigs/pruned/chr.{lg_range}.pruned.la",
+        err = temp("10_PlaceAndOrientContigs/pruned/err/chr.{lg_range}.pruned.err")
+    message: "Pruning contig blocks without map support and removing overlaps"
+    params:
+        chrom = lg
+    shell: "awk -f software/LepAnchor/scripts/prune.awk {input} > {output.chrom} 2> {output.err}"
+
+rule prune_post:
+    input:
+        bedfile = "10_PlaceAndOrientContigs/map.propogated2.bed",
+        prunedchrom = expand("10_PlaceAndOrientContigs/pruned/chr.{lgs}.pruned.la", lgs = lg_range),
+        prunederr = expand("10_PlaceAndOrientContigs/pruned/err/chr.{lgs}.pruned.err", lgs = lg_range)
+    output: 
+        overlaps = "10_PlaceAndOrientContigs/overlaps.removed.la",
+        pruned = "10_PlaceAndOrientContigs/pruned.la"
+    message: "Removing overlaps"
+    threads: 1
+    shell:
+        """
+        cat {input.prunederr} > {output.pruned}
+        awk -f software/LepAnchor/scripts/removeOverlaps.awk {input.bedfile} {input.prunedchrom} > {output.overlaps}
+        """
\ No newline at end of file

From 0649e73daafa654a4d01b2f61f2c4c68ae61f121 Mon Sep 17 00:00:00 2001
From: Pavel Dimens <pdimens@live.com>
Date: Thu, 3 Feb 2022 20:12:57 -0500
Subject: [PATCH 07/46] fix shebang

---
 LepWrap | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/LepWrap b/LepWrap
index 4561ff7..8443514 100755
--- a/LepWrap
+++ b/LepWrap
@@ -1,4 +1,4 @@
-LepWrap#! /usr/bin/env bash
+#! /usr/bin/env bash
 
 if which snakemake &>/dev/null; then
   foo=1
@@ -227,4 +227,4 @@ if [ $LA == "true" ]; then
   lepanchor $1 $CONF
 else
   echo "Skipping LepAnchor"
-fi
\ No newline at end of file
+fi

From 70e91a34b384b980e94d805ce59f87749532c740 Mon Sep 17 00:00:00 2001
From: Pavel Dimens <pdimens@live.com>
Date: Thu, 3 Feb 2022 20:28:03 -0500
Subject: [PATCH 08/46] update i/o names

---
 rules/LepAnchor/build_agp.smk       |  2 +-
 rules/LepAnchor/generate_inputs.smk |  6 +++---
 rules/LepAnchor/mask_and_chain.smk  | 17 ++++++++---------
 rules/LepAnchor/place_orient3.smk   |  8 ++++----
 4 files changed, 16 insertions(+), 17 deletions(-)

diff --git a/rules/LepAnchor/build_agp.smk b/rules/LepAnchor/build_agp.smk
index 125850f..eb51e42 100644
--- a/rules/LepAnchor/build_agp.smk
+++ b/rules/LepAnchor/build_agp.smk
@@ -17,7 +17,7 @@ rule construct_agp:
 rule unused:
   input:
     lengths = "10_PlaceAndOrientContigs/contigs.length",
-    haplos = "10_PlaceAndOrientContigs/fullHaplotypes50.txt",
+    haplos = "10_PlaceAndOrientContigs/suspected.haplotypes",
     cleaned = "10_PlaceAndOrientContigs/overlaps.removed.la",
   output: 
     txt = "11_AGP/not_used_final.txt",
diff --git a/rules/LepAnchor/generate_inputs.smk b/rules/LepAnchor/generate_inputs.smk
index 6c34c83..affe53d 100644
--- a/rules/LepAnchor/generate_inputs.smk
+++ b/rules/LepAnchor/generate_inputs.smk
@@ -36,7 +36,7 @@ rule contiglengths:
 
 rule find_haplotypes:
   input: "9_Chain/chainfile.gz"
-  output: report("10_PlaceAndOrientContigs/suspected.haplotypes.before", category = "Logs")
+  output: report("10_PlaceAndOrientContigs/suspected.haplotypes.initial", category = "Logs")
   message: "Finding non-haplotype contigs not included in map.bed"
   shell: 
     """
@@ -48,7 +48,7 @@ rule liftover:
   input: 
     chain = "9_Chain/chainfile.gz",
     intervals = "10_PlaceAndOrientContigs/lepanchor.input",
-    haplos = "10_PlaceAndOrientContigs/suspected.haplotypes.before"
+    haplos = "10_PlaceAndOrientContigs/suspected.haplotypes.initial"
   output: 
     lift = report("10_PlaceAndOrientContigs/liftover.la", category = "Lifted Intervals"),
     sortedlift = report("10_PlaceAndOrientContigs/liftover.sorted.la", category = "Lifted Intervals")
@@ -84,7 +84,7 @@ rule map2bed:
 rule ungrouped:
   input:
     lengths = "10_PlaceAndOrientContigs/contigs.length",
-    haplos = "10_PlaceAndOrientContigs/suspected.haplotypes.before",
+    haplos = "10_PlaceAndOrientContigs/suspected.haplotypes.initial",
     bedfile = "10_PlaceAndOrientContigs/map.bed"
   output:
     bedfile = "10_PlaceAndOrientContigs/map_extra.bed"
diff --git a/rules/LepAnchor/mask_and_chain.smk b/rules/LepAnchor/mask_and_chain.smk
index 2e26d64..d286810 100644
--- a/rules/LepAnchor/mask_and_chain.smk
+++ b/rules/LepAnchor/mask_and_chain.smk
@@ -1,10 +1,10 @@
 rule prep_geno:
   input: geno
-  output: "8_Repeatmask/inputgenome/lepanchorinput.fa"
+  output: "8_RepeatMask/inputgenome/lepanchorinput.fa"
   message: "Preparing genome for repeat masking"
   shell:
     """
-    mkdir -p 8_Repeatmask/inputgenome
+    mkdir -p 8_RepeatMask/inputgenome
     if (file {input} | grep -q compressed); then
       echo "- Assembly is compressed, creating decompressed copy: {output}"
       gunzip --stdout {input} > {output}
@@ -16,23 +16,22 @@ rule prep_geno:
 
 
 rule repeatmask:
-  input: "8_Repeatmask/inputgenome/lepanchorinput.fa"
-  output: "8_Repeatmask/repeatmasked.fa.gz"
-  log: "8_Repeatmask/Red.log"
+  input: "8_RepeatMask/inputgenome/lepanchorinput.fa"
+  output: "8_RepeatMask/repeatmasked.fa.gz"
+  log: "8_RepeatMask/Red.log"
   message: "Using Red to repeat-mask {input}"
   threads: 30
   shell:
     """
-    echo "- Running Red"
-    software/LepAnchor/deps/Red -gnm 8_Repeatmask/inputgenome -msk 8_Repeatmask -sco 8_Repeatmask -cnd 8_Repeatmask -rpt 8_Repeatmask > {log} 2>> {log}
+    software/LepAnchor/deps/Red -gnm 8_RepeatMask/inputgenome -msk 8_RepeatMask -sco 8_RepeatMask -cnd 8_RepeatMask -rpt 8_RepeatMask > {log} 2>> {log}
     echo "- Compressing repeat-masked genome from Red"
-    gzip --stdout 8_Repeatmask/*.msk > {output} && rm 8_Repeatmask/*.msk
+    gzip --stdout 8_RepeatMask/*.msk > {output} && rm 8_RepeatMask/*.msk
     """
     
 
 rule chain_1:
   input: 
-    geno = "8_Repeatmask/repeatmasked.fa.gz",
+    geno = "8_RepeatMask/repeatmasked.fa.gz",
     ctrl = "software/LepAnchor/deps/all_lastz.ctl",
     scoremtx = "software/LepAnchor/deps/scoreMatrix.q"
   output: 
diff --git a/rules/LepAnchor/place_orient3.smk b/rules/LepAnchor/place_orient3.smk
index 26bf843..0457664 100644
--- a/rules/LepAnchor/place_orient3.smk
+++ b/rules/LepAnchor/place_orient3.smk
@@ -21,11 +21,11 @@ rule place_orient3:
     gunzip -fc {input.chain} | java -cp software/LepAnchor PlaceAndOrientContigs numThreads={threads} $(awk -f software/LepAnchor/scripts/pickorientation.awk {input.chrom}) bed={input.bedfile} chromosome={params.chrom} map={input.lift} chain=- paf={input.paf} proximity={input.prox} evaluateAnchoring={input.propogated} improveAnchoring=1 {params.datatype} {params.extras} > {output.chrom} 2> {output.errors}
     """
     
-rule findhaplotypes:
+rule find_haplotypes2:
   input:
     errors = expand("10_PlaceAndOrientContigs/orient_3/errors/chr.{lgs}.err", lgs = lg_range)
   output:
-    haplos = "10_PlaceAndOrientContigs/fullHaplotypes50.txt"
+    haplos = "10_PlaceAndOrientContigs/suspected.haplotypes"
   message: "Finding full haplotypes"
   params:
     haplo = haplo_limit
@@ -40,7 +40,7 @@ rule liftoverHaplotypes:
   input:
     chain = "9_Chain/chainfile.gz",
     chrom = "10_PlaceAndOrientContigs/orient_1/chr.{lg_range}.la",
-    haplos = "10_PlaceAndOrientContigs/fullHaplotypes50.txt"
+    haplos = "10_PlaceAndOrientContigs/suspected.haplotypes"
   output: "10_PlaceAndOrientContigs/liftover/chr.{lg_range}.liftover"
   message: "Running liftoverHaplotypes for {input.chrom}"
   threads: 1
@@ -52,7 +52,7 @@ rule liftoverHaplotypes:
 rule removehaplotypes:
   input:
     mapfile = "10_PlaceAndOrientContigs/map.propogated2.bed", 
-    haplos = "10_PlaceAndOrientContigs/fullHaplotypes50.txt"
+    haplos = "10_PlaceAndOrientContigs/suspected.haplotypes"
   output:
     bedfile = "10_PlaceAndOrientContigs/map.propogated2.nohaplo.bed"
   message: "Removing haplotypes from the map"

From 4868a3aa8a87237ad12922bf8a5a7d9aa248660c Mon Sep 17 00:00:00 2001
From: Pavel Dimens <pdimens@live.com>
Date: Thu, 3 Feb 2022 20:31:17 -0500
Subject: [PATCH 09/46] rm redundant call

---
 rules/LepAnchor/place_orient4.smk | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/rules/LepAnchor/place_orient4.smk b/rules/LepAnchor/place_orient4.smk
index 6c46ec1..b6fe2ab 100644
--- a/rules/LepAnchor/place_orient4.smk
+++ b/rules/LepAnchor/place_orient4.smk
@@ -19,7 +19,7 @@ rule place_orient4:
     threads: 5
     shell:
         """
-        gunzip -fc {input.chain} | java -cp software/LepAnchor PlaceAndOrientContigs numThreads={threads} $(awk -f software/LepAnchor/scripts/pickorientation.awk {input.chrom}) bed={input.bedfile} chromosome={params.chrom} map=$MAPL chain=- paf={input.paf} proximity={input.prox} {params.datatype} {params.extras} keepEmptyIntervals=1 evaluateAnchoring={input.chromlast} improveAnchoring=1 > {output.chrom} 2> {output.err}
+        gunzip -fc {input.chain} | java -cp software/LepAnchor PlaceAndOrientContigs numThreads={threads} $(awk -f software/LepAnchor/scripts/pickorientation.awk {input.chrom}) bed={input.bedfile} chromosome={params.chrom} map=$MAPL chain=- paf={input.paf} proximity={input.prox} {params.datatype} {params.extras} evaluateAnchoring={input.chromlast} improveAnchoring=1 > {output.chrom} 2> {output.err}
         """
 
 rule prune_contigblocks:

From e188863a4bfa68d08f533874f90a72eb1c5706bd Mon Sep 17 00:00:00 2001
From: Pavel Dimens <pdimens@live.com>
Date: Thu, 3 Feb 2022 22:31:30 -0500
Subject: [PATCH 10/46] cleanup

---
 rules/LepAnchor/place_orient1.smk       |  19 +-
 rules/LepAnchor/place_orient2.smk       |   5 +-
 rules/LepAnchor/place_orient3.smk       |   2 +-
 rules/LepAnchor/place_orient4.smk       |   2 +-
 software/LepAnchor/lepanchor_wrapper.sh | 246 ------------------------
 5 files changed, 6 insertions(+), 268 deletions(-)
 delete mode 100644 software/LepAnchor/lepanchor_wrapper.sh

diff --git a/rules/LepAnchor/place_orient1.smk b/rules/LepAnchor/place_orient1.smk
index ccf2ffe..8c4e3f3 100644
--- a/rules/LepAnchor/place_orient1.smk
+++ b/rules/LepAnchor/place_orient1.smk
@@ -7,24 +7,16 @@ rule place_orient:
     lift = "10_PlaceAndOrientContigs/liftover.la"
   output:
     chrom = "10_PlaceAndOrientContigs/orient_1/chr.{lg_range}.la",
-    haplos = "10_PlaceAndOrientContigs/orient_1/haplotypes/chr.{lg_range}.haplo.suspected",
     chromerr = report("10_PlaceAndOrientContigs/orient_1/logs/chr.{lg_range}.la.log", category = "Anchoring I Logs")
-  log:
-    errors = "10_PlaceAndOrientContigs/orient_1/errors/chr.{lg_range}.errors",
-    haplos = "10_PlaceAndOrientContigs/orient_1/haplotypes/chr.{lg_range}.haplo.all"
   params:
     chrom = "{lg_range}",
     extras = place_orient_extra,
-    datatype = data_type,
-    haplo = haplo_limit
-  threads: 3
+    datatype = data_type
+  threads: 2
   message: "Running the 1st round of PlaceAndOrientContigs for linkage group {params.chrom}"
   shell:
     """
     gunzip -fc {input.chain} | java -cp software/LepAnchor PlaceAndOrientContigs numThreads={threads} bed={input.bedfile} chromosome={params.chrom} map={input.lift} chain=- paf={input.paf} proximity={input.prox} {params.datatype} {params.extras} > {output.chrom} 2> {output.chromerr}
-    sort -n -r {log.chrom} | awk '($NF=="haplotype" && (!(($5 SUBSEP $6 SUBSEP $7) in h))){{h[$2,$3,$4]; print}}' > {log.haplos}
-    sort -n -r {log.chrom} | awk -vlimit={params.haplo} '($NF=="haplotype" && ($1>=($4-$3+1-limit)/limit) && (!(($5 SUBSEP $6 SUBSEP $7) in h))){{h[$2,$3,$4]; print}}'  > {output.haplos}  
-    grep "error$" {log.chrom} > {log.errors}
     """
 
 rule propogate1:
@@ -38,11 +30,4 @@ rule propogate1:
   shell:
     """
     awk -f software/LepAnchor/scripts/propagate4.awk pass=1 {input.placed} pass=2 {input.errors} | awk -f software/LepAnchor/scripts/pickbed.awk - {input.bedfile} > {output.propogated}
-    #awk -f propagate4.awk pass=1 chr*[0-9].la pass=2 chr*[0-9].la.err|awk -f pickbed.awk - map_extra.bed >map_extra_prop.bed
     """
-
-rule mergehaplos:
-  input: expand("10_PlaceAndOrientContigs/orient_1/haplotypes/chr.{lg}.haplo.suspected", lg = lg_range)
-  output: "10_PlaceAndOrientContigs/suspected.haplotypes.after"
-  message: "Merging suspected haplotype contig information from the linkage groups"
-  shell: "cat {input} | sort | uniq > {output}"
diff --git a/rules/LepAnchor/place_orient2.smk b/rules/LepAnchor/place_orient2.smk
index 44cd219..6fffa40 100644
--- a/rules/LepAnchor/place_orient2.smk
+++ b/rules/LepAnchor/place_orient2.smk
@@ -12,9 +12,8 @@ rule place_orient2:
   params:
     chrom = "{lg_range}",
     extras = place_orient_extra,
-    datatype = data_type,
-    haplo = haplo_limit
-  threads: 5
+    datatype = data_type
+  threads: 2
   message: "Running 2nd round of PlaceAndOrientContigs for linkage group {params.chrom}"
   shell:
     """
diff --git a/rules/LepAnchor/place_orient3.smk b/rules/LepAnchor/place_orient3.smk
index 0457664..bd1a60f 100644
--- a/rules/LepAnchor/place_orient3.smk
+++ b/rules/LepAnchor/place_orient3.smk
@@ -15,7 +15,7 @@ rule place_orient3:
     extras = place_orient_extra,
     datatype = data_type,
   message: "Running 3rd round of PlaceAndOrientContigs for linkage group {params.chrom}"
-  threads: 5
+  threads: 2
   shell:
     """
     gunzip -fc {input.chain} | java -cp software/LepAnchor PlaceAndOrientContigs numThreads={threads} $(awk -f software/LepAnchor/scripts/pickorientation.awk {input.chrom}) bed={input.bedfile} chromosome={params.chrom} map={input.lift} chain=- paf={input.paf} proximity={input.prox} evaluateAnchoring={input.propogated} improveAnchoring=1 {params.datatype} {params.extras} > {output.chrom} 2> {output.errors}
diff --git a/rules/LepAnchor/place_orient4.smk b/rules/LepAnchor/place_orient4.smk
index b6fe2ab..e6f9b74 100644
--- a/rules/LepAnchor/place_orient4.smk
+++ b/rules/LepAnchor/place_orient4.smk
@@ -16,7 +16,7 @@ rule place_orient4:
         chrom = "{lg_range}",
         extras = place_orient_extra,
         datatype = data_type,
-    threads: 5
+    threads: 2
     shell:
         """
         gunzip -fc {input.chain} | java -cp software/LepAnchor PlaceAndOrientContigs numThreads={threads} $(awk -f software/LepAnchor/scripts/pickorientation.awk {input.chrom}) bed={input.bedfile} chromosome={params.chrom} map=$MAPL chain=- paf={input.paf} proximity={input.prox} {params.datatype} {params.extras} evaluateAnchoring={input.chromlast} improveAnchoring=1 > {output.chrom} 2> {output.err}
diff --git a/software/LepAnchor/lepanchor_wrapper.sh b/software/LepAnchor/lepanchor_wrapper.sh
deleted file mode 100644
index d80a0ab..0000000
--- a/software/LepAnchor/lepanchor_wrapper.sh
+++ /dev/null
@@ -1,246 +0,0 @@
-#!/bin/bash
-##########################################################
-#
-#  Lep-Anchor wrapper
-#
-#  usage: lepanchor_wrapper.sh -f ref.fasta -n num_chr -c chain_file -p paf_file -r prox_file -m map_file1 -m map_file2, ... 
-#
-#  output: LA_REF.fa.gz anchored reference genome
-#          LA_REF.agp   agp file describing the genome
-#          marey*.png   Marey maps for visual verification
-#          chr*.agp     agp files for each chromosome
-#          scaffolds_chr*.agp agp files for each chromosome in scaffolds (each block of linked contigs as a scaffold)
-#
-#
-#  Pasi Rastas, (c) 2020, pasi.rastas@gmail.com
-#
-##########################################################
-
-#parse parameters
-
-function print_usage()
-{
-echo "##########################################################"
-echo "#"
-echo "#  Lep-Anchor wrapper"
-echo "#"
-echo "#  usage: lepanchor_wrapper.sh -t threads -f ref.fasta -n num_chr -c chain_file -r prox_file -p paf_file -m map_file1 -m map_file2, ... "
-echo "#"
-echo "#  download Lep-Anchor by"
-echo "#  wget https://sourceforge.net/projects/lep-anchor/files/binary%2Bcode.zip/download -O la.zip;unzip la.zip"
-echo "#"
-echo "#  Pasi Rastas, (c) 2020, pasi.rastas@gmail.com"
-echo "#"
-echo "##########################################################"
-}
-
-while getopts ":n:c:p:m:f:t:r:" OPTION; do
-	case ${OPTION} in
-	t)
-	THREADS=$OPTARG;;
-	n)
-	CHR=$OPTARG;;
-	c)
-	CHAIN=$OPTARG;;
-	p)
-	PAF=$OPTARG;;
-	r)
-	PROX=$OPTARG;;
-	m)
-	MAP="$MAP $OPTARG";;
-	f)
-	REF=$OPTARG;;
-	*)
-        echo "Incorrect options provided"
-        exit 1;;
-    esac
-done
-
-if [[ $MAP =~ ^$ ]];then
-	print_usage
-	echo "Please provide at least one map"
-	exit 1
-fi
-
-if [[ $REF =~ ^$ ]];then
-    if [[ ! -e "contigs.length" ]];then
-	print_usage
-	echo "Please provide either reference fasta or contigs.length file"
-	exit 1
-    fi
-fi
-
-if [[ $CHR =~ ^[0-9]+$ ]];then
-	echo "Number of chromosomes = $CHR"
-else
-	print_usage
-	echo "Please provide parameter n (number of chromosomes)"
-	exit 1
-fi
-
-if [[ $CHAIN =~ ^$ ]];then
-	echo "No chain provided"
-	CHAIN="/dev/null"
-fi
-
-if [[ $PROX =~ ^$ ]];then
-        echo "No proximity data provided"
-        PROX="/dev/null"
-fi
-
-
-if [[ $PAF =~ ^$ ]];then
-	echo "No paf provided" 
-	PAF="/dev/null"
-fi
-
-#number of threads
-if [[ $THREADS =~ ^$ ]];then
-	THREADS=8
-fi
-
-#get Lep-Anchor
-#wget https://sourceforge.net/projects/lep-anchor/files/binary%2Bcode.zip/download -O la.zip
-#unzip la.zip
-
-#where Lep-Anchor binaries are located
-LABIN=bin/
-
-#java runtime located here
-JAVA=java
-
-#parallel 
-if ! command -v "parallel"
-then
-	echo "command parallel not found, using only one thread"
-	PARALLEL=bash
-else
-	PARALLEL="parallel --jobs $THREADS"
-fi
-
-if [[ ! $REF =~ ^$ ]];then
-	echo "calculating contigs.length file..."
-	echo "gunzip -fc $REF | awk -f scripts/contigLength.awk > contigs.length" | bash
-fi
-
-
-echo "finding full haplotypes..."
-echo "gunzip -fc $CHAIN | awk -f scripts/findFullHaplotypes.awk > fullHaplotypes50.txt" | bash
-wc -l fullHaplotypes50.txt
-
-
-echo "running liftoverHaplotypes for all input maps..."
-for i in $MAP
-do
-echo "gunzip -fc $CHAIN | $JAVA -cp $LABIN LiftoverHaplotypes map=$i haplotypes=fullHaplotypes50.txt chain=- > $i.liftover"
-done | $PARALLEL
-
-#store lift overed maps to $MAPL
-for i in $MAP
-do
-	MAPL="$MAPL $i.liftover"
-done
-
-
-#make input for CleanMap
-for i in $MAP
-do
-	cat $i.liftover
-done | sort -V -k 1,1 -k 2,2n > map_all_sorted.liftover
-
-
-#CleanMap
-echo "running CleanMap..."
-$JAVA -cp $LABIN CleanMap map=map_all_sorted.liftover > map_all.clean
-
-#Map2Bed
-echo "running Map2Bed..."
-$JAVA -cp $LABIN Map2Bed map=map_all.clean contigLength=contigs.length > map.bed
-
-#find contigs not put into chromosomes
-cut -f 1 contigs.length | grep -v -w -F -f <(cut -f 2 fullHaplotypes50.txt; cut -f 1 map.bed) > not_used.txt
-
-grep -w -F -f not_used.txt contigs.length | awk -vn=$CHR '{s=$1"\t1\t"$2"\t?\t"; for (i=1;i<=n;++i) print s i}' > chr0.bed
-cat map.bed chr0.bed > map_extra.bed
-
-
-#PlaceAndOrientContigs
-echo "running PlaceAndOrientContigs (first iteration)..."
-for i in $(seq $CHR)
-do
-echo "gunzip -fc $CHAIN | $JAVA -cp $LABIN PlaceAndOrientContigs bed=map_extra.bed chromosome=$i map=$MAPL chain=- paf=$PAF proximity=$PROX keepEmptyIntervals=1 > chr$i.la 2> chr$i.la.err"
-done | $PARALLEL
-
-
-#propagate
-echo "running propagate..."
-
-awk -f scripts/propagate.awk chr*.la > tmp1.la
-awk -f scripts/propagate.awk tmp1.la > tmp2.la
-i=2
-
-while ! cmp -s "tmp$i.la" "tmp$(( $i-1 )).la" ;do
-	awk -f scripts/propagate.awk tmp$i.la > tmp$[$i+1].la
-	i=$[$i+1]
-done
-
-#create prop*.la
-awk '/^[^#]/{++d[$1 "\t" $7+0 "\t" $8+0]; data[++line]=$0}END{for (i = 1; i <= line; ++i) {$0=data[i];if (d[$1 "\t" $7+0 "\t" $8+0] == 1) fn="prop"$5".la"; else if ($5==1) fn="prop0.la"; else fn=""; if (fn != "") print $0>fn}}' tmp$i.la
-
-#create a new bed by combining prop[1-9]*.la and map.bed
-awk '(NR==FNR){print;c[$1]}(NR!=FNR && !($1 in c)){print $1 "\t" $7+0 "\t" $8+0"\t?\t"$5}' map.bed prop[1-9]*.la > map_prop.bed
-
-#PlaceAndOrientContigs
-echo "running PlaceAndOrientContigs (second iteration)..."
-for i in $(seq $CHR)
-do
-echo "gunzip -fc $CHAIN | $JAVA -cp $LABIN PlaceAndOrientContigs bed=map_prop.bed chromosome=$i map=$MAPL chain=- paf=$PAF proximity=$PROX keepEmptyIntervals=1 > ichr$i.la 2> ichr$i.la.err"
-done | $PARALLEL
-
-#pruning contig blocks without map support
-for i in $(seq $CHR)
-do
-	awk -f scripts/prune.awk ichr$i.la > ichr${i}_pruned.la
-done 2> pruned.la
-
-#remove overlap(s)
-awk -f scripts/removeOverlaps.awk map_prop.bed ichr*_pruned.la > iall.la
-
-#construct agp files
-for i in $(seq $CHR)
-do
-awk -vn=$i '($5==n)' iall.la | awk -vprefix="LG" -vlg=$i -f scripts/makeagp_full2.awk - > chr$i.agp
-awk -vn=$i '($5==n)' iall.la | awk -vprefix="LG" -vlg=$i -f scripts/makeagp2.awk - > scaffolds_chr$i.agp
-done
-
-#find contigs not used
-cut -f 1 contigs.length | grep -v -w -F -f <(cut -f 2 fullHaplotypes50.txt;awk '($5!="U"){print $6}' chr*.agp) > not_used_final.txt
-
-grep -F -w -f not_used_final.txt contigs.length | awk '{print $1,1,$2,1,"W",$1,1,$2,"+"}' > not_used.agp
-
-cat chr*.agp not_used.agp > REF_LA.agp
-#one could use scaffolds_chr*.agp as well instead of chr*.agp
-cat scaffolds_chr*.agp not_used.agp > REF_LA_scaffolds.agp
-
-#make final fasta
-if [[ ! $REF =~ ^$ ]];then
-	echo "constructing final fasta (REF_LA.fa.gz)..."
-	echo "gunzip -fc $REF | awk -f scripts/makefasta.awk - REF_LA.agp | gzip > REF_LA.fa.gz" | bash
-
-	echo "constructing final fasta (REF_LA_scaffolds.fa.gz)..."
-	echo "gunzip -fc $REF | awk -f scripts/makefasta.awk - REF_LA_scaffolds.agp | gzip > REF_LA_scaffolds.fa.gz" | bash
-fi
-
-#construct Marey map
-echo "constructing Marey maps... (marey*.png)"
-j=1
-for m in $MAP
-do
-	for c in $(seq $CHR)
-	do
-	awk -vn=$c '($3==n)' $m.liftover | awk -f scripts/liftover.awk chr$c.agp - |awk -vm=$j '(/LG/ && NF>=4){if (NF==4) $5=$4;print $1"\t"$2"\t"$3"\t"m"\t"$4"\t"$5}'
-	done
-	j=$[$j + 1]
-done | gzip > marey.data.gz
-
-Rscript scripts/plot_marey.R
\ No newline at end of file

From 1d70ec57bad663e39fbd93cc33655290cb02dce2 Mon Sep 17 00:00:00 2001
From: Pavel Dimens <pdimens@live.com>
Date: Thu, 3 Feb 2022 22:33:50 -0500
Subject: [PATCH 11/46] move chromosome={params.chrom} to front of call

---
 rules/LepAnchor/place_orient1.smk | 2 +-
 rules/LepAnchor/place_orient2.smk | 2 +-
 rules/LepAnchor/place_orient3.smk | 2 +-
 rules/LepAnchor/place_orient4.smk | 2 +-
 4 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/rules/LepAnchor/place_orient1.smk b/rules/LepAnchor/place_orient1.smk
index 8c4e3f3..f25d197 100644
--- a/rules/LepAnchor/place_orient1.smk
+++ b/rules/LepAnchor/place_orient1.smk
@@ -16,7 +16,7 @@ rule place_orient:
   message: "Running the 1st round of PlaceAndOrientContigs for linkage group {params.chrom}"
   shell:
     """
-    gunzip -fc {input.chain} | java -cp software/LepAnchor PlaceAndOrientContigs numThreads={threads} bed={input.bedfile} chromosome={params.chrom} map={input.lift} chain=- paf={input.paf} proximity={input.prox} {params.datatype} {params.extras} > {output.chrom} 2> {output.chromerr}
+    gunzip -fc {input.chain} | java -cp software/LepAnchor PlaceAndOrientContigs chromosome={params.chrom} numThreads={threads} bed={input.bedfile} map={input.lift} chain=- paf={input.paf} proximity={input.prox} {params.datatype} {params.extras} > {output.chrom} 2> {output.chromerr}
     """
 
 rule propogate1:
diff --git a/rules/LepAnchor/place_orient2.smk b/rules/LepAnchor/place_orient2.smk
index 6fffa40..d5a4611 100644
--- a/rules/LepAnchor/place_orient2.smk
+++ b/rules/LepAnchor/place_orient2.smk
@@ -17,7 +17,7 @@ rule place_orient2:
   message: "Running 2nd round of PlaceAndOrientContigs for linkage group {params.chrom}"
   shell:
     """
-    gunzip -fc {input.chain} | java -cp software/LepAnchor PlaceAndOrientContigs numThreads={threads} $(awk -f software/LepAnchor/scripts/pickorientation.awk {input.chrom}) bed={input.bedfile} chromosome={params.chrom} map={input.lift} chain=- paf={input.paf} proximity={input.prox} {params.datatype} {params.extras} > {output.chrom} 2> {output.chromerr}
+    gunzip -fc {input.chain} | java -cp software/LepAnchor PlaceAndOrientContigs chromosome={params.chrom} numThreads={threads} $(awk -f software/LepAnchor/scripts/pickorientation.awk {input.chrom}) bed={input.bedfile} map={input.lift} chain=- paf={input.paf} proximity={input.prox} {params.datatype} {params.extras} > {output.chrom} 2> {output.chromerr}
     """
 
 rule propogate2:
diff --git a/rules/LepAnchor/place_orient3.smk b/rules/LepAnchor/place_orient3.smk
index bd1a60f..4df922d 100644
--- a/rules/LepAnchor/place_orient3.smk
+++ b/rules/LepAnchor/place_orient3.smk
@@ -18,7 +18,7 @@ rule place_orient3:
   threads: 2
   shell:
     """
-    gunzip -fc {input.chain} | java -cp software/LepAnchor PlaceAndOrientContigs numThreads={threads} $(awk -f software/LepAnchor/scripts/pickorientation.awk {input.chrom}) bed={input.bedfile} chromosome={params.chrom} map={input.lift} chain=- paf={input.paf} proximity={input.prox} evaluateAnchoring={input.propogated} improveAnchoring=1 {params.datatype} {params.extras} > {output.chrom} 2> {output.errors}
+    gunzip -fc {input.chain} | java -cp software/LepAnchor PlaceAndOrientContigs chromosome={params.chrom} numThreads={threads} $(awk -f software/LepAnchor/scripts/pickorientation.awk {input.chrom}) bed={input.bedfile} map={input.lift} chain=- paf={input.paf} proximity={input.prox} evaluateAnchoring={input.propogated} improveAnchoring=1 {params.datatype} {params.extras} > {output.chrom} 2> {output.errors}
     """
     
 rule find_haplotypes2:
diff --git a/rules/LepAnchor/place_orient4.smk b/rules/LepAnchor/place_orient4.smk
index e6f9b74..03b9503 100644
--- a/rules/LepAnchor/place_orient4.smk
+++ b/rules/LepAnchor/place_orient4.smk
@@ -19,7 +19,7 @@ rule place_orient4:
     threads: 2
     shell:
         """
-        gunzip -fc {input.chain} | java -cp software/LepAnchor PlaceAndOrientContigs numThreads={threads} $(awk -f software/LepAnchor/scripts/pickorientation.awk {input.chrom}) bed={input.bedfile} chromosome={params.chrom} map=$MAPL chain=- paf={input.paf} proximity={input.prox} {params.datatype} {params.extras} evaluateAnchoring={input.chromlast} improveAnchoring=1 > {output.chrom} 2> {output.err}
+        gunzip -fc {input.chain} | java -cp software/LepAnchor PlaceAndOrientContigs chromosome={params.chrom} numThreads={threads} $(awk -f software/LepAnchor/scripts/pickorientation.awk {input.chrom}) bed={input.bedfile} map=$MAPL chain=- paf={input.paf} proximity={input.prox} {params.datatype} {params.extras} evaluateAnchoring={input.chromlast} improveAnchoring=1 > {output.chrom} 2> {output.err}
         """
 
 rule prune_contigblocks:

From e2073d7f9aee681ef8b5662d06ae15f628e097ff Mon Sep 17 00:00:00 2001
From: Pavel Dimens <pdimens@live.com>
Date: Sun, 6 Feb 2022 12:50:02 -0500
Subject: [PATCH 12/46] fixes

---
 rules/LepAnchor/place_orient2.smk | 14 ++++++++------
 rules/LepAnchor/place_orient3.smk |  4 ++--
 rules/LepAnchor/place_orient4.smk |  7 +++----
 3 files changed, 13 insertions(+), 12 deletions(-)

diff --git a/rules/LepAnchor/place_orient2.smk b/rules/LepAnchor/place_orient2.smk
index d5a4611..000934f 100644
--- a/rules/LepAnchor/place_orient2.smk
+++ b/rules/LepAnchor/place_orient2.smk
@@ -22,18 +22,20 @@ rule place_orient2:
 
 rule propogate2:
   input:
-    placed = expand("10_PlaceAndOrientContigs/orient_2/logs/chr.{lgs}.err", lgs = lg_range),
+    placed = expand("10_PlaceAndOrientContigs/orient_2/chr.{lgs}.la", lgs = lg_range),
+    #placed = expand("10_PlaceAndOrientContigs/orient_2/logs/chr.{lgs}.err", lgs = lg_range),
     bedfile = "10_PlaceAndOrientContigs/map.propogated.bed"
   output:
-    prop = expand("10_PlaceAndOrientContigs/propogate/propogated.{lgs}.la", lgs = range(lg + 1)),
+    prop = expand("10_PlaceAndOrientContigs/propogate/propogated.{lgs}.la", lgs = lg_range),
     propogated = "10_PlaceAndOrientContigs/map.propogated2.bed",
     iter1 = temp("10_PlaceAndOrientContigs/tmp1.la"),
-    iter2 = temp("10_PlaceAndOrientContigs/tmp2.la")
+    iter2 = temp("10_PlaceAndOrientContigs/tmp2.la"),
+    iter3 = temp("10_PlaceAndOrientContigs/tmp3.la")
   message: "Second round of propogation"
   shell:
     """
-    awk -f software/LepAnchor/scripts/propagate.awk {input.placed} > 10_PlaceAndOrientContigs/tmp1.la
-    awk -f software/LepAnchor/scripts/propagate.awk 10_PlaceAndOrientContigs/tmp1.la > 10_PlaceAndOrientContigs/tmp2.la
+    awk -f software/LepAnchor/scripts/propagate.awk {input.placed} > {output.iter1}
+    awk -f software/LepAnchor/scripts/propagate.awk {output.iter1} > {output.iter2}
     i=2
 
     while ! cmp -s "10_PlaceAndOrientContigs/tmp$i.la" "10_PlaceAndOrientContigs/tmp$(( $i-1 )).la" ;do
@@ -42,6 +44,6 @@ rule propogate2:
     done
 
     #create prop*.la
-    awk -f software/LepAnchor/scripts/propagate2.awk tmp$i.la | awk '(/^[^#]/ && NF>=8){{++d[$1"\t"($7+0)"\t"($8+0)]; data[++line]=$0}}END{{for (i=1; i<=line; ++i) {{$0=data[i];if (d[$1"\t"($7+0)"\t"($8+0)] == 1) {{fn="10_PlaceAndOrientContigs/propogate/propogated."$5".la";print $0>fn}}}}}}'
+    awk -f software/LepAnchor/scripts/propagate2.awk 10_PlaceAndOrientContigs/tmp$i.la | awk '(/^[^#]/ && NF>=8){{++d[$1"\t"($7+0)"\t"($8+0)]; data[++line]=$0}}END{{for (i=1; i<=line; ++i) {{$0=data[i];if (d[$1"\t"($7+0)"\t"($8+0)] == 1) {{fn="10_PlaceAndOrientContigs/propogate/propogated."$5".la";print $0>fn}}}}}}'
     awk '{{print $1"\t"($7+0)"\t"($8+0)"\t?\t"$5}}' {output.prop} | awk -f software/LepAnchor/scripts/pickbed.awk - {input.bedfile} > {output.propogated}
     """
\ No newline at end of file
diff --git a/rules/LepAnchor/place_orient3.smk b/rules/LepAnchor/place_orient3.smk
index 4df922d..ae7f45c 100644
--- a/rules/LepAnchor/place_orient3.smk
+++ b/rules/LepAnchor/place_orient3.smk
@@ -13,7 +13,7 @@ rule place_orient3:
   params:
     chrom = "{lg_range}",
     extras = place_orient_extra,
-    datatype = data_type,
+    datatype = data_type
   message: "Running 3rd round of PlaceAndOrientContigs for linkage group {params.chrom}"
   threads: 2
   shell:
@@ -46,7 +46,7 @@ rule liftoverHaplotypes:
   threads: 1
   shell:
     """
-    gunzip -fc {input.chain} | java -cp software/LepAnchor LiftoverHaplotypes map={input.chrom} haplotypes={input.haplos} chain=- > $i.liftover
+    gunzip -fc {input.chain} | java -cp software/LepAnchor LiftoverHaplotypes map={input.chrom} haplotypes={input.haplos} chain=- > {output}
     """
 
 rule removehaplotypes:
diff --git a/rules/LepAnchor/place_orient4.smk b/rules/LepAnchor/place_orient4.smk
index 03b9503..dd86e03 100644
--- a/rules/LepAnchor/place_orient4.smk
+++ b/rules/LepAnchor/place_orient4.smk
@@ -6,8 +6,7 @@ rule place_orient4:
         prox = proximity,
         lift = "10_PlaceAndOrientContigs/liftover.la",
         chrom = "10_PlaceAndOrientContigs/orient_1/chr.{lg_range}.la",
-        chromlast = "10_PlaceAndOrientContigs/orient_3/chr.{lg_range}.la",
-        liftover = expand("10_PlaceAndOrientContigs/liftover/chr.{lgs}.liftover", lgs = lg_range)
+        chromlast = "10_PlaceAndOrientContigs/orient_3/chr.{lg_range}.la"
     output:
         chrom = "10_PlaceAndOrientContigs/orient_4/chr.{lg_range}.la",
         err = "10_PlaceAndOrientContigs/orient_4/errors/chr.{lg_range}.errors"
@@ -15,11 +14,11 @@ rule place_orient4:
     params:
         chrom = "{lg_range}",
         extras = place_orient_extra,
-        datatype = data_type,
+        datatype = data_type
     threads: 2
     shell:
         """
-        gunzip -fc {input.chain} | java -cp software/LepAnchor PlaceAndOrientContigs chromosome={params.chrom} numThreads={threads} $(awk -f software/LepAnchor/scripts/pickorientation.awk {input.chrom}) bed={input.bedfile} map=$MAPL chain=- paf={input.paf} proximity={input.prox} {params.datatype} {params.extras} evaluateAnchoring={input.chromlast} improveAnchoring=1 > {output.chrom} 2> {output.err}
+        gunzip -fc {input.chain} | java -cp software/LepAnchor PlaceAndOrientContigs chromosome={params.chrom} numThreads={threads} $(awk -f software/LepAnchor/scripts/pickorientation.awk {input.chrom}) bed={input.bedfile} map={input.lift} chain=- paf={input.paf} proximity={input.prox} {params.datatype} {params.extras} evaluateAnchoring={input.chromlast} improveAnchoring=1 > {output.chrom} 2> {output.err}
         """
 
 rule prune_contigblocks:

From 70b4e8b0e37b9f628349e541c32875a722f1decb Mon Sep 17 00:00:00 2001
From: "Pavel V. Dimens" <pdimens@live.com>
Date: Sun, 6 Feb 2022 12:51:20 -0500
Subject: [PATCH 13/46] Update config.yml

---
 config.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/config.yml b/config.yml
index b65ff0f..afdc5be 100644
--- a/config.yml
+++ b/config.yml
@@ -126,9 +126,9 @@ extra_params_Map2Bed: ""
 #lepanchor_input: "noIntervals=0"  # data is intervals
 lepanchor_input: "noIntervals=1"  # data is distances
 
-# The size limit for detecting potential haplotype contigs (default: ~5000)
+# The size limit for detecting potential haplotype contigs (LepAnchor default: 2000)
 # Set this value really high (50000+) to ignore haplotype removal in between PlaceOrient iterations
-haplotype_limit: 5000
+haplotype_limit: 2000
 
 # Additional parameters you would like to use for PlaceAndOrientContigs, if any (e.g. randomOrder=1)
 extra_params_PlaceOrient: "keepEmptyIntervals=1 numRuns=10"

From d6ab3d2dcafbc498f796b124b16ffd76e00b01cd Mon Sep 17 00:00:00 2001
From: "Pavel V. Dimens" <pdimens@live.com>
Date: Sun, 6 Feb 2022 12:52:10 -0500
Subject: [PATCH 14/46] Update LepWrap

---
 LepWrap | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/LepWrap b/LepWrap
index 8443514..2f80969 100755
--- a/LepWrap
+++ b/LepWrap
@@ -148,9 +148,9 @@ extra_params_Map2Bed: ""
 #lepanchor_input: "noIntervals=0"  # data is intervals
 lepanchor_input: "noIntervals=1"  # data is distances
 
-# The size limit for detecting potential haplotype contigs (default: ~5000)
+# The size limit for detecting potential haplotype contigs (LepAnchor default: 2000)
 # Set this value really high (50000+) to ignore haplotype removal in between PlaceOrient iterations
-haplotype_limit: 5000
+haplotype_limit: 2000
 
 # Additional parameters you would like to use for PlaceAndOrientContigs, if any (e.g. randomOrder=1)
 extra_params_PlaceOrient: "keepEmptyIntervals=1 numRuns=10"

From 1ee7a46ea075c21134bef442dbf2ce840d9413f6 Mon Sep 17 00:00:00 2001
From: Pavel Dimens <pdimens@live.com>
Date: Sun, 6 Feb 2022 13:22:57 -0500
Subject: [PATCH 15/46] cleanup and sanity checks

---
 LepWrap | 86 +++++++++++++++++++++++++++++++++++----------------------
 1 file changed, 53 insertions(+), 33 deletions(-)

diff --git a/LepWrap b/LepWrap
index 2f80969..753f48d 100755
--- a/LepWrap
+++ b/LepWrap
@@ -1,5 +1,18 @@
 #! /usr/bin/env bash
 
+# Help text
+if [[ -z "$1" ]]; then
+  echo "Perform the modules of Lep-Map3 and/or Lep-Anchor" 
+  echo "Make sure the config file (default: config.yml) is properly configured for how you want to run things"
+  echo "The second positional argument is optional if your config file is named config.yml"
+  echo ""
+  echo "[usage]   LepWrap <# of threads> <config.yml>"
+  echo "[example] LepWrap 16"
+  echo "[example] LepWrap 30 kosambi.20iterations.yml"
+  exit 1
+fi
+
+# Check for snakemake
 if which snakemake &>/dev/null; then
   foo=1
 else
@@ -11,15 +24,8 @@ else
   exit 1
 fi
 
-if [[ -z "$2" ]]; then
-    if [ ! -f config.yml ]; then
-      echo -n "Error: "
-      printf "\033[01;32m"
-      printf "config.yml"
-      printf "\033[0m"
-      echo " not found"
-      echo "The file 'config.yml' was created for you, please edit it and run LepWrap again"
-    cat <<EOF >config.yml
+function generateconfig {
+  cat <<EOF >$1
 # Configuration file for LepWrap
 #=======================================================#
 #                       Lep-Map 3                       #
@@ -163,36 +169,50 @@ extra_params_PlaceOrient: "keepEmptyIntervals=1 numRuns=10"
 
 # Set edge_length to the percent number of markers you would like to examine from either end of the linkage group
 # Value can be an integer or decimal, i.e. 15 is the same as 0.15, which both mean "15%" (10-15 is reasonable)
-LA_edge_length: 20
+LA_edge_length: 15
 
-# Set trim_cuttoff to the centiMorgan distance cutoff (5 is reasonable)
+# Set trim_cuttoff to the centiMorgan distance cutoff (5-10 is reasonable)
 LA_trim_cutoff: 5
 EOF
-  exit 1
-  fi
-    CONF=config.yml
+}
+
+export -f generateconfig
+
+# make sure the first argument is a number (number of threads)
+# function from https://stackoverflow.com/a/61835747
+is_int()  { case ${1#[-+]} in '' | *[!0-9]*              ) return 1;; esac ;}
+
+if $(is_int $1); then
+  foo=1
 else
-    if [ ! -f $2 ]; then
-      echo -n "Error: Config file "
-      printf "\033[01;32m"
-      printf "$2"
-      printf "\033[0m"
-      echo " not found"
-      exit 1
-    else
-      CONF=$2
-    fi
+  echo "Error: the first argument must the number of threads, as an integer."
+  exit 1
 fi
 
-if [[ -z "$1" ]]; then
-  echo "Perform the modules of Lep-Map3 and/or Lep-Anchor" 
-  echo "Make sure the config file (default: config.yml) is properly configured for how you want to run things"
-  echo "The second positional argument is optional if your config file is named config.yml"
-  echo ""
-  echo "[usage]   LepWrap <# of threads> <config.yml>"
-  echo "[example] LepWrap 16"
-  echo "[example] LepWrap 30 kosambi.20iterations.yml"
-  exit 1
+if [[ ! -z "$2" ]]; then
+  if [ ! -f $2 ]; then
+    echo -n "Error: Config file "
+    printf "\033[01;32m"
+    printf "$2"
+    printf "\033[0m"
+    echo " was not found, but it was created for you. Please edit it and run LepWrap again"
+    generateconfig $2
+    exit 1
+  else
+    CONF=$2
+  fi
+else 
+  if [ ! -f config.yml ]; then
+    echo -n "Error: "
+    printf "\033[01;32m"
+    printf "config.yml"
+    printf "\033[0m"
+    echo " not found"
+    echo " was not found, but it was created for you. Please edit it and run LepWrap again"
+    generateconfig config.yml
+    exit 1
+  fi
+    CONF=config.yml
 fi
 
 lepmap(){

From ec7258f06b26682698f6a53a1b96fef00f6a5490 Mon Sep 17 00:00:00 2001
From: Pavel Dimens <pdimens@live.com>
Date: Sun, 6 Feb 2022 13:27:22 -0500
Subject: [PATCH 16/46] bind LM3 error to LA run. Nicer printing

---
 LepWrap | 12 +++++++-----
 1 file changed, 7 insertions(+), 5 deletions(-)

diff --git a/LepWrap b/LepWrap
index 753f48d..4a18c97 100755
--- a/LepWrap
+++ b/LepWrap
@@ -216,13 +216,17 @@ else
 fi
 
 lepmap(){
-  echo "Running Lep-Map3"
+  printf "\033[01;32m"
+  printf "Running Lep-Map3\n"
+  printf "\033[0m"
   sleep 2s
   snakemake --cores $1 --snakefile ./rules/LepMap3/LepMap3.smk --configfile $CONF --directory .
 }
 
 lepanchor(){
-  echo -e "\nRunning Lep-Anchor"
+  printf "\033[01;32m"
+  printf "Running Lep-Anchor\n"
+  printf "\033[0m"
   sleep 2s
   snakemake --cores $1 --snakefile ./rules/LepAnchor/LepAnchor.smk --configfile $CONF --directory .
 }
@@ -241,9 +245,7 @@ if [ $LM == "true" ]; then
   lepmap $1 $CONF
 else
   echo "Skipping Lep-Map3"
-fi
-
-if [ $LA == "true" ]; then
+fi && if [ $LA == "true" ]; then
   lepanchor $1 $CONF
 else
   echo "Skipping LepAnchor"

From 638b2e26f7b902decae68b2bc89b9c6e231bde76 Mon Sep 17 00:00:00 2001
From: Pavel Dimens <pdimens@live.com>
Date: Sun, 6 Feb 2022 13:31:36 -0500
Subject: [PATCH 17/46] QoL

---
 LepWrap | 17 +++++++++++++----
 1 file changed, 13 insertions(+), 4 deletions(-)

diff --git a/LepWrap b/LepWrap
index 4a18c97..5c37ce5 100755
--- a/LepWrap
+++ b/LepWrap
@@ -3,12 +3,21 @@
 # Help text
 if [[ -z "$1" ]]; then
   echo "Perform the modules of Lep-Map3 and/or Lep-Anchor" 
-  echo "Make sure the config file (default: config.yml) is properly configured for how you want to run things"
+  echo "The config file (default: config.yml) must be configured"
   echo "The second positional argument is optional if your config file is named config.yml"
   echo ""
-  echo "[usage]   LepWrap <# of threads> <config.yml>"
-  echo "[example] LepWrap 16"
-  echo "[example] LepWrap 30 kosambi.20iterations.yml"
+  printf "\033[01;32m"
+  printf "[usage]"
+  printf "\033[0m"
+  echo "   LepWrap <# of threads> <config.yml>"
+    printf "\033[01;32m"
+  printf "[example]"
+  printf "\033[0m"
+  echo " LepWrap 16"
+  printf "\033[01;32m"
+  printf "[example]"
+  printf "\033[0m"
+  echo " LepWrap 30 kosambi.20iterations.yml"
   exit 1
 fi
 

From f2c157d1bb7e9451e298d6395492731717e67777 Mon Sep 17 00:00:00 2001
From: Pavel Dimens <pdimens@live.com>
Date: Sun, 6 Feb 2022 14:06:11 -0500
Subject: [PATCH 18/46] housekeeping

---
 rules/LepAnchor/LA_extra.smk        | 11 ----------
 rules/LepAnchor/build_agp.smk       |  7 +++----
 rules/LepAnchor/build_fasta.smk     | 32 ++++++++---------------------
 rules/LepAnchor/generate_inputs.smk |  8 +++-----
 rules/LepAnchor/place_orient1.smk   |  8 ++++----
 rules/LepAnchor/place_orient2.smk   |  9 ++++----
 rules/LepAnchor/place_orient3.smk   | 10 ++++-----
 rules/LepAnchor/place_orient4.smk   | 10 ++++-----
 8 files changed, 32 insertions(+), 63 deletions(-)
 delete mode 100644 rules/LepAnchor/LA_extra.smk

diff --git a/rules/LepAnchor/LA_extra.smk b/rules/LepAnchor/LA_extra.smk
deleted file mode 100644
index d98b15d..0000000
--- a/rules/LepAnchor/LA_extra.smk
+++ /dev/null
@@ -1,11 +0,0 @@
-rule remove_haplos:
-  input: 
-    bedfile = "10_Anchoring/map_extra.bed",
-    haplotypes = "10_Anchoring/suspected.haplotypes.after"
-  output: "10_Anchoring/map.nohaplotypes.bed"
-  message: "Creating bedfile with suspected haplotypes removed"
-  shell: 
-    """
-    grep -w -v -f <(cut -f 2 {input.haplotypes}) {input.bedfile} > {output}
-    #awk -f software/LepAnchor/scripts/removeHaplotypes.awk {input.bedfile} {input.haplotypes} > {output}"
-    """
\ No newline at end of file
diff --git a/rules/LepAnchor/build_agp.smk b/rules/LepAnchor/build_agp.smk
index eb51e42..8a9116b 100644
--- a/rules/LepAnchor/build_agp.smk
+++ b/rules/LepAnchor/build_agp.smk
@@ -1,6 +1,5 @@
 rule construct_agp:
-  input:
-    cleaned = "10_PlaceAndOrientContigs/overlaps.removed.la"
+  input: "10_PlaceAndOrientContigs/overlaps.removed.la"
   output:
     agp = report("11_AGP/contigs/chr.{lg_range}.agp", category = "Contig AGP Files"),
     scaff_agp = report("11_AGP/scaffolds/chr.{lg_range}.scaffolds.agp", category = "Scaffold AGP Files")
@@ -9,8 +8,8 @@ rule construct_agp:
     chrom = "{lg_range}"
   shell:
     """
-    awk -vn={params.chrom} '($5==n)' {input.cleaned} | awk -vprefix="LG" -vlg={params.chrom} -f software/LepAnchor/scripts/makeagp_full2.awk - > {output.agp}
-    awk -vn={params.chrom} '($5==n)' {input.cleaned} | awk -vprefix="LG" -vlg={params.chrom} -f software/LepAnchor/scripts/makeagp2.awk - > {output.scaff_agp}
+    awk -vn={params.chrom} '($5==n)' {input} | awk -vprefix="LG" -vlg={params.chrom} -f software/LepAnchor/scripts/makeagp_full2.awk - > {output.agp}
+    awk -vn={params.chrom} '($5==n)' {input} | awk -vprefix="LG" -vlg={params.chrom} -f software/LepAnchor/scripts/makeagp2.awk - > {output.scaff_agp}
     """
 
 
diff --git a/rules/LepAnchor/build_fasta.smk b/rules/LepAnchor/build_fasta.smk
index 8aefe0a..c9fd642 100644
--- a/rules/LepAnchor/build_fasta.smk
+++ b/rules/LepAnchor/build_fasta.smk
@@ -2,49 +2,33 @@ rule build_scaffold_only_fasta:
   input:
     assembly = geno,
     agp = "11_AGP/lepanchor.contigs.only.agp"
-  output:
-    fasta = "12_Fasta/Anchored.scaffolds.only.fa.gz",
+  output: "12_Fasta/Anchored.scaffolds.only.fa.gz"
   message: "Constructing final scaffold-only fasta file {output.fasta}"
-  shell:
-    """
-    gunzip -fc {input.assembly} | awk -f software/LepAnchor/scripts/makefasta.awk - {input.agp} | gzip > {output.fasta}
-    """
+  shell: "gunzip -fc {input.assembly} | awk -f software/LepAnchor/scripts/makefasta.awk - {input.agp} | gzip > {output}"
 
 
 rule build_scaffold_contig_fasta:
   input:
     assembly = geno,
     agp = "11_AGP/lepanchor.contigs.all.agp"
-  output:
-    fasta = "12_Fasta/Anchored.scaffolds.fa.gz",
+  output: "12_Fasta/Anchored.scaffolds.fa.gz"
   message: "Constructing final scaffold fasta file {output.fasta}"
-  shell:
-    """
-    gunzip -fc {input.assembly} | awk -f software/LepAnchor/scripts/makefasta.awk - {input.agp} | gzip > {output.fasta}
-    """
+  shell: "gunzip -fc {input.assembly} | awk -f software/LepAnchor/scripts/makefasta.awk - {input.agp} | gzip > {output}"
 
 
 rule build_contig_only_fasta:
   input:
     assembly = geno,
     scaff_agp = "11_AGP/lepanchor.scaffolds.only.agp"
-  output:
-    fasta = "12_Fasta/Anchored.contigs.only.fa.gz"
+  output: "12_Fasta/Anchored.contigs.only.fa.gz"
   message: "Constructing final contig-only fasta file {output.fasta}"
-  shell:
-    """
-    gunzip -fc {input.assembly} | awk -f software/LepAnchor/scripts/makefasta.awk - {input.scaff_agp} | gzip > {output.fasta}
-    """
+  shell: "gunzip -fc {input.assembly} | awk -f software/LepAnchor/scripts/makefasta.awk - {input.scaff_agp} | gzip > {output}"
 
 
 rule build_contig_fasta:
   input:
     assembly = geno,
     scaff_agp = "11_AGP/lepanchor.scaffolds.all.agp"
-  output:
-    fasta = "12_Fasta/Anchored.contigs.fa.gz"
+  output: "12_Fasta/Anchored.contigs.fa.gz"
   message: "Constructing final contig fasta file {output.fasta}"
-  shell:
-    """
-    gunzip -fc {input.assembly} | awk -f software/LepAnchor/scripts/makefasta.awk - {input.scaff_agp} | gzip > {output.fasta}
-    """
\ No newline at end of file
+  shell: "gunzip -fc {input.assembly} | awk -f software/LepAnchor/scripts/makefasta.awk - {input.scaff_agp} | gzip > {output}"
\ No newline at end of file
diff --git a/rules/LepAnchor/generate_inputs.smk b/rules/LepAnchor/generate_inputs.smk
index affe53d..8dfb335 100644
--- a/rules/LepAnchor/generate_inputs.smk
+++ b/rules/LepAnchor/generate_inputs.smk
@@ -8,7 +8,7 @@ rule extract_markers:
 rule generate_input_data:
   input:
     markers = "snps.txt",
-    data = expand("7_Intervals/ordered.{x}.intervals", x = range(1, lg + 1)) if data_type == "noIntervals=0" else expand("7_Distances/ordered.{x}.distances", x = range(1, lg + 1))
+    data = expand("7_Intervals/ordered.{x}.intervals", x = lg_range) if data_type == "noIntervals=0" else expand("7_Distances/ordered.{x}.distances", x = lg_range)
   output: 
     data = report("10_PlaceAndOrientContigs/lepanchor.input", category = "Data")
   message: "Combining {params} Lep-Map3 files into single LepAnchor input {output}"
@@ -38,10 +38,7 @@ rule find_haplotypes:
   input: "9_Chain/chainfile.gz"
   output: report("10_PlaceAndOrientContigs/suspected.haplotypes.initial", category = "Logs")
   message: "Finding non-haplotype contigs not included in map.bed"
-  shell: 
-    """
-    gunzip -fc {input} | awk -f software/LepAnchor/scripts/findFullHaplotypes.awk > {output}
-    """
+  shell: "gunzip -fc {input} | awk -f software/LepAnchor/scripts/findFullHaplotypes.awk > {output}"
 
 
 rule liftover:
@@ -69,6 +66,7 @@ rule cleanmap:
     extras = cleanmap_extra
   shell: "java -cp software/LepAnchor CleanMap map={input} {params.extras} > {output} 2> {log}"
 
+
 rule map2bed:
   input: 
     cleanmap = "10_PlaceAndOrientContigs/map_all.clean",
diff --git a/rules/LepAnchor/place_orient1.smk b/rules/LepAnchor/place_orient1.smk
index f25d197..eb21666 100644
--- a/rules/LepAnchor/place_orient1.smk
+++ b/rules/LepAnchor/place_orient1.smk
@@ -6,8 +6,8 @@ rule place_orient:
     prox = proximity,
     lift = "10_PlaceAndOrientContigs/liftover.la"
   output:
-    chrom = "10_PlaceAndOrientContigs/orient_1/chr.{lg_range}.la",
-    chromerr = report("10_PlaceAndOrientContigs/orient_1/logs/chr.{lg_range}.la.log", category = "Anchoring I Logs")
+    chrom = "10_PlaceAndOrientContigs/1_orient/chr.{lg_range}.la",
+    chromerr = "10_PlaceAndOrientContigs/1_orient/logs/chr.{lg_range}.la.log"
   params:
     chrom = "{lg_range}",
     extras = place_orient_extra,
@@ -21,8 +21,8 @@ rule place_orient:
 
 rule propogate1:
   input: 
-    placed = expand("10_PlaceAndOrientContigs/orient_1/chr.{lgs}.la", lgs = lg_range),
-    errors = expand("10_PlaceAndOrientContigs/orient_1/logs/chr.{lgs}.la.log", lgs = lg_range),
+    placed = expand("10_PlaceAndOrientContigs/1_orient/chr.{lgs}.la", lgs = lg_range),
+    errors = expand("10_PlaceAndOrientContigs/1_orient/logs/chr.{lgs}.la.log", lgs = lg_range),
     bedfile = "10_PlaceAndOrientContigs/map_extra.bed"
   output:
     propogated = "10_PlaceAndOrientContigs/map.propogated.bed",
diff --git a/rules/LepAnchor/place_orient2.smk b/rules/LepAnchor/place_orient2.smk
index 000934f..912b9ba 100644
--- a/rules/LepAnchor/place_orient2.smk
+++ b/rules/LepAnchor/place_orient2.smk
@@ -5,10 +5,10 @@ rule place_orient2:
     paf = paf,
     prox = proximity,
     lift = "10_PlaceAndOrientContigs/liftover.la",
-    chrom = "10_PlaceAndOrientContigs/orient_1/chr.{lg_range}.la"
+    chrom = "10_PlaceAndOrientContigs/1_orient/chr.{lg_range}.la"
   output:
-    chrom = "10_PlaceAndOrientContigs/orient_2/chr.{lg_range}.la",
-    chromerr = "10_PlaceAndOrientContigs/orient_2/logs/chr.{lg_range}.err"
+    chrom = "10_PlaceAndOrientContigs/2_orient/chr.{lg_range}.la",
+    chromerr = "10_PlaceAndOrientContigs/2_orient/logs/chr.{lg_range}.err"
   params:
     chrom = "{lg_range}",
     extras = place_orient_extra,
@@ -22,8 +22,7 @@ rule place_orient2:
 
 rule propogate2:
   input:
-    placed = expand("10_PlaceAndOrientContigs/orient_2/chr.{lgs}.la", lgs = lg_range),
-    #placed = expand("10_PlaceAndOrientContigs/orient_2/logs/chr.{lgs}.err", lgs = lg_range),
+    placed = expand("10_PlaceAndOrientContigs/2_orient/chr.{lgs}.la", lgs = lg_range),
     bedfile = "10_PlaceAndOrientContigs/map.propogated.bed"
   output:
     prop = expand("10_PlaceAndOrientContigs/propogate/propogated.{lgs}.la", lgs = lg_range),
diff --git a/rules/LepAnchor/place_orient3.smk b/rules/LepAnchor/place_orient3.smk
index ae7f45c..7ab8ffa 100644
--- a/rules/LepAnchor/place_orient3.smk
+++ b/rules/LepAnchor/place_orient3.smk
@@ -5,11 +5,11 @@ rule place_orient3:
     paf = paf,
     prox = proximity,
     lift = "10_PlaceAndOrientContigs/liftover.la",
-    chrom = "10_PlaceAndOrientContigs/orient_1/chr.{lg_range}.la",
+    chrom = "10_PlaceAndOrientContigs/1_orient/chr.{lg_range}.la",
     propogated = "10_PlaceAndOrientContigs/propogate/propogated.{lg_range}.la"
   output:
-    chrom = "10_PlaceAndOrientContigs/orient_3/chr.{lg_range}.la",
-    errors = "10_PlaceAndOrientContigs/orient_3/errors/chr.{lg_range}.err"
+    chrom = "10_PlaceAndOrientContigs/3_orient/chr.{lg_range}.la",
+    errors = "10_PlaceAndOrientContigs/3_orient/errors/chr.{lg_range}.err"
   params:
     chrom = "{lg_range}",
     extras = place_orient_extra,
@@ -23,7 +23,7 @@ rule place_orient3:
     
 rule find_haplotypes2:
   input:
-    errors = expand("10_PlaceAndOrientContigs/orient_3/errors/chr.{lgs}.err", lgs = lg_range)
+    errors = expand("10_PlaceAndOrientContigs/3_orient/errors/chr.{lgs}.err", lgs = lg_range)
   output:
     haplos = "10_PlaceAndOrientContigs/suspected.haplotypes"
   message: "Finding full haplotypes"
@@ -39,7 +39,7 @@ rule find_haplotypes2:
 rule liftoverHaplotypes:
   input:
     chain = "9_Chain/chainfile.gz",
-    chrom = "10_PlaceAndOrientContigs/orient_1/chr.{lg_range}.la",
+    chrom = "10_PlaceAndOrientContigs/1_orient/chr.{lg_range}.la",
     haplos = "10_PlaceAndOrientContigs/suspected.haplotypes"
   output: "10_PlaceAndOrientContigs/liftover/chr.{lg_range}.liftover"
   message: "Running liftoverHaplotypes for {input.chrom}"
diff --git a/rules/LepAnchor/place_orient4.smk b/rules/LepAnchor/place_orient4.smk
index dd86e03..0928e9c 100644
--- a/rules/LepAnchor/place_orient4.smk
+++ b/rules/LepAnchor/place_orient4.smk
@@ -5,11 +5,11 @@ rule place_orient4:
         paf = paf,
         prox = proximity,
         lift = "10_PlaceAndOrientContigs/liftover.la",
-        chrom = "10_PlaceAndOrientContigs/orient_1/chr.{lg_range}.la",
-        chromlast = "10_PlaceAndOrientContigs/orient_3/chr.{lg_range}.la"
+        chrom = "10_PlaceAndOrientContigs/1_orient/chr.{lg_range}.la",
+        chromlast = "10_PlaceAndOrientContigs/3_orient/chr.{lg_range}.la"
     output:
-        chrom = "10_PlaceAndOrientContigs/orient_4/chr.{lg_range}.la",
-        err = "10_PlaceAndOrientContigs/orient_4/errors/chr.{lg_range}.errors"
+        chrom = "10_PlaceAndOrientContigs/4_orient/chr.{lg_range}.la",
+        err = "10_PlaceAndOrientContigs/4_orient/errors/chr.{lg_range}.errors"
     message: "Running 4th round of PlaceAndOrientContigs for linkage group {params.chrom}"
     params:
         chrom = "{lg_range}",
@@ -22,7 +22,7 @@ rule place_orient4:
         """
 
 rule prune_contigblocks:
-    input: "10_PlaceAndOrientContigs/orient_4/chr.{lg_range}.la"
+    input: "10_PlaceAndOrientContigs/4_orient/chr.{lg_range}.la"
     output: 
         chrom = "10_PlaceAndOrientContigs/pruned/chr.{lg_range}.pruned.la",
         err = temp("10_PlaceAndOrientContigs/pruned/err/chr.{lg_range}.pruned.err")

From a556c4ee41cbe6fad426fd10d7aa37bffaa4d287 Mon Sep 17 00:00:00 2001
From: Pavel Dimens <pdimens@live.com>
Date: Sun, 6 Feb 2022 14:19:44 -0500
Subject: [PATCH 19/46] restore my changes

---
 software/LepAnchor/scripts/plot_marey.R | 108 ++++++++++++------------
 1 file changed, 55 insertions(+), 53 deletions(-)

diff --git a/software/LepAnchor/scripts/plot_marey.R b/software/LepAnchor/scripts/plot_marey.R
index 3cd3ced..8bf6538 100644
--- a/software/LepAnchor/scripts/plot_marey.R
+++ b/software/LepAnchor/scripts/plot_marey.R
@@ -1,55 +1,57 @@
-library(scales)
+#! /usr/bin/env Rscript
+# Written by Pasi Rastas (2021)
+# modified by Pavel Dimens for Lep-Wrap (2021)
 
-map=read.table(gzfile("marey.data.gz")) 
-
-NN=unique(map$V3)
-MM=unique(map$V4)
-
-cl=rainbow(length(MM))
-
-
-for(lg in NN) {
-	print(lg)
-	png(paste0("marey", lg, ".png"),width=1024,height=1024)
-	ymax = 0
-	xmax = 0
-	for (m in MM) {
-		map_tmp = map[map$V1==paste0("LG",lg) & map$V3==lg & map$V4==m,]
-		if (nrow(map_tmp) > 0) {
-			ymax = max(ymax, max(map_tmp$V5))
-			xmax = max(xmax, max(map_tmp$V2))
-		}
-	}
-
-	index = 1
-	for (m in MM) {
-		map_tmp = map[map$V1==paste0("LG",lg) & map$V3==lg & map$V4==m,]
-		if (nrow(map_tmp) > 0) {
-			orientation=glm(map_tmp$V2 ~ map_tmp$V5)$coefficients[2] 
-			if (!is.na(orientation) && orientation < 0) {
-				map_tmp$V5 = max(map_tmp$V6) - map_tmp$V5
-				map_tmp$V6 = max(map_tmp$V6) - map_tmp$V6
-			}
-		}
-		if (index == 1) {
-			plot(map_tmp$V2, map_tmp$V5, xlab="Position (Mb)",ylab="Recombination Distance",xaxt="n", main=paste0("LG", lg), col=alpha(cl[index],0.3), pch=20, cex=1.0, ylim=c(0,ymax), xlim=c(0,xmax))
-			points(map_tmp$V2, map_tmp$V6, col=alpha(cl[index],0.3), pch=20, cex=1.0)
-        		arrows(map_tmp$V2, map_tmp$V5, map_tmp$V2, map_tmp$V6, length=0.0, col=alpha(cl[index],0.5),lwd=1.5)
-		}
-		else {
-			points(map_tmp$V2, map_tmp$V5, col=alpha(cl[index],0.3), pch=20, cex=1.0)
-			points(map_tmp$V2, map_tmp$V6, col=alpha(cl[index],0.3), pch=20, cex=1.0)
-        		arrows(map_tmp$V2, map_tmp$V5, map_tmp$V2, map_tmp$V6, length=0.0, col=alpha(cl[index],0.5),lwd=1.5)
-		}
-		index = index + 1
-	}
-
-	agp <- read.table(paste0("chr", lg, ".agp"))
-	agp=agp[agp$V1==paste0("LG",lg) & agp$V5=="W",c(1:3)]
-
-	segments(agp$V2,2*c(1:2),agp$V3,2*c(1:2),col=c("red","blue"),lwd=2,lend=1)
-	axis(1,seq(0,500000000,5000000),seq(0,500,5))
-	segments(agp$V2,0,agp$V2,ymax,lwd=0.5,col=rgb(0.5,0.5,0.5,0.2))
-	dev.off()
-}
+library(scales)
 
+args <- commandArgs(trailingOnly = TRUE)
+
+# args[1] = path/to/marey.data.gz
+# args[2] = directory/of/chrom AGP files
+
+map <- read.table(gzfile(args[1]))
+
+basedir <- dirname(args[1])
+
+NN <- unique(map$V3)
+MM <- unique(map$V4)
+
+cl <- rainbow(length(MM))
+
+for (lg in NN) {
+    #print(lg)
+    png(paste0(basedir, "/LG.", lg ,".mareymap", ".png"), width = 1024, height = 1024)
+    ymax <- 0
+    for (m in MM) {
+        map_tmp <- map[map$V3 == lg & map$V4 == m, ]
+        ymax <- max(ymax, max(map_tmp$V5))
+    }
+
+    index <- 1
+    for (m in MM) {
+        map_tmp <- map[map$V3 == lg & map$V4 == m, ]
+        if (glm(map_tmp$V2 ~ map_tmp$V5)$coefficients[2] < 0) {
+            map_tmp$V5 <- max(map_tmp$V5) - map_tmp$V5
+            map_tmp$V6 <- max(map_tmp$V6) - map_tmp$V6
+        }
+        if (index == 1) {
+            plot(map_tmp$V2, map_tmp$V5, xlab = "Position (Mb)", ylab = "Recombination Distance (cM)", xaxt = "n", main = paste0("LG", lg), col = alpha(cl[index], 0.3), pch = 20, cex = 1.0, ylim = c(0, ymax))
+            points(map_tmp$V2, map_tmp$V6, col = alpha(cl[index], 0.3), pch = 20, cex = 1.0)
+            arrows(map_tmp$V2, map_tmp$V5, map_tmp$V2, map_tmp$V6, length = 0.0, col = alpha(cl[index], 0.5), lwd = 1.5)
+        }
+        else {
+            points(map_tmp$V2, map_tmp$V5, col = alpha(cl[index], 0.3), pch = 20, cex = 1.0)
+            points(map_tmp$V2, map_tmp$V6, col = alpha(cl[index], 0.3), pch = 20, cex = 1.0)
+            arrows(map_tmp$V2, map_tmp$V5, map_tmp$V2, map_tmp$V6, length = 0.0, col = alpha(cl[index], 0.5), lwd = 1.5)
+        }
+        index <- index + 1
+    }
+
+    agp <- read.table(paste0(normalizePath(args[2]), "/chr.", lg, ".agp"))
+    agp <- agp[agp$V1 == paste0("LG", lg) & agp$V5 == "W", c(1:3)]
+
+    segments(agp$V2, 2 * c(1:2), agp$V3, 2 * c(1:2), col = c("red", "blue"), lwd = 2, lend = 1)
+    axis(1, seq(0, 500000000, 5000000), seq(0, 500, 5))
+    segments(agp$V2, 0, agp$V2, ymax, lwd = 0.5, col = rgb(0.5, 0.5, 0.5, 0.2))
+    dev.off()
+}
\ No newline at end of file

From 106c0861c33d745ac67d18904b56f5d25b0ad210 Mon Sep 17 00:00:00 2001
From: Pavel Dimens <pdimens@live.com>
Date: Sun, 6 Feb 2022 15:21:55 -0500
Subject: [PATCH 20/46] consolidate LAtrim and LepWrapTrim

---
 rules/LepAnchor/trim_edges.smk |   2 +-
 scripts/LATrim.r               | 162 ---------------------------------
 scripts/LepWrapTrim.r          |  45 ++++++---
 3 files changed, 33 insertions(+), 176 deletions(-)
 delete mode 100755 scripts/LATrim.r

diff --git a/rules/LepAnchor/trim_edges.smk b/rules/LepAnchor/trim_edges.smk
index 627c025..f6d2372 100644
--- a/rules/LepAnchor/trim_edges.smk
+++ b/rules/LepAnchor/trim_edges.smk
@@ -19,7 +19,7 @@ rule trim_newintervals:
   params:
     edge = edgelen,
     dist = trimdist
-  shell: "Rscript scripts/LATrim.r {input} {params.dist} {params.edge} 15_Trim"
+  shell: "Rscript scripts/LepWrapTrim.r {input} {params.dist} {params.edge} 15_Trim"
 
 
 rule merge_trimplots:
diff --git a/scripts/LATrim.r b/scripts/LATrim.r
deleted file mode 100755
index c4581d8..0000000
--- a/scripts/LATrim.r
+++ /dev/null
@@ -1,162 +0,0 @@
-#! /usr/bin/env Rscript
-
-suppressMessages(if (!require("tidyverse")) install.packages("tidyverse"))
-suppressMessages(library("tidyverse"))
-suppressMessages(if (!require("cowplot")) install.packages("cowplot"))
-library(cowplot)
-
-args <- commandArgs(trailingOnly = TRUE)
-# args[1] is the OrderMarkers2 output file
-# args[2] is the centimorgan cutoff distance
-# args[3] is the % of edge markers to scan
-# args[4] is the name of the output folder
-
-lgfile <- read.delim(
-  args[1], 
-  header = FALSE, 
-  sep = "\t", 
-  comment.char="#"
-) %>%
-  mutate(Mpass = T, Fpass = T)
-
-## setup output file names ##
-# split the filename by path
-filename <- unlist(strsplit(args[1], "/"))
-# pop out just the filename
-filename <- filename[length(filename)]
-lg <- (strsplit(lgfile[1,1], "LG") %>% unlist())[2] %>% as.numeric()
-
-#========= output instantiation ========#
-
-dir.create(args[4], showWarnings = FALSE)
-dir.create(paste0(args[4],"/plots"), showWarnings = FALSE)
-dir.create(paste0(args[4],"/logs"), showWarnings = FALSE)
-dir.create(paste0(args[4],"/QC_raw"), showWarnings = FALSE)
-outfile_base <- paste(args[4], filename, sep = "/")
-outfile_log_base <- paste(args[4], "logs", filename, sep = "/")
-plotfile_base <- paste(args[4], "plots", filename, sep = "/")
-plotfile <- paste(plotfile_base, "trim.pdf", sep = ".")
-rawfile_base <- paste(args[4], "QC_raw", filename, sep = "/")
-
-##### Pruning the ends #####
-dist_thresh <- as.numeric(args[2])
-if(dist_thresh >= 1){
-  dist_thresh <- dist_thresh * .01
-}
-
-dist_thresh_all <- c(
-  abs(max(lgfile[, 5]) - min(lgfile[, 5])) * dist_thresh,     # male
-  abs(max(lgfile[, 6]) - min(lgfile[, 6])) * dist_thresh      # female
-)
-
-# if the percent threshold is given as an integer, convert it to a decimal
-edge_length <- as.numeric(args[3])
-if(edge_length >= 1){
-  edge_length <- edge_length * .01
-}
-n_markers <- nrow(lgfile)
-forward_start <- round(n_markers * edge_length, digits = 0)
-reverse_start <- round(n_markers - forward_start, digits = 0)
-
-for (j in 5:6){   # iterate over male (5) and female (6)
-  # sort on column
-  lgfile <- arrange(lgfile, j)
-  dist_thresh <- dist_thresh_all[j-4]
-  # trim beginning
-  # the loop goes towards the edges to be effecient with the break() call, removing the
-  # entire cluster once one bad marker is found
-  for(a in forward_start:2){ #first n% of total markers starting from the forward edge, going out
-    diff <- abs(lgfile[a,j]-lgfile[a-1,j]) # difference between two points
-    if( diff > dist_thresh ){ # is the difference between the two points > distance argument?
-      lgfile[(a-1):1, j+2] <- FALSE # mark that marker and all markers BEFORE it as FAIL
-      break()
-    }
-  }
-  # trim end
-  for(z in reverse_start:(n_markers-1)){ #last n% total markers starting from the reverse edge going out
-    diff <- abs(lgfile[z+1,j]-lgfile[z,j]) # difference between two points
-    if( diff > dist_thresh ){ # is the difference between the two points > distance argument?
-      lgfile[(z+1):n_markers,j+2] <- FALSE # mark that marker and all markers AFTER it as FAIL
-      break()
-    }
-  }
-}
-
-# create new table of markers passing QC
-cleaned_markers <- (lgfile %>% filter(Mpass & Fpass))[,1:6]
-# re-scale cleaned markers to 0 by subtracting the minimum genetic position
-cleaned_markers <- cleaned_markers %>%
-    mutate(V5 = V5 - min(V5), V6 = V6 - min(V6))
-
-# isolate bad markers
-removed_markers <- (lgfile %>% filter(!Mpass | !Fpass))[,1:6]
-
-# get simple counts
-rm_male <- lgfile %>% filter(!Mpass & Fpass) %>% nrow()
-rm_female <- lgfile %>% filter(!Fpass & Mpass) %>% nrow()
-rm_both <- lgfile %>% filter(!Mpass & !Fpass) %>% nrow()
-
-pdf(NULL)
-
-plot_male <- lgfile %>% arrange(V5) %>%
-  ggplot(aes(x = seq_along(V5), y = V5, color = Mpass)) +
-  geom_point(shape = 19) +
-  scale_color_manual(values = c("dodgerblue", "indianred2"), limits = c(T, F)) +
-  geom_vline(xintercept = forward_start, linetype = "dashed", size = 0.2) +
-  geom_vline(xintercept = reverse_start, linetype = "dashed", size = 0.2) +
-  labs(
-    title = "",
-    subtitle = paste0(rm_male, " male markers >", dist_thresh_all[1], "cM trimmed"),
-    caption = paste0(edge_length, "% edge markers, ", dist_thresh, "% cM"),
-    x = "Marker Number", 
-    y = "Position (cM)", 
-    color = "Pass Filtering"
-  )
-
-plot_female <- lgfile %>% arrange(V6) %>%
-  ggplot(aes(x = seq_along(V6), y = V6, color = Fpass)) +
-  geom_point(shape = 19) +
-  scale_color_manual(values = c("dodgerblue", "indianred2"), limits = c(T, F)) +
-  geom_vline(xintercept = forward_start, linetype = "dashed", size = 0.2) +
-  geom_vline(xintercept = reverse_start, linetype = "dashed", size = 0.2) +
-  labs(
-    title = paste("Edge Cluster Trimming for LG:", lg),
-    subtitle = paste0(rm_female, " female markers >", dist_thresh_all[2], "cM trimmed"),
-    caption = paste0("Markers failing both M+F: ", rm_both),
-    x = "Marker Number", 
-    y = "Position (cM)", 
-    color = "Pass Filtering",
-    legend.position = "none"
-  )
-
-plot_grid(plot_female, plot_male, ncol = 2, nrow = 1)
-
-suppressMessages(ggsave(plotfile, width = 7, height = 3, units = "in"))
-
-write.table(
-  cleaned_markers, 
-  file = paste(outfile_base, "trimmed", sep = "."), 
-  sep = "\t",
-  quote = FALSE, 
-  row.names = FALSE,
-  col.names = FALSE,
-)
-
-write.table(
-  lgfile, 
-  file = paste(rawfile_base, "filtered.raw", sep = "."), 
-  sep = "\t",
-  quote = FALSE, 
-  row.names = FALSE,
-  col.names = FALSE,
-)
-
-write.table(
-  removed_markers,
-  file=paste(outfile_log_base, "removed", sep = "."),
-  append=FALSE, 
-  sep = "\t", 
-  quote = FALSE, 
-  row.names = FALSE, 
-  col.names = FALSE
-)
\ No newline at end of file
diff --git a/scripts/LepWrapTrim.r b/scripts/LepWrapTrim.r
index 6a6e17a..d1c0166 100755
--- a/scripts/LepWrapTrim.r
+++ b/scripts/LepWrapTrim.r
@@ -4,7 +4,7 @@ suppressMessages(if (!require("tidyverse")) install.packages("tidyverse"))
 suppressMessages(library("tidyverse"))
 
 args <- commandArgs(trailingOnly = TRUE)
-# args[1] is the OrderMarkers2 output file
+# args[1] is the OrderMarkers2/LepAnchor output file
 # args[2] is the centiMorgan cutoff threshold
 # args[3] is the % of edge markers to scan
 # args[4] is the output directory
@@ -39,12 +39,27 @@ lgfile <- read.delim(
 ) %>%
   mutate(Mpass = T, Fpass = T)
 
+# Modify which columns to look at based on input format
+# LM3 input has 5 columns + 2 from M|Fpass
+# LA input has 6 columns + 2 from M|Fpass
+if(ncol(lgfile) == 7) {
+  # LepMap3 input file
+  idxcol <- c(2,3)
+  keepcol <- 1:5
+  lgidx <- 2
+} else {
+  # LepAnchor input file
+  idxcol <- c(5, 6)
+  keepcol <- 1:6
+  lgidx <- 3
+}
+
 ## setup output file names ##
 # split the filename by path
 filename <- unlist(strsplit(args[1], "/"))
 # pop out just the filename
 filename <- filename[length(filename)]
-lg <- unlist(strsplit(filename, "\\."))[2]
+lg <- unlist(strsplit(filename, "\\."))[lgidx]
 
 #========= instantiate output ========#
 dir.create(args[4], showWarnings = FALSE)
@@ -66,8 +81,8 @@ if(dist_thresh >= 1){
 }
 
 dist_thresh_all <- c(
-  abs(max(lgfile[, 2]) - min(lgfile[, 2])) * dist_thresh,     # male
-  abs(max(lgfile[, 3]) - min(lgfile[, 3])) * dist_thresh      # female
+  abs(max(lgfile[, idxcol[1]]) - min(lgfile[, idxcol[1]])) * dist_thresh,     # male
+  abs(max(lgfile[, idxcol[2]]) - min(lgfile[, idxcol[2]])) * dist_thresh      # female
 )
 
 edge_length <- as.numeric(args[3])
@@ -80,10 +95,11 @@ forward_start <- round(n_markers * edge_length, digits = 0)
 reverse_start <- round(n_markers - forward_start, digits = 0)
 
 # iterate over male (2) and female (3)
-for (j in 2:3){
+threshidx <- 1
+for (j in idxcol){
   # sort on column
   lgfile <- arrange(lgfile, j)
-  dist_thresh <- dist_thresh_all[j-1]
+  dist_thresh <- dist_thresh_all[threshidx]
   # trim beginning
   for(a in forward_start:2){ #first n% of total markers from the beginning
     diff <- abs(lgfile[a,j]-lgfile[a-1,j]) # difference between two points
@@ -100,6 +116,7 @@ for (j in 2:3){
       break()
     }
   }
+  threshidx <- threshidx + 1
 }
 
 # isolate bad markers
@@ -115,7 +132,7 @@ rm_both <- lgfile %>% filter(!Mpass & !Fpass) %>% nrow()
 pdf(NULL)
 
 plot_df <- lgfile %>%
-  rename(Male = V2, Female = V3) %>%
+  rename(Male = idxcol[1], Female = idxcol[2]) %>%
   arrange(Male) %>%
   mutate(Marker = seq_along(Mpass)) %>%
   rowwise() %>%
@@ -126,15 +143,17 @@ plot_df <- lgfile %>%
   mutate(Fail = QAfix(Fail, Sex))
 
 plot_df %>%
-  ggplot(aes(Marker, Position, color = Fail)) +
-  geom_point(shape = 19, alpha = 0.3) +
+  ggplot(aes(Marker, Position, color = Fail, shape = Fail)) +
+  geom_point(alpha = 0.5) +
   scale_color_manual(values = c("dodgerblue", "indianred2"), limits = c(T, F)) +
+  scale_shape_manual(values = c(19, 17), limits = c(T, F), guide = "none") +
   geom_vline(xintercept = forward_start, linetype = "dashed", size = 0.2) +
   geom_vline(xintercept = reverse_start, linetype = "dashed", size = 0.2) +
+  guides(color = guide_legend(override.aes = list(size = c(2,2), shape = c(19, 17)))) +
   labs(
     title = paste("Edge Cluster Trimming Results for Linkage Group", lg),
     subtitle = paste0("Markers Failing QC: ", rm_female, " female, ", rm_male, " male, ", rm_both, " both (", rm_female+rm_male+rm_both, " total)" ),
-    caption = paste0(edge_length*100, "% of edge markers, ", args[2], "% cM threshold: ", dist_thresh_all[2], "(F)  &  ", dist_thresh_all[1], "(M)"),
+    caption = paste0(edge_length*100, "% of edge markers, ", args[2], "% cM threshold: ", round(dist_thresh_all[2], digits = 2), "(F)  &  ", round(dist_thresh_all[1], digits = 2), "(M)"),
     x = "Marker Number", 
     y = "Position (cM)", 
     color = "Pass QA"
@@ -151,14 +170,14 @@ fail_idx <- which(!lgfile$QC)
 # prepend a comment to the flagged markers so LepMap3 ignores them
 lgfile[fail_idx, 1] <- paste0("#", lgfile[fail_idx, 1])
 # re-scale remaining markers to 0 by subtracting the minimum genetic position for each sex
-lgfile[,2] <- round(lgfile[,2] - (min(lgfile[lgfile$QC,2])), digits = 3)
-lgfile[,3] <- round(lgfile[,3] - (min(lgfile[lgfile$QC,3])), digits = 3)
+lgfile[,idxcol[1]] <- round(lgfile[,idxcol[1]] - (min(lgfile[lgfile$QC,idxcol[1]])), digits = 3)
+lgfile[,idxcol[2]] <- round(lgfile[,idxcol[2]] - (min(lgfile[lgfile$QC,idxcol[2]])), digits = 3)
 
 # write header to a new file
 writeLines(readLines(args[1], n=2), con = paste(outfile_base, "trimmed", sep = "."))
 # write the remainder to that file
 write.table(
-  lgfile[,1:5], 
+  lgfile[, keepcol], 
   file =  paste(outfile_base, "trimmed", sep = "."), 
   sep = "\t",
   quote = FALSE, 

From 821a2a7cb8489c769d01b9471f40078291cf3eef Mon Sep 17 00:00:00 2001
From: Pavel Dimens <pdimens@live.com>
Date: Sun, 6 Feb 2022 15:24:57 -0500
Subject: [PATCH 21/46] pedantic codefix

---
 LepWrap | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/LepWrap b/LepWrap
index 5c37ce5..62173a3 100755
--- a/LepWrap
+++ b/LepWrap
@@ -4,8 +4,7 @@
 if [[ -z "$1" ]]; then
   echo "Perform the modules of Lep-Map3 and/or Lep-Anchor" 
   echo "The config file (default: config.yml) must be configured"
-  echo "The second positional argument is optional if your config file is named config.yml"
-  echo ""
+  echo -e "The second positional argument is optional if your config file is named config.yml\n"
   printf "\033[01;32m"
   printf "[usage]"
   printf "\033[0m"
@@ -17,7 +16,7 @@ if [[ -z "$1" ]]; then
   printf "\033[01;32m"
   printf "[example]"
   printf "\033[0m"
-  echo " LepWrap 30 kosambi.20iterations.yml"
+  echo -e " LepWrap 30 kosambi.20iterations.yml"
   exit 1
 fi
 

From 9d649c137843eafd417393f36aca3b0be1783141 Mon Sep 17 00:00:00 2001
From: Pavel Dimens <pdimens@live.com>
Date: Sun, 6 Feb 2022 15:33:05 -0500
Subject: [PATCH 22/46] fix legacy code

---
 LepWrap                         | 2 +-
 rules/LepAnchor/build_fasta.smk | 8 ++++----
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/LepWrap b/LepWrap
index 62173a3..ca90068 100755
--- a/LepWrap
+++ b/LepWrap
@@ -193,7 +193,7 @@ is_int()  { case ${1#[-+]} in '' | *[!0-9]*              ) return 1;; esac ;}
 if $(is_int $1); then
   foo=1
 else
-  echo "Error: the first argument must the number of threads, as an integer."
+  echo "Error: the first argument must be the number of threads, as an integer."
   exit 1
 fi
 
diff --git a/rules/LepAnchor/build_fasta.smk b/rules/LepAnchor/build_fasta.smk
index c9fd642..4e9d7b5 100644
--- a/rules/LepAnchor/build_fasta.smk
+++ b/rules/LepAnchor/build_fasta.smk
@@ -3,7 +3,7 @@ rule build_scaffold_only_fasta:
     assembly = geno,
     agp = "11_AGP/lepanchor.contigs.only.agp"
   output: "12_Fasta/Anchored.scaffolds.only.fa.gz"
-  message: "Constructing final scaffold-only fasta file {output.fasta}"
+  message: "Constructing final scaffold-only fasta file {output}"
   shell: "gunzip -fc {input.assembly} | awk -f software/LepAnchor/scripts/makefasta.awk - {input.agp} | gzip > {output}"
 
 
@@ -12,7 +12,7 @@ rule build_scaffold_contig_fasta:
     assembly = geno,
     agp = "11_AGP/lepanchor.contigs.all.agp"
   output: "12_Fasta/Anchored.scaffolds.fa.gz"
-  message: "Constructing final scaffold fasta file {output.fasta}"
+  message: "Constructing final scaffold fasta file {output}"
   shell: "gunzip -fc {input.assembly} | awk -f software/LepAnchor/scripts/makefasta.awk - {input.agp} | gzip > {output}"
 
 
@@ -21,7 +21,7 @@ rule build_contig_only_fasta:
     assembly = geno,
     scaff_agp = "11_AGP/lepanchor.scaffolds.only.agp"
   output: "12_Fasta/Anchored.contigs.only.fa.gz"
-  message: "Constructing final contig-only fasta file {output.fasta}"
+  message: "Constructing final contig-only fasta file {output}"
   shell: "gunzip -fc {input.assembly} | awk -f software/LepAnchor/scripts/makefasta.awk - {input.scaff_agp} | gzip > {output}"
 
 
@@ -30,5 +30,5 @@ rule build_contig_fasta:
     assembly = geno,
     scaff_agp = "11_AGP/lepanchor.scaffolds.all.agp"
   output: "12_Fasta/Anchored.contigs.fa.gz"
-  message: "Constructing final contig fasta file {output.fasta}"
+  message: "Constructing final contig fasta file {output}"
   shell: "gunzip -fc {input.assembly} | awk -f software/LepAnchor/scripts/makefasta.awk - {input.scaff_agp} | gzip > {output}"
\ No newline at end of file

From 7dabf47c145dd3532783fb60aa7fb31d93ee4089 Mon Sep 17 00:00:00 2001
From: Pavel Dimens <pdimens@live.com>
Date: Sun, 6 Feb 2022 15:33:39 -0500
Subject: [PATCH 23/46] add missing message

---
 rules/LepAnchor/trim_edges.smk | 1 +
 1 file changed, 1 insertion(+)

diff --git a/rules/LepAnchor/trim_edges.smk b/rules/LepAnchor/trim_edges.smk
index f6d2372..e00a10e 100644
--- a/rules/LepAnchor/trim_edges.smk
+++ b/rules/LepAnchor/trim_edges.smk
@@ -39,4 +39,5 @@ rule merge_trimmedintervals:
 rule plot_trimmedintervals:
   input: "16_MareyMapsTrimmed/data.marey.trimmed.gz"
   output: report("16_MareyMapsTrimmed/LepAnchor.mareymaps.pdf", category = "Trimmed Marey Maps")
+  message: "Plotting results of edge trimming"
   shell: "Rscript scripts/LASummary.r {input}"
\ No newline at end of file

From ab4ee98229d2421a5358b03a163bce6bba7b423d Mon Sep 17 00:00:00 2001
From: Pavel Dimens <pdimens@live.com>
Date: Sun, 6 Feb 2022 19:05:53 -0500
Subject: [PATCH 24/46] fix plot script

---
 scripts/LepWrapTrim.r | 23 ++++++++++++-----------
 1 file changed, 12 insertions(+), 11 deletions(-)

diff --git a/scripts/LepWrapTrim.r b/scripts/LepWrapTrim.r
index d1c0166..d4c6290 100755
--- a/scripts/LepWrapTrim.r
+++ b/scripts/LepWrapTrim.r
@@ -39,6 +39,12 @@ lgfile <- read.delim(
 ) %>%
   mutate(Mpass = T, Fpass = T)
 
+## setup output file names ##
+# split the filename by path
+filename <- unlist(strsplit(args[1], "/"))
+# pop out just the filename
+filename <- filename[length(filename)]
+
 # Modify which columns to look at based on input format
 # LM3 input has 5 columns + 2 from M|Fpass
 # LA input has 6 columns + 2 from M|Fpass
@@ -46,21 +52,16 @@ if(ncol(lgfile) == 7) {
   # LepMap3 input file
   idxcol <- c(2,3)
   keepcol <- 1:5
-  lgidx <- 2
+  lg <- unlist(strsplit(filename, "\\."))[2]
+  colshift <- 4
 } else {
   # LepAnchor input file
   idxcol <- c(5, 6)
   keepcol <- 1:6
-  lgidx <- 3
+  lg <- unlist(strsplit(filename, "\\."))[3]
+  colshift <- 2
 }
 
-## setup output file names ##
-# split the filename by path
-filename <- unlist(strsplit(args[1], "/"))
-# pop out just the filename
-filename <- filename[length(filename)]
-lg <- unlist(strsplit(filename, "\\."))[lgidx]
-
 #========= instantiate output ========#
 dir.create(args[4], showWarnings = FALSE)
 dir.create(paste0(args[4],"/plots"), showWarnings = FALSE)
@@ -104,7 +105,7 @@ for (j in idxcol){
   for(a in forward_start:2){ #first n% of total markers from the beginning
     diff <- abs(lgfile[a,j]-lgfile[a-1,j]) # difference between two points
     if( diff > dist_thresh ){ # is the difference between the two points > distance argument?
-      lgfile[(a-1):1, j+4] <- FALSE # all markers BEFORE it as FAIL
+      lgfile[(a-1):1, j + colshift] <- FALSE # all markers BEFORE it as FAIL
       break()
     }
   }
@@ -112,7 +113,7 @@ for (j in idxcol){
   for(z in reverse_start:(n_markers-1)){ #last n% total markers starting from the back edge going out
     diff <- abs(lgfile[z+1,j]-lgfile[z,j]) # difference between two points
     if( diff > dist_thresh ){ # is the difference between the two points > distance argument?
-      lgfile[(z+1):n_markers,j+4] <- FALSE # all markers AFTER it as FAIL
+      lgfile[(z+1):n_markers, j + colshift] <- FALSE # all markers AFTER it as FAIL
       break()
     }
   }

From 44fe78f6454580cab1f35995d93be7fff94d4a61 Mon Sep 17 00:00:00 2001
From: Pavel Dimens <pdimens@live.com>
Date: Tue, 8 Feb 2022 20:03:05 -0500
Subject: [PATCH 25/46] omit place iteration 4

---
 rules/LepAnchor/LepAnchor.smk     |  2 +-
 rules/LepAnchor/place_orient3.smk | 97 ++++++++++++++++++++-----------
 rules/LepAnchor/place_orient4.smk |  3 +-
 3 files changed, 64 insertions(+), 38 deletions(-)

diff --git a/rules/LepAnchor/LepAnchor.smk b/rules/LepAnchor/LepAnchor.smk
index e15c3fe..c318868 100644
--- a/rules/LepAnchor/LepAnchor.smk
+++ b/rules/LepAnchor/LepAnchor.smk
@@ -24,7 +24,7 @@ include: "mask_and_chain.smk"
 include: "place_orient1.smk"
 include: "place_orient2.smk"
 include: "place_orient3.smk"
-include: "place_orient4.smk"
+#include: "place_orient4.smk" 
 include: "build_agp.smk"
 include: "build_fasta.smk"
 include: "mareymaps_untrimmed.smk"
diff --git a/rules/LepAnchor/place_orient3.smk b/rules/LepAnchor/place_orient3.smk
index 7ab8ffa..ad820af 100644
--- a/rules/LepAnchor/place_orient3.smk
+++ b/rules/LepAnchor/place_orient3.smk
@@ -21,40 +21,67 @@ rule place_orient3:
     gunzip -fc {input.chain} | java -cp software/LepAnchor PlaceAndOrientContigs chromosome={params.chrom} numThreads={threads} $(awk -f software/LepAnchor/scripts/pickorientation.awk {input.chrom}) bed={input.bedfile} map={input.lift} chain=- paf={input.paf} proximity={input.prox} evaluateAnchoring={input.propogated} improveAnchoring=1 {params.datatype} {params.extras} > {output.chrom} 2> {output.errors}
     """
     
-rule find_haplotypes2:
-  input:
-    errors = expand("10_PlaceAndOrientContigs/3_orient/errors/chr.{lgs}.err", lgs = lg_range)
-  output:
-    haplos = "10_PlaceAndOrientContigs/suspected.haplotypes"
-  message: "Finding full haplotypes"
-  params:
-    haplo = haplo_limit
-  shell:
-    """
-    awk '($NF=="haplotype")' {input.errors} | 
-      sort -n -r | 
-      awk -vlimit={params.haplo} '($NF=="haplotype" && ($1>=($4-$3+1-limit)/limit) && (!(($5 SUBSEP $6 SUBSEP $7) in h))){{h[$2,$3,$4]; print}}' > {output.haplos}
-    """
+rule prune_contigblocks:
+    input: "expand(10_PlaceAndOrientContigs/3_orient/chr.{lg_range}.la")
+    output: 
+        chrom = "10_PlaceAndOrientContigs/pruned/chr.{lg_range}.pruned.la",
+        err = "10_PlaceAndOrientContigs/pruned/err/chr.{lg_range}.pruned.err"
+    message: "Pruning contig blocks without map support and removing overlaps"
+    params:
+        chrom = lg
+    shell: "awk -f software/LepAnchor/scripts/prune.awk {input} > {output.chrom} 2> {output.err}"
 
-rule liftoverHaplotypes:
-  input:
-    chain = "9_Chain/chainfile.gz",
-    chrom = "10_PlaceAndOrientContigs/1_orient/chr.{lg_range}.la",
-    haplos = "10_PlaceAndOrientContigs/suspected.haplotypes"
-  output: "10_PlaceAndOrientContigs/liftover/chr.{lg_range}.liftover"
-  message: "Running liftoverHaplotypes for {input.chrom}"
-  threads: 1
-  shell:
-    """
-    gunzip -fc {input.chain} | java -cp software/LepAnchor LiftoverHaplotypes map={input.chrom} haplotypes={input.haplos} chain=- > {output}
-    """
+rule prune_post:
+    input:
+        bedfile = "10_PlaceAndOrientContigs/map.propogated2.bed",
+        prunedchrom = expand("10_PlaceAndOrientContigs/pruned/chr.{lgs}.pruned.la", lgs = lg_range),
+        prunederr = expand("10_PlaceAndOrientContigs/pruned/err/chr.{lgs}.pruned.err", lgs = lg_range)
+    output: 
+        overlaps = "10_PlaceAndOrientContigs/overlaps.removed.la",
+        pruned = "10_PlaceAndOrientContigs/pruned.la"
+    message: "Removing overlaps"
+    threads: 1
+    shell:
+        """
+        cat {input.prunederr} > {output.pruned}
+        awk -f software/LepAnchor/scripts/removeOverlaps.awk {input.bedfile} {input.prunedchrom} > {output.overlaps}
+        """
 
-rule removehaplotypes:
-  input:
-    mapfile = "10_PlaceAndOrientContigs/map.propogated2.bed", 
-    haplos = "10_PlaceAndOrientContigs/suspected.haplotypes"
-  output:
-    bedfile = "10_PlaceAndOrientContigs/map.propogated2.nohaplo.bed"
-  message: "Removing haplotypes from the map"
-  threads: 1
-  shell: "awk -f software/LepAnchor/scripts/removeHaplotypes.awk {input} > {output}"
+#rule find_haplotypes2:
+#  input:
+#    errors = expand("10_PlaceAndOrientContigs/3_orient/errors/chr.{lgs}.err", lgs = lg_range)
+#  output:
+#    haplos = "10_PlaceAndOrientContigs/suspected.haplotypes"
+#  message: "Finding full haplotypes"
+#  params:
+#    haplo = haplo_limit
+#  shell:
+#    """
+#    awk '($NF=="haplotype")' {input.errors} | 
+#      sort -n -r | 
+#      awk -vlimit={params.haplo} '($NF=="haplotype" && ($1>=($4-$3+1-limit)/limit) && (!(($5 SUBSEP $6 SUBSEP $7) in h))){{h[$2,$3,$4]; print}}' > {output.haplos}
+#    """
+#
+#rule liftoverHaplotypes:
+#  input:
+#    chain = "9_Chain/chainfile.gz",
+#    chrom = "10_PlaceAndOrientContigs/1_orient/chr.{lg_range}.la",
+#    haplos = "10_PlaceAndOrientContigs/suspected.haplotypes"
+#  output: "10_PlaceAndOrientContigs/liftover/chr.{lg_range}.liftover"
+#  message: "Running liftoverHaplotypes for {input.chrom}"
+#  threads: 1
+#  shell:
+#    """
+#    gunzip -fc {input.chain} | java -cp software/LepAnchor LiftoverHaplotypes map={input.chrom} haplotypes={input.haplos} chain=- > {output}
+#    """
+#
+#rule removehaplotypes:
+#  input:
+#    mapfile = "10_PlaceAndOrientContigs/map.propogated2.bed", 
+#    haplos = "10_PlaceAndOrientContigs/suspected.haplotypes"
+#  output:
+#    bedfile = "10_PlaceAndOrientContigs/map.propogated2.nohaplo.bed"
+#  message: "Removing haplotypes from the map"
+#  threads: 1
+#  shell: "awk -f software/LepAnchor/scripts/removeHaplotypes.awk {input} > {output}"
+#
\ No newline at end of file
diff --git a/rules/LepAnchor/place_orient4.smk b/rules/LepAnchor/place_orient4.smk
index 0928e9c..f7c0f40 100644
--- a/rules/LepAnchor/place_orient4.smk
+++ b/rules/LepAnchor/place_orient4.smk
@@ -22,10 +22,9 @@ rule place_orient4:
         """
 
 rule prune_contigblocks:
-    input: "10_PlaceAndOrientContigs/4_orient/chr.{lg_range}.la"
+    input: "expand(10_PlaceAndOrientContigs/4_orient/chr.{lgs}.la", lgs = lg_range)
     output: 
         chrom = "10_PlaceAndOrientContigs/pruned/chr.{lg_range}.pruned.la",
-        err = temp("10_PlaceAndOrientContigs/pruned/err/chr.{lg_range}.pruned.err")
     message: "Pruning contig blocks without map support and removing overlaps"
     params:
         chrom = lg

From bcbf9d4809b4a6934147c04381c0fe689a1e2660 Mon Sep 17 00:00:00 2001
From: Pavel Dimens <pdimens@live.com>
Date: Tue, 8 Feb 2022 20:06:31 -0500
Subject: [PATCH 26/46] fix indentation

---
 rules/LepAnchor/place_orient3.smk | 44 +++++++++++++++----------------
 1 file changed, 22 insertions(+), 22 deletions(-)

diff --git a/rules/LepAnchor/place_orient3.smk b/rules/LepAnchor/place_orient3.smk
index ad820af..8c736fe 100644
--- a/rules/LepAnchor/place_orient3.smk
+++ b/rules/LepAnchor/place_orient3.smk
@@ -22,30 +22,30 @@ rule place_orient3:
     """
     
 rule prune_contigblocks:
-    input: "expand(10_PlaceAndOrientContigs/3_orient/chr.{lg_range}.la")
-    output: 
-        chrom = "10_PlaceAndOrientContigs/pruned/chr.{lg_range}.pruned.la",
-        err = "10_PlaceAndOrientContigs/pruned/err/chr.{lg_range}.pruned.err"
-    message: "Pruning contig blocks without map support and removing overlaps"
-    params:
-        chrom = lg
-    shell: "awk -f software/LepAnchor/scripts/prune.awk {input} > {output.chrom} 2> {output.err}"
+  input: "expand(10_PlaceAndOrientContigs/3_orient/chr.{lg_range}.la")
+  output: 
+    chrom = "10_PlaceAndOrientContigs/pruned/chr.{lg_range}.pruned.la",
+    err = "10_PlaceAndOrientContigs/pruned/err/chr.{lg_range}.pruned.err"
+  message: "Pruning contig blocks without map support and removing overlaps"
+  params:
+    chrom = lg
+  shell: "awk -f software/LepAnchor/scripts/prune.awk {input} > {output.chrom} 2> {output.err}"
 
 rule prune_post:
-    input:
-        bedfile = "10_PlaceAndOrientContigs/map.propogated2.bed",
-        prunedchrom = expand("10_PlaceAndOrientContigs/pruned/chr.{lgs}.pruned.la", lgs = lg_range),
-        prunederr = expand("10_PlaceAndOrientContigs/pruned/err/chr.{lgs}.pruned.err", lgs = lg_range)
-    output: 
-        overlaps = "10_PlaceAndOrientContigs/overlaps.removed.la",
-        pruned = "10_PlaceAndOrientContigs/pruned.la"
-    message: "Removing overlaps"
-    threads: 1
-    shell:
-        """
-        cat {input.prunederr} > {output.pruned}
-        awk -f software/LepAnchor/scripts/removeOverlaps.awk {input.bedfile} {input.prunedchrom} > {output.overlaps}
-        """
+  input:
+    bedfile = "10_PlaceAndOrientContigs/map.propogated2.bed",
+    prunedchrom = expand("10_PlaceAndOrientContigs/pruned/chr.{lgs}.pruned.la", lgs = lg_range),
+    prunederr = expand("10_PlaceAndOrientContigs/pruned/err/chr.{lgs}.pruned.err", lgs = lg_range)
+  output: 
+    overlaps = "10_PlaceAndOrientContigs/overlaps.removed.la",
+    pruned = "10_PlaceAndOrientContigs/pruned.la"
+  message: "Removing overlaps"
+  threads: 1
+  shell:
+    """
+    cat {input.prunederr} > {output.pruned}
+    awk -f software/LepAnchor/scripts/removeOverlaps.awk {input.bedfile} {input.prunedchrom} > {output.overlaps}
+      """
 
 #rule find_haplotypes2:
 #  input:

From f7c1115a9afcdda02de762c247e658396efcff88 Mon Sep 17 00:00:00 2001
From: Pavel Dimens <pdimens@live.com>
Date: Tue, 8 Feb 2022 20:07:43 -0500
Subject: [PATCH 27/46] remove expand call

---
 rules/LepAnchor/place_orient3.smk | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/rules/LepAnchor/place_orient3.smk b/rules/LepAnchor/place_orient3.smk
index 8c736fe..8193be7 100644
--- a/rules/LepAnchor/place_orient3.smk
+++ b/rules/LepAnchor/place_orient3.smk
@@ -22,7 +22,7 @@ rule place_orient3:
     """
     
 rule prune_contigblocks:
-  input: "expand(10_PlaceAndOrientContigs/3_orient/chr.{lg_range}.la")
+  input: "10_PlaceAndOrientContigs/3_orient/chr.{lg_range}.la"
   output: 
     chrom = "10_PlaceAndOrientContigs/pruned/chr.{lg_range}.pruned.la",
     err = "10_PlaceAndOrientContigs/pruned/err/chr.{lg_range}.pruned.err"

From b8029573a07131e00be2500699b475b308f73321 Mon Sep 17 00:00:00 2001
From: Pavel Dimens <pdimens@live.com>
Date: Tue, 8 Feb 2022 20:24:11 -0500
Subject: [PATCH 28/46] fix unused contig finding

---
 rules/LepAnchor/build_agp.smk | 10 ++++------
 1 file changed, 4 insertions(+), 6 deletions(-)

diff --git a/rules/LepAnchor/build_agp.smk b/rules/LepAnchor/build_agp.smk
index 8a9116b..0854114 100644
--- a/rules/LepAnchor/build_agp.smk
+++ b/rules/LepAnchor/build_agp.smk
@@ -12,23 +12,21 @@ rule construct_agp:
     awk -vn={params.chrom} '($5==n)' {input} | awk -vprefix="LG" -vlg={params.chrom} -f software/LepAnchor/scripts/makeagp2.awk - > {output.scaff_agp}
     """
 
-
 rule unused:
   input:
     lengths = "10_PlaceAndOrientContigs/contigs.length",
-    haplos = "10_PlaceAndOrientContigs/suspected.haplotypes",
-    cleaned = "10_PlaceAndOrientContigs/overlaps.removed.la",
+    haplos = "10_PlaceAndOrientContigs/suspected.haplotypes.initial",
+    agp = expand("11_AGP/contigs/chr.{lgs}.agp", lgs = lg_range)
   output: 
-    txt = "11_AGP/not_used_final.txt",
+    txt = "11_AGP/not_used.txt",
     agp = "11_AGP/not_used.agp"
   message: "Finding unused contigs"
   shell:
     """
-    cut -f 1 {input.lengths} | grep -v -w -F -f <(cut -f2 {input.haplos}; cut -f1 {input.cleaned}) > {output.txt}
+    cut -f 1 {input.lengths} | grep -v -w -F -f <(cut -f 2 {input.haplos}; awk '($5!="U"){{print $6}}' {input.agp}) > {output.txt}
     grep -F -w -f {output.txt} {input.lengths} | awk '{{print $1,1,$2,1,"W",$1,1,$2,"+"}}' > {output.agp}
     """
 
-
 rule build_final_agp:
   input:
     agp = expand("11_AGP/contigs/chr.{lgs}.agp", lgs = lg_range),

From d542e59417886e7ad417148c32879ba1af7512a1 Mon Sep 17 00:00:00 2001
From: "Pavel V. Dimens" <pdimens@live.com>
Date: Mon, 14 Feb 2022 11:34:50 -0500
Subject: [PATCH 29/46] Create install.sh

---
 .misc/install.sh | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)
 create mode 100644 .misc/install.sh

diff --git a/.misc/install.sh b/.misc/install.sh
new file mode 100644
index 0000000..344251a
--- /dev/null
+++ b/.misc/install.sh
@@ -0,0 +1,18 @@
+# install LepWrap into conda PATH
+mkdir -p $CONDA_PREFIX/bin
+# LepWrap executable
+cp LepWrap $CONDA_PREFIX/bin/
+chmod +x $CONDA_PREFIX/bin/LepWrap
+# associated scripts
+chmod +x scripts/*
+cp scripts/* $CONDA_PREFIX/bin/
+# LepMap3 modules and scripts
+cp software/LepMap3/*.class $CONDA_PREFIX/bin
+cp software/LepMap3/scripts/* $CONDA_PREFIX/bin
+# LepAnchor modules and scripts
+cp software/LepAnchor/*.class software/LepAnchor/lepanchor_wrapper.sh $CONDA_PREFIX/bin
+cp software/LepAnchor/scripts/* $CONDA_PREFIX/bin
+cp software/LepAnchor/deps/ucsc_binaries/* $CONDA_PREFIX/bin
+cp software/LepAnchor/deps/*.pl software/LepAnchor/deps/Red software/LepAnchor/deps/all_lastz.ctl software/LepAnchor/deps/scoreMatrix.q software/LepAnchor/deps/step* $CONDA_PREFIX/bin
+# Snakemake rules
+cp rules/LepAnchor/*.smk rules/LepMap3/*.smk $CONDA_PREFIX/bin

From 7bcabadacc5287b496b3ae8e07ddd5d3f3a2ca01 Mon Sep 17 00:00:00 2001
From: "Pavel V. Dimens" <pdimens@live.com>
Date: Mon, 14 Feb 2022 11:35:30 -0500
Subject: [PATCH 30/46] Create build.sh

---
 .misc/build.sh | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)
 create mode 100644 .misc/build.sh

diff --git a/.misc/build.sh b/.misc/build.sh
new file mode 100644
index 0000000..1d0a5ad
--- /dev/null
+++ b/.misc/build.sh
@@ -0,0 +1,19 @@
+#!/bin/bash
+# for installing conda package
+mkdir -p $PREFIX/bin
+# LepWrap executable
+cp LepWrap $PREFIX/bin/
+chmod +x $PREFIX/bin/LepWrap
+# associated scripts
+chmod +x scripts/*
+cp scripts/* $PREFIX/bin/
+# LepMap3 modules and scripts
+cp software/LepMap3/*.class $PREFIX/bin
+cp software/LepMap3/scripts/* $PREFIX/bin
+# LepAnchor modules and scripts
+cp software/LepAnchor/*.class software/LepAnchor/lepanchor_wrapper.sh $PREFIX/bin
+cp software/LepAnchor/scripts/* $PREFIX/bin
+cp software/LepAnchor/deps/ucsc_binaries/* $PREFIX/bin
+cp software/LepAnchor/deps/*.pl software/LepAnchor/deps/Red software/LepAnchor/deps/all_lastz.ctl software/LepAnchor/deps/scoreMatrix.q software/LepAnchor/deps/step* $PREFIX/bin
+# Snakemake rules
+cp rules/LepAnchor/*.smk rules/LepMap3/*.smk $PREFIX/bin

From 50cb858481e3e7559dd6842b302db7bc74527767 Mon Sep 17 00:00:00 2001
From: "Pavel V. Dimens" <pdimens@live.com>
Date: Mon, 14 Feb 2022 11:35:48 -0500
Subject: [PATCH 31/46] Update install.sh

---
 .misc/install.sh | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.misc/install.sh b/.misc/install.sh
index 344251a..6cbc7b5 100644
--- a/.misc/install.sh
+++ b/.misc/install.sh
@@ -1,3 +1,5 @@
+#! /usr/bin/env bash
+
 # install LepWrap into conda PATH
 mkdir -p $CONDA_PREFIX/bin
 # LepWrap executable

From c1a86455c2dca48dc0a9499555b9cf027c7a5d7e Mon Sep 17 00:00:00 2001
From: "Pavel V. Dimens" <pdimens@live.com>
Date: Mon, 14 Feb 2022 11:36:06 -0500
Subject: [PATCH 32/46] Update build.sh

---
 .misc/build.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.misc/build.sh b/.misc/build.sh
index 1d0a5ad..608c20a 100644
--- a/.misc/build.sh
+++ b/.misc/build.sh
@@ -1,4 +1,4 @@
-#!/bin/bash
+#! usr/bin/env bash
 # for installing conda package
 mkdir -p $PREFIX/bin
 # LepWrap executable

From e100c558d1970bc0ec0ff9d699e3410a9ad8ca22 Mon Sep 17 00:00:00 2001
From: "Pavel V. Dimens" <pdimens@live.com>
Date: Mon, 14 Feb 2022 11:36:52 -0500
Subject: [PATCH 33/46] Create meta.yml

---
 .misc/meta.yml | 45 +++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 45 insertions(+)
 create mode 100644 .misc/meta.yml

diff --git a/.misc/meta.yml b/.misc/meta.yml
new file mode 100644
index 0000000..26e8868
--- /dev/null
+++ b/.misc/meta.yml
@@ -0,0 +1,45 @@
+{% set version = "3.6.2" %}
+{% set sha256 = "0f0998ecd50b586d69b50e53d9a0b3d5aa3afa70bd96fe85c2fa3ba02e58278b" %}
+
+package:
+  name: lepwrap
+  version: '{{ version }}'
+
+source:
+  url: https://github.com/pdimens/LepWrap/archive/refs/tags/{{ version }}.tar.gz
+  sha256: {{ sha256 }}
+
+build:
+  number: 3
+  noarch: generic
+
+requirements:
+  build:
+  host:
+  run:
+    - bzip2
+    - font-ttf-dejavu-sans-mono
+    - font-ttf-ubuntu
+    - pygraphviz
+    - graphviz
+    - imagemagick
+    - openjdk
+    - pandoc
+    - python >=3.9
+    - r-base >=4
+    - r-tidyverse
+    - sed
+    - snakemake >=6.4
+
+test:
+  commands:
+    - "java --version"
+    - "R --version"
+about:
+  home: "https://github.com/pdimens/LepWrap/"
+  license: "The GNU General Public License v3.0 (GPL3)"
+  summary: "The Snakemake pipeline to use Lep-Map3 to create linkage maps and LepAnchor for anchoring+orienting genome assemblies."
+
+extra:
+  container:
+    extended-base: True

From bfae878a432b9f382d9f87a3463d477b19781823 Mon Sep 17 00:00:00 2001
From: Pavel Dimens <pdimens@live.com>
Date: Mon, 14 Feb 2022 12:26:31 -0500
Subject: [PATCH 34/46] first attempt at consolidation

---
 .misc/build.sh                          |   3 +-
 .misc/install.sh                        |   2 +-
 HM.all_lastz.log                        |   0
 HM.axtChainRecipBestNet.log             |   1 +
 HM.initiation.log                       |   1 +
 HM2.all_lastz.log                       |   3 +
 LepWrap                                 | 170 +-----------------------
 rules/LepAnchor/build_agp.smk           |   4 +-
 rules/LepAnchor/build_fasta.smk         |   8 +-
 rules/LepAnchor/generate_inputs.smk     |  10 +-
 rules/LepAnchor/mareymaps_untrimmed.smk |  10 +-
 rules/LepAnchor/mask_and_chain.smk      |  22 ++-
 rules/LepAnchor/place_orient1.smk       |   4 +-
 rules/LepAnchor/place_orient2.smk       |  12 +-
 rules/LepAnchor/place_orient3.smk       |  12 +-
 rules/LepAnchor/place_orient4.smk       |   6 +-
 rules/LepAnchor/trim_edges.smk          |   4 +-
 rules/LepMap3/distances.smk             |   4 +-
 rules/LepMap3/generate_map.smk          |   6 +-
 rules/LepMap3/order.smk                 |   7 +-
 rules/LepMap3/prepare_data.smk          |   4 +-
 rules/LepMap3/reorder.smk               |   4 +-
 rules/LepMap3/trim.smk                  |   6 +-
 scripts/FilterLinkageMap.r              |   2 +
 scripts/RecombinationSummary.r          |   1 +
 scripts/generate_config.sh              | 151 +++++++++++++++++++++
 scripts/generate_lastzctl.sh            |  48 +++++++
 scripts/generate_qscoremtx.sh           |   9 ++
 scripts/iterate_js2all.sh               |   2 +-
 scripts/refinemap.sh                    |   2 +-
 scripts/usage                           |   4 +-
 thingsx.seq                             |   1 +
 thingsx.sizes                           |   1 +
 x.seq                                   |   1 +
 x.sizes                                 |   1 +
 35 files changed, 299 insertions(+), 227 deletions(-)
 create mode 100644 HM.all_lastz.log
 create mode 100644 HM.axtChainRecipBestNet.log
 create mode 100644 HM.initiation.log
 create mode 100644 HM2.all_lastz.log
 create mode 100755 scripts/generate_config.sh
 create mode 100755 scripts/generate_lastzctl.sh
 create mode 100755 scripts/generate_qscoremtx.sh
 create mode 120000 thingsx.seq
 create mode 120000 thingsx.sizes
 create mode 120000 x.seq
 create mode 120000 x.sizes

diff --git a/.misc/build.sh b/.misc/build.sh
index 608c20a..2ba015f 100644
--- a/.misc/build.sh
+++ b/.misc/build.sh
@@ -1,4 +1,5 @@
 #! usr/bin/env bash
+
 # for installing conda package
 mkdir -p $PREFIX/bin
 # LepWrap executable
@@ -12,7 +13,7 @@ cp software/LepMap3/*.class $PREFIX/bin
 cp software/LepMap3/scripts/* $PREFIX/bin
 # LepAnchor modules and scripts
 cp software/LepAnchor/*.class software/LepAnchor/lepanchor_wrapper.sh $PREFIX/bin
-cp software/LepAnchor/scripts/* $PREFIX/bin
+cp $CONDA_PREFIX/bin/* $PREFIX/bin
 cp software/LepAnchor/deps/ucsc_binaries/* $PREFIX/bin
 cp software/LepAnchor/deps/*.pl software/LepAnchor/deps/Red software/LepAnchor/deps/all_lastz.ctl software/LepAnchor/deps/scoreMatrix.q software/LepAnchor/deps/step* $PREFIX/bin
 # Snakemake rules
diff --git a/.misc/install.sh b/.misc/install.sh
index 6cbc7b5..d87f015 100644
--- a/.misc/install.sh
+++ b/.misc/install.sh
@@ -13,7 +13,7 @@ cp software/LepMap3/*.class $CONDA_PREFIX/bin
 cp software/LepMap3/scripts/* $CONDA_PREFIX/bin
 # LepAnchor modules and scripts
 cp software/LepAnchor/*.class software/LepAnchor/lepanchor_wrapper.sh $CONDA_PREFIX/bin
-cp software/LepAnchor/scripts/* $CONDA_PREFIX/bin
+cp $CONDA_PREFIX/bin/* $CONDA_PREFIX/bin
 cp software/LepAnchor/deps/ucsc_binaries/* $CONDA_PREFIX/bin
 cp software/LepAnchor/deps/*.pl software/LepAnchor/deps/Red software/LepAnchor/deps/all_lastz.ctl software/LepAnchor/deps/scoreMatrix.q software/LepAnchor/deps/step* $CONDA_PREFIX/bin
 # Snakemake rules
diff --git a/HM.all_lastz.log b/HM.all_lastz.log
new file mode 100644
index 0000000..e69de29
diff --git a/HM.axtChainRecipBestNet.log b/HM.axtChainRecipBestNet.log
new file mode 100644
index 0000000..9efda7c
--- /dev/null
+++ b/HM.axtChainRecipBestNet.log
@@ -0,0 +1 @@
+Can't open perl script "../software/LepAnchor/deps/HM_axtChainRecipBestNet.pl": No such file or directory
diff --git a/HM.initiation.log b/HM.initiation.log
new file mode 100644
index 0000000..1134612
--- /dev/null
+++ b/HM.initiation.log
@@ -0,0 +1 @@
+Can't open perl script "../software/LepAnchor/deps/initiation.pl": No such file or directory
diff --git a/HM2.all_lastz.log b/HM2.all_lastz.log
new file mode 100644
index 0000000..7b3c223
--- /dev/null
+++ b/HM2.all_lastz.log
@@ -0,0 +1,3 @@
+Can't open perl script "../software/LepAnchor/deps/HM_all_lastz_mThreads.pl": No such file or directory
+Can't open perl script "../software/LepAnchor/deps/HM_all_lastz_mThreads.pl": No such file or directory
+Can't open perl script "../software/LepAnchor/deps/HM_all_lastz_mThreads.pl": No such file or directory
diff --git a/LepWrap b/LepWrap
index ca90068..2b78c49 100755
--- a/LepWrap
+++ b/LepWrap
@@ -32,160 +32,6 @@ else
   exit 1
 fi
 
-function generateconfig {
-  cat <<EOF >$1
-# Configuration file for LepWrap
-#=======================================================#
-#                       Lep-Map 3                       #
-#=======================================================#
-# Change this to false if you want to skip Lep-Map3
-run_lepmap: true
-
-  #----- ParentCall2 ------#
-# The filtered VCF file with your genotype likelihoods:
-vcf: "mydata.vcf"
-
-# Instructions to create pedigree file: https://sourceforge.net/p/lep-map3/wiki/software/LepMap3 Home/#parentcall2
-# the pedigree file associated with your data
-pedigree: "pedigree.txt"
-
-# Additional parameters for ParentCall2 (e.g. halfSibs=1), if any
-extra_params_ParentCall: "removeNonInformative=1"
-
-
-  #----- Filtering2 -----#
-# Data tolerance value-- set this to 0 if you want to skip the Filtering2 module
-data_tol: 0
-
-# Additional parameters for Filtering2 (e.g. convert2Biallelic=1), if any
-extra_params_Filtering: ""
-
-
-  #----- SeperateChromosomes2 -----#
-# LepWrap will iteratively perform SeperateChromosomes2 for each
-# LOD score in the range of lod_min to lod_max
-
-# The minimum LOD for SeperateChromosomes2
-lod_min: 10
-
-# The maximum LOD for SeperateChromosomes2
-lod_max: 50
-
-# Use only markers with informative father (1), mother(2), both parents(3) or neither parent(0)
-informative: "informativeMask=3"
-
-# Additional parameters for SeparateChromosomes2 (e.g. distrotionLOD=1), if any
-extra_params_SeparateChromosomes: "sizeLimit=5 distortionLod=1"
-
-
-  #----- JoinSingles2ALL -----#
-# Set this to false if you want to skip joining singles (0) to linkage groups
-run_joinsingles2all: false
-
-# These are the parameters for JoinSingles2ALL, and are highly data-dependent
-# Start with lower values for lod_limit and increase as necessary
-lod_limit: "lodLimit=2"
-
-# Start with lower values for lod_limit and increase as necessary
-lod_difference: "lodDifference=2"
-
-# Additional parameters for JoinSingles2All (e.g. iterate=1), if any
-extra_params_JoinSingles: "iterate=1 distortionLod=1"
- 
-
-  #----- OrderMarkers2 -----#
-# Set exp_lg to your expected number of chromosomes for iterative ordering
-exp_lg: 24
-
-# Additional parameters for OrderMarkers2 (e.g. hyperPhaser=1), if any
-# I recommend setting numMergeIterations to ~100 (Lep-Map3 default is 6)
-extra_params_OrderMarkers: "useKosambi=1 phasingIterations=2 numMergeIterations=100"
-
-
-  #----- Edge Trimming -----#
-# Edge trimming will examine the first and last X% of markers in a linkage group
-# and remove clusters that are N% centimorgans (of the total cM span) away from 
-# the next marker. You can "skip" trimming by setting trim_cutoff really high (e.g. 80-100).
-
-# Set edge_length to the percent number of markers you would like to examine from either end of the linkage group
-# Value can be an integer or decimal, i.e. 15 is the same as 0.15, which both mean "15%" (10-20 is reasonable)
-edge_length: 20
-
-# Set trim_cuttoff to the centiMorgan distance cutoff (5-10 is reasonable)
-trim_cutoff: 100 
-
-
-  #----- Re-OrderMarkers2 -----#
-# The second round of OrderMarkers will use the same basic parameters as the first round (but not the extra params)
-# If there are additional parameters you would like to use, add them here:
-extra_params_reOrderMarkers: "improveOrder=1 useKosambi=1 numMergeIterations=75"
-
-  #----- Calculate Distances -----#
-# If you used useKosambi=1 or useMorgan=1 for Ordering/reOrdering, add that same
-# parameter to distance_method, otherwise leave it as a blank string
-distance_method: "useKosambi=1"
-
-
-#=======================================================#
-#                       Lep-Anchor                      #
-#=======================================================#
-  #---- global settings ----#
-# Change this to false if you want to skip Lep-Anchor
-run_lepanchor: true
-
-# The path to the genome assembly you are trying to anchor 
-assembly: "assembly.fasta"
-
-# The number of linkage groups you have
-lg_count: 24
-
-# If you have a PAF file of long reads mapped to your genome, add it here, otherwise leave the text as "/dev/null"
-PAF_file: "/dev/null"
-
-# If you have a proximity file add it here, otherwise leave the text as "/dev/null".
-# This isn't yet implemented in Lep-Anchor.
-proximity_file: "/dev/null"
-
-
-  #----- CleanMap -----#
-# Additional parameters for CleanMap (e.g. chimericDistance=500), if any
-extra_params_CleanMap: ""
-
-
-  #----- Map2Bed -----#
-# Additional parameters for Map2Bed (e.g. markerSupport=4), if any
-extra_params_Map2Bed: ""
-
-
-  #----- PlaceAndOrientContigs -----#
-# Choose which of the input types you want to generate by leaving it uncommented. Intervals are the default, but either works.
-#lepanchor_input: "noIntervals=0"  # data is intervals
-lepanchor_input: "noIntervals=1"  # data is distances
-
-# The size limit for detecting potential haplotype contigs (LepAnchor default: 2000)
-# Set this value really high (50000+) to ignore haplotype removal in between PlaceOrient iterations
-haplotype_limit: 2000
-
-# Additional parameters you would like to use for PlaceAndOrientContigs, if any (e.g. randomOrder=1)
-extra_params_PlaceOrient: "keepEmptyIntervals=1 numRuns=10"
-
-
-  #----- Edge Trimming -----#
-# Edge trimming will examine the first and last X% of markers in a linkage group
-# and remove clusters that are N% centimorgans (of the total cM span) away from 
-# the next marker. You can "skip" trimming by setting  LA_trim_cutoff really high (e.g. 80-100) 
-
-# Set edge_length to the percent number of markers you would like to examine from either end of the linkage group
-# Value can be an integer or decimal, i.e. 15 is the same as 0.15, which both mean "15%" (10-15 is reasonable)
-LA_edge_length: 15
-
-# Set trim_cuttoff to the centiMorgan distance cutoff (5-10 is reasonable)
-LA_trim_cutoff: 5
-EOF
-}
-
-export -f generateconfig
-
 # make sure the first argument is a number (number of threads)
 # function from https://stackoverflow.com/a/61835747
 is_int()  { case ${1#[-+]} in '' | *[!0-9]*              ) return 1;; esac ;}
@@ -204,7 +50,7 @@ if [[ ! -z "$2" ]]; then
     printf "$2"
     printf "\033[0m"
     echo " was not found, but it was created for you. Please edit it and run LepWrap again"
-    generateconfig $2
+    generate_config.sh > $2
     exit 1
   else
     CONF=$2
@@ -217,7 +63,7 @@ else
     printf "\033[0m"
     echo " not found"
     echo " was not found, but it was created for you. Please edit it and run LepWrap again"
-    generateconfig config.yml
+    generate_config.sh > config.yml
     exit 1
   fi
     CONF=config.yml
@@ -228,7 +74,7 @@ lepmap(){
   printf "Running Lep-Map3\n"
   printf "\033[0m"
   sleep 2s
-  snakemake --cores $1 --snakefile ./rules/LepMap3/LepMap3.smk --configfile $CONF --directory .
+  snakemake --cores $1 --snakefile $CONDA_PREFIX/bin/LepMap3.smk --configfile $CONF --directory .
 }
 
 lepanchor(){
@@ -236,14 +82,12 @@ lepanchor(){
   printf "Running Lep-Anchor\n"
   printf "\033[0m"
   sleep 2s
-  snakemake --cores $1 --snakefile ./rules/LepAnchor/LepAnchor.smk --configfile $CONF --directory .
+  snakemake --cores $1 --snakefile $CONDA_PREFIX/bin/LepAnchor.smk --configfile $CONF --directory .
 }
 
-# copy lastz binaries into conda path if they aren't already there
 if [ -z "$CONDA_PREFIX" ]; then
-  echo "No active conda environment detected"
-else
-  cp -n software/LepAnchor/deps/ucsc_binaries/* $CONDA_PREFIX/bin
+  echo "No active conda environment detected. The LepWrap conda environment is required for the pipeline to work."
+  exit 1
 fi
 
 LM=$(grep "run_lepmap" config.yml | cut -d":" -f2 | xargs | tr '[:upper:]' '[:lower:]')
@@ -256,5 +100,5 @@ else
 fi && if [ $LA == "true" ]; then
   lepanchor $1 $CONF
 else
-  echo "Skipping LepAnchor"
+  echo "Skipping Lep-Anchor"
 fi
diff --git a/rules/LepAnchor/build_agp.smk b/rules/LepAnchor/build_agp.smk
index 0854114..983d57a 100644
--- a/rules/LepAnchor/build_agp.smk
+++ b/rules/LepAnchor/build_agp.smk
@@ -8,8 +8,8 @@ rule construct_agp:
     chrom = "{lg_range}"
   shell:
     """
-    awk -vn={params.chrom} '($5==n)' {input} | awk -vprefix="LG" -vlg={params.chrom} -f software/LepAnchor/scripts/makeagp_full2.awk - > {output.agp}
-    awk -vn={params.chrom} '($5==n)' {input} | awk -vprefix="LG" -vlg={params.chrom} -f software/LepAnchor/scripts/makeagp2.awk - > {output.scaff_agp}
+    awk -vn={params.chrom} '($5==n)' {input} | awk -vprefix="LG" -vlg={params.chrom} -f $CONDA_PREFIX/bin/makeagp_full2.awk - > {output.agp}
+    awk -vn={params.chrom} '($5==n)' {input} | awk -vprefix="LG" -vlg={params.chrom} -f $CONDA_PREFIX/bin/makeagp2.awk - > {output.scaff_agp}
     """
 
 rule unused:
diff --git a/rules/LepAnchor/build_fasta.smk b/rules/LepAnchor/build_fasta.smk
index 4e9d7b5..9d20133 100644
--- a/rules/LepAnchor/build_fasta.smk
+++ b/rules/LepAnchor/build_fasta.smk
@@ -4,7 +4,7 @@ rule build_scaffold_only_fasta:
     agp = "11_AGP/lepanchor.contigs.only.agp"
   output: "12_Fasta/Anchored.scaffolds.only.fa.gz"
   message: "Constructing final scaffold-only fasta file {output}"
-  shell: "gunzip -fc {input.assembly} | awk -f software/LepAnchor/scripts/makefasta.awk - {input.agp} | gzip > {output}"
+  shell: "gunzip -fc {input.assembly} | awk -f $CONDA_PREFIX/bin/makefasta.awk - {input.agp} | gzip > {output}"
 
 
 rule build_scaffold_contig_fasta:
@@ -13,7 +13,7 @@ rule build_scaffold_contig_fasta:
     agp = "11_AGP/lepanchor.contigs.all.agp"
   output: "12_Fasta/Anchored.scaffolds.fa.gz"
   message: "Constructing final scaffold fasta file {output}"
-  shell: "gunzip -fc {input.assembly} | awk -f software/LepAnchor/scripts/makefasta.awk - {input.agp} | gzip > {output}"
+  shell: "gunzip -fc {input.assembly} | awk -f $CONDA_PREFIX/bin/makefasta.awk - {input.agp} | gzip > {output}"
 
 
 rule build_contig_only_fasta:
@@ -22,7 +22,7 @@ rule build_contig_only_fasta:
     scaff_agp = "11_AGP/lepanchor.scaffolds.only.agp"
   output: "12_Fasta/Anchored.contigs.only.fa.gz"
   message: "Constructing final contig-only fasta file {output}"
-  shell: "gunzip -fc {input.assembly} | awk -f software/LepAnchor/scripts/makefasta.awk - {input.scaff_agp} | gzip > {output}"
+  shell: "gunzip -fc {input.assembly} | awk -f $CONDA_PREFIX/bin/makefasta.awk - {input.scaff_agp} | gzip > {output}"
 
 
 rule build_contig_fasta:
@@ -31,4 +31,4 @@ rule build_contig_fasta:
     scaff_agp = "11_AGP/lepanchor.scaffolds.all.agp"
   output: "12_Fasta/Anchored.contigs.fa.gz"
   message: "Constructing final contig fasta file {output}"
-  shell: "gunzip -fc {input.assembly} | awk -f software/LepAnchor/scripts/makefasta.awk - {input.scaff_agp} | gzip > {output}"
\ No newline at end of file
+  shell: "gunzip -fc {input.assembly} | awk -f $CONDA_PREFIX/bin/makefasta.awk - {input.scaff_agp} | gzip > {output}"
\ No newline at end of file
diff --git a/rules/LepAnchor/generate_inputs.smk b/rules/LepAnchor/generate_inputs.smk
index 8dfb335..f1e3aa8 100644
--- a/rules/LepAnchor/generate_inputs.smk
+++ b/rules/LepAnchor/generate_inputs.smk
@@ -31,14 +31,14 @@ rule contiglengths:
   input: geno
   output: report("10_PlaceAndOrientContigs/contigs.length", category = "Data")
   message: "Getting contig lengths"
-  shell: "gunzip -fc {input} | awk -f software/LepAnchor/scripts/contigLength.awk > {output}"
+  shell: "gunzip -fc {input} | awk -f $CONDA_PREFIX/bin/contigLength.awk > {output}"
 
 
 rule find_haplotypes:
   input: "9_Chain/chainfile.gz"
   output: report("10_PlaceAndOrientContigs/suspected.haplotypes.initial", category = "Logs")
   message: "Finding non-haplotype contigs not included in map.bed"
-  shell: "gunzip -fc {input} | awk -f software/LepAnchor/scripts/findFullHaplotypes.awk > {output}"
+  shell: "gunzip -fc {input} | awk -f $CONDA_PREFIX/bin/findFullHaplotypes.awk > {output}"
 
 
 rule liftover:
@@ -52,7 +52,7 @@ rule liftover:
   message: "Running liftoverHaplotypes for the input maps"
   shell: 
     """
-    gunzip -fc {input.chain} | java -cp software/LepAnchor LiftoverHaplotypes map={input.intervals} haplotypes={input.haplos} chain=- > {output.lift}
+    gunzip -fc {input.chain} | java -cp $CONDA_PREFIX/bin/ LiftoverHaplotypes map={input.intervals} haplotypes={input.haplos} chain=- > {output.lift}
     cat {output.lift} | sort -V -k 1,1 -k 2,2n > {output.sortedlift}
     """
 
@@ -64,7 +64,7 @@ rule cleanmap:
   message: "Running CleanMap"
   params:
     extras = cleanmap_extra
-  shell: "java -cp software/LepAnchor CleanMap map={input} {params.extras} > {output} 2> {log}"
+  shell: "java -cp $CONDA_PREFIX/bin/ CleanMap map={input} {params.extras} > {output} 2> {log}"
 
 
 rule map2bed:
@@ -76,7 +76,7 @@ rule map2bed:
   message: "Running Map2Bed"
   params:
     extras = map2bed_extra
-  shell: "java -cp software/LepAnchor Map2Bed map={input.cleanmap} contigLength={input.lengths} {params.extras} > {output} 2> {log}"
+  shell: "java -cp $CONDA_PREFIX/bin/ Map2Bed map={input.cleanmap} contigLength={input.lengths} {params.extras} > {output} 2> {log}"
 
 
 rule ungrouped:
diff --git a/rules/LepAnchor/mareymaps_untrimmed.smk b/rules/LepAnchor/mareymaps_untrimmed.smk
index bf93a90..d285a5b 100644
--- a/rules/LepAnchor/mareymaps_untrimmed.smk
+++ b/rules/LepAnchor/mareymaps_untrimmed.smk
@@ -19,12 +19,12 @@ rule mareymap_data:
     """
     for c in $(seq 1 {params.chrom})
     do
-      awk -vn=$c '($3==n)' {input.lift} | awk -f software/LepAnchor/scripts/liftover.awk 11_AGP/contigs/chr.$c.agp - | awk -vm=1 '(/LG/ && NF>=4){{if (NF==4) $5=$4;print $1"\t"$2"\t"$3"\t"m"\t"$4"\t"$5}}' | gzip
+      awk -vn=$c '($3==n)' {input.lift} | awk -f $CONDA_PREFIX/bin/liftover.awk 11_AGP/contigs/chr.$c.agp - | awk -vm=1 '(/LG/ && NF>=4){{if (NF==4) $5=$4;print $1"\t"$2"\t"$3"\t"m"\t"$4"\t"$5}}' | gzip
     done > {output.mareydata} 2> {log}
    
     for c in $(seq 1 {params.chrom})
     do
-      awk -vn=$c '($3==n)' {input.lift} | awk -f software/LepAnchor/scripts/liftover.awk 11_AGP/contigs/chr.$c.agp - | awk -vm=1 '(/LG/ && NR>=4){{if (NF>4) s=0.5; else s=1;print $1"\t"$2"\t"$3"\t"m"\t"s*($4+$5)}}' | gzip
+      awk -vn=$c '($3==n)' {input.lift} | awk -f $CONDA_PREFIX/bin/liftover.awk 11_AGP/contigs/chr.$c.agp - | awk -vm=1 '(/LG/ && NR>=4){{if (NF>4) s=0.5; else s=1;print $1"\t"$2"\t"$3"\t"m"\t"s*($4+$5)}}' | gzip
     done > {output.sexavg} 2> /dev/null
     """
 
@@ -43,7 +43,7 @@ rule mareymaps:
   message: "Creating Marey Maps"
   shell: 
     """
-    Rscript software/LepAnchor/scripts/plot_marey.R {input.data} 11_AGP/contigs
-    Rscript scripts/LASummary.r {input.data} true
-    Rscript scripts/LASummarySexAvg.r {input.sexavg}
+    Rscript $CONDA_PREFIX/bin/plot_marey.R {input.data} 11_AGP/contigs
+    LASummary.r {input.data} true
+    LASummarySexAvg.r {input.sexavg}
     """
\ No newline at end of file
diff --git a/rules/LepAnchor/mask_and_chain.smk b/rules/LepAnchor/mask_and_chain.smk
index d286810..eaa763c 100644
--- a/rules/LepAnchor/mask_and_chain.smk
+++ b/rules/LepAnchor/mask_and_chain.smk
@@ -27,13 +27,23 @@ rule repeatmask:
     echo "- Compressing repeat-masked genome from Red"
     gzip --stdout 8_RepeatMask/*.msk > {output} && rm 8_RepeatMask/*.msk
     """
-    
+
+rule lastz_config:
+  output: 
+    ctl = "9_Chain/all_lastz.ctl",
+    scoremtx = "9_Chain/scoreMatrix.q"
+  message: "Creating LASTZ configuration inputs"
+  shell: 
+    """
+    generate_lastzctl.sh > {output.ctl}
+    generate_qscoremtx.sh > {output.scoremtx}
+    """
 
 rule chain_1:
   input: 
     geno = "8_RepeatMask/repeatmasked.fa.gz",
-    ctrl = "software/LepAnchor/deps/all_lastz.ctl",
-    scoremtx = "software/LepAnchor/deps/scoreMatrix.q"
+    ctrl = "9_Chain/all_lastz.ctl",
+    scoremtx = "9_Chain/scoreMatrix.q"
   output: 
     out1 = "9_Chain/repeatmaskedx.sizes",
     out2 = "9_Chain/repeatmasked.sizes"
@@ -41,9 +51,9 @@ rule chain_1:
   threads: 30
   shell:
     """
-    ln -srf {input} 9_Chain/
+    ln -srf {input.geno} 9_Chain/
     cd 9_Chain
-    ../software/LepAnchor/deps/step1.HM2 repeatmasked {threads}
+    step1.HM2 repeatmasked {threads}
     """
 
 
@@ -59,6 +69,6 @@ rule chain_2:
   shell:
     """   
     cd 9_Chain
-    ../software/LepAnchor/deps/step2.HM2 repeatmasked {threads} && rm -r repeatmasked.repeatmaskedx.result/raw.axt
+    step2.HM2 repeatmasked {threads} && rm -r repeatmasked.repeatmaskedx.result/raw.axt
     ln -sr ../{output.original} ../{output.slink}
     """
diff --git a/rules/LepAnchor/place_orient1.smk b/rules/LepAnchor/place_orient1.smk
index eb21666..4b97cca 100644
--- a/rules/LepAnchor/place_orient1.smk
+++ b/rules/LepAnchor/place_orient1.smk
@@ -16,7 +16,7 @@ rule place_orient:
   message: "Running the 1st round of PlaceAndOrientContigs for linkage group {params.chrom}"
   shell:
     """
-    gunzip -fc {input.chain} | java -cp software/LepAnchor PlaceAndOrientContigs chromosome={params.chrom} numThreads={threads} bed={input.bedfile} map={input.lift} chain=- paf={input.paf} proximity={input.prox} {params.datatype} {params.extras} > {output.chrom} 2> {output.chromerr}
+    gunzip -fc {input.chain} | java -cp $CONDA_PREFIX/bin/ PlaceAndOrientContigs chromosome={params.chrom} numThreads={threads} bed={input.bedfile} map={input.lift} chain=- paf={input.paf} proximity={input.prox} {params.datatype} {params.extras} > {output.chrom} 2> {output.chromerr}
     """
 
 rule propogate1:
@@ -29,5 +29,5 @@ rule propogate1:
   message: "First round of propogation with propogate4.awk"
   shell:
     """
-    awk -f software/LepAnchor/scripts/propagate4.awk pass=1 {input.placed} pass=2 {input.errors} | awk -f software/LepAnchor/scripts/pickbed.awk - {input.bedfile} > {output.propogated}
+    awk -f $CONDA_PREFIX/bin/propagate4.awk pass=1 {input.placed} pass=2 {input.errors} | awk -f $CONDA_PREFIX/bin/pickbed.awk - {input.bedfile} > {output.propogated}
     """
diff --git a/rules/LepAnchor/place_orient2.smk b/rules/LepAnchor/place_orient2.smk
index 912b9ba..b6ad01d 100644
--- a/rules/LepAnchor/place_orient2.smk
+++ b/rules/LepAnchor/place_orient2.smk
@@ -17,7 +17,7 @@ rule place_orient2:
   message: "Running 2nd round of PlaceAndOrientContigs for linkage group {params.chrom}"
   shell:
     """
-    gunzip -fc {input.chain} | java -cp software/LepAnchor PlaceAndOrientContigs chromosome={params.chrom} numThreads={threads} $(awk -f software/LepAnchor/scripts/pickorientation.awk {input.chrom}) bed={input.bedfile} map={input.lift} chain=- paf={input.paf} proximity={input.prox} {params.datatype} {params.extras} > {output.chrom} 2> {output.chromerr}
+    gunzip -fc {input.chain} | java -cp $CONDA_PREFIX/bin/ PlaceAndOrientContigs chromosome={params.chrom} numThreads={threads} $(awk -f $CONDA_PREFIX/bin/pickorientation.awk {input.chrom}) bed={input.bedfile} map={input.lift} chain=- paf={input.paf} proximity={input.prox} {params.datatype} {params.extras} > {output.chrom} 2> {output.chromerr}
     """
 
 rule propogate2:
@@ -33,16 +33,16 @@ rule propogate2:
   message: "Second round of propogation"
   shell:
     """
-    awk -f software/LepAnchor/scripts/propagate.awk {input.placed} > {output.iter1}
-    awk -f software/LepAnchor/scripts/propagate.awk {output.iter1} > {output.iter2}
+    awk -f $CONDA_PREFIX/bin/propagate.awk {input.placed} > {output.iter1}
+    awk -f $CONDA_PREFIX/bin/propagate.awk {output.iter1} > {output.iter2}
     i=2
 
     while ! cmp -s "10_PlaceAndOrientContigs/tmp$i.la" "10_PlaceAndOrientContigs/tmp$(( $i-1 )).la" ;do
-      awk -f software/LepAnchor/scripts/propagate.awk 10_PlaceAndOrientContigs/tmp$i.la > 10_PlaceAndOrientContigs/tmp$[$i+1].la
+      awk -f $CONDA_PREFIX/bin/propagate.awk 10_PlaceAndOrientContigs/tmp$i.la > 10_PlaceAndOrientContigs/tmp$[$i+1].la
       i=$[$i+1]
     done
 
     #create prop*.la
-    awk -f software/LepAnchor/scripts/propagate2.awk 10_PlaceAndOrientContigs/tmp$i.la | awk '(/^[^#]/ && NF>=8){{++d[$1"\t"($7+0)"\t"($8+0)]; data[++line]=$0}}END{{for (i=1; i<=line; ++i) {{$0=data[i];if (d[$1"\t"($7+0)"\t"($8+0)] == 1) {{fn="10_PlaceAndOrientContigs/propogate/propogated."$5".la";print $0>fn}}}}}}'
-    awk '{{print $1"\t"($7+0)"\t"($8+0)"\t?\t"$5}}' {output.prop} | awk -f software/LepAnchor/scripts/pickbed.awk - {input.bedfile} > {output.propogated}
+    awk -f $CONDA_PREFIX/bin/propagate2.awk 10_PlaceAndOrientContigs/tmp$i.la | awk '(/^[^#]/ && NF>=8){{++d[$1"\t"($7+0)"\t"($8+0)]; data[++line]=$0}}END{{for (i=1; i<=line; ++i) {{$0=data[i];if (d[$1"\t"($7+0)"\t"($8+0)] == 1) {{fn="10_PlaceAndOrientContigs/propogate/propogated."$5".la";print $0>fn}}}}}}'
+    awk '{{print $1"\t"($7+0)"\t"($8+0)"\t?\t"$5}}' {output.prop} | awk -f $CONDA_PREFIX/bin/pickbed.awk - {input.bedfile} > {output.propogated}
     """
\ No newline at end of file
diff --git a/rules/LepAnchor/place_orient3.smk b/rules/LepAnchor/place_orient3.smk
index 8193be7..57f7651 100644
--- a/rules/LepAnchor/place_orient3.smk
+++ b/rules/LepAnchor/place_orient3.smk
@@ -18,7 +18,7 @@ rule place_orient3:
   threads: 2
   shell:
     """
-    gunzip -fc {input.chain} | java -cp software/LepAnchor PlaceAndOrientContigs chromosome={params.chrom} numThreads={threads} $(awk -f software/LepAnchor/scripts/pickorientation.awk {input.chrom}) bed={input.bedfile} map={input.lift} chain=- paf={input.paf} proximity={input.prox} evaluateAnchoring={input.propogated} improveAnchoring=1 {params.datatype} {params.extras} > {output.chrom} 2> {output.errors}
+    gunzip -fc {input.chain} | java -cp $CONDA_PREFIX/bin PlaceAndOrientContigs chromosome={params.chrom} numThreads={threads} $(awk -f $CONDA_PREFIX/bin/pickorientation.awk {input.chrom}) bed={input.bedfile} map={input.lift} chain=- paf={input.paf} proximity={input.prox} evaluateAnchoring={input.propogated} improveAnchoring=1 {params.datatype} {params.extras} > {output.chrom} 2> {output.errors}
     """
     
 rule prune_contigblocks:
@@ -29,7 +29,7 @@ rule prune_contigblocks:
   message: "Pruning contig blocks without map support and removing overlaps"
   params:
     chrom = lg
-  shell: "awk -f software/LepAnchor/scripts/prune.awk {input} > {output.chrom} 2> {output.err}"
+  shell: "awk -f $CONDA_PREFIX/bin/prune.awk {input} > {output.chrom} 2> {output.err}"
 
 rule prune_post:
   input:
@@ -44,8 +44,8 @@ rule prune_post:
   shell:
     """
     cat {input.prunederr} > {output.pruned}
-    awk -f software/LepAnchor/scripts/removeOverlaps.awk {input.bedfile} {input.prunedchrom} > {output.overlaps}
-      """
+    awk -f $CONDA_PREFIX/bin/removeOverlaps.awk {input.bedfile} {input.prunedchrom} > {output.overlaps}
+    """
 
 #rule find_haplotypes2:
 #  input:
@@ -72,7 +72,7 @@ rule prune_post:
 #  threads: 1
 #  shell:
 #    """
-#    gunzip -fc {input.chain} | java -cp software/LepAnchor LiftoverHaplotypes map={input.chrom} haplotypes={input.haplos} chain=- > {output}
+#    gunzip -fc {input.chain} | java -cp $CONDA_PREFIX/bin/ LiftoverHaplotypes map={input.chrom} haplotypes={input.haplos} chain=- > {output}
 #    """
 #
 #rule removehaplotypes:
@@ -83,5 +83,5 @@ rule prune_post:
 #    bedfile = "10_PlaceAndOrientContigs/map.propogated2.nohaplo.bed"
 #  message: "Removing haplotypes from the map"
 #  threads: 1
-#  shell: "awk -f software/LepAnchor/scripts/removeHaplotypes.awk {input} > {output}"
+#  shell: "awk -f $CONDA_PREFIX/bin/removeHaplotypes.awk {input} > {output}"
 #
\ No newline at end of file
diff --git a/rules/LepAnchor/place_orient4.smk b/rules/LepAnchor/place_orient4.smk
index f7c0f40..1640b17 100644
--- a/rules/LepAnchor/place_orient4.smk
+++ b/rules/LepAnchor/place_orient4.smk
@@ -18,7 +18,7 @@ rule place_orient4:
     threads: 2
     shell:
         """
-        gunzip -fc {input.chain} | java -cp software/LepAnchor PlaceAndOrientContigs chromosome={params.chrom} numThreads={threads} $(awk -f software/LepAnchor/scripts/pickorientation.awk {input.chrom}) bed={input.bedfile} map={input.lift} chain=- paf={input.paf} proximity={input.prox} {params.datatype} {params.extras} evaluateAnchoring={input.chromlast} improveAnchoring=1 > {output.chrom} 2> {output.err}
+        gunzip -fc {input.chain} | java -cp $CONDA_PREFIX/bin/ PlaceAndOrientContigs chromosome={params.chrom} numThreads={threads} $(awk -f $CONDA_PREFIX/bin/pickorientation.awk {input.chrom}) bed={input.bedfile} map={input.lift} chain=- paf={input.paf} proximity={input.prox} {params.datatype} {params.extras} evaluateAnchoring={input.chromlast} improveAnchoring=1 > {output.chrom} 2> {output.err}
         """
 
 rule prune_contigblocks:
@@ -28,7 +28,7 @@ rule prune_contigblocks:
     message: "Pruning contig blocks without map support and removing overlaps"
     params:
         chrom = lg
-    shell: "awk -f software/LepAnchor/scripts/prune.awk {input} > {output.chrom} 2> {output.err}"
+    shell: "awk -f $CONDA_PREFIX/bin/prune.awk {input} > {output.chrom} 2> {output.err}"
 
 rule prune_post:
     input:
@@ -43,5 +43,5 @@ rule prune_post:
     shell:
         """
         cat {input.prunederr} > {output.pruned}
-        awk -f software/LepAnchor/scripts/removeOverlaps.awk {input.bedfile} {input.prunedchrom} > {output.overlaps}
+        awk -f $CONDA_PREFIX/bin/removeOverlaps.awk {input.bedfile} {input.prunedchrom} > {output.overlaps}
         """
\ No newline at end of file
diff --git a/rules/LepAnchor/trim_edges.smk b/rules/LepAnchor/trim_edges.smk
index e00a10e..5c41824 100644
--- a/rules/LepAnchor/trim_edges.smk
+++ b/rules/LepAnchor/trim_edges.smk
@@ -19,7 +19,7 @@ rule trim_newintervals:
   params:
     edge = edgelen,
     dist = trimdist
-  shell: "Rscript scripts/LepWrapTrim.r {input} {params.dist} {params.edge} 15_Trim"
+  shell: "LepWrapTrim.r {input} {params.dist} {params.edge} 15_Trim"
 
 
 rule merge_trimplots:
@@ -40,4 +40,4 @@ rule plot_trimmedintervals:
   input: "16_MareyMapsTrimmed/data.marey.trimmed.gz"
   output: report("16_MareyMapsTrimmed/LepAnchor.mareymaps.pdf", category = "Trimmed Marey Maps")
   message: "Plotting results of edge trimming"
-  shell: "Rscript scripts/LASummary.r {input}"
\ No newline at end of file
+  shell: "LASummary.r {input}"
\ No newline at end of file
diff --git a/rules/LepMap3/distances.smk b/rules/LepMap3/distances.smk
index ef94e55..65ce7f7 100644
--- a/rules/LepMap3/distances.smk
+++ b/rules/LepMap3/distances.smk
@@ -19,10 +19,10 @@ rule calculate_distances:
         """
         cp {input.lg} {output.distance}
         
-        zcat {input.data_call} | java -cp software/LepMap3 OrderMarkers2 data=- evaluateOrder={input.lg} {params.dist_method} numThreads={threads} improveOrder=0 sexAveraged=1 &> {output.sex_averagedtmp}
+        zcat {input.data_call} | java -cp $CONDA_PREFIX/bin/ OrderMarkers2 evaluateOrder={input.lg} data=- {params.dist_method} numThreads={threads} improveOrder=0 sexAveraged=1 &> {output.sex_averagedtmp}
         sed -i -e 's/LG \= 0/LG \= {params.lg}/g' {output.sex_averagedtmp}
         sed -n '/\*\*\* LG \=/,$p' {output.sex_averagedtmp} > {output.sex_averaged} 
         awk '/#java/{{flag=1}} flag; /*** LG =/{{flag=0}}' {output.sex_averagedtmp} > {log.sex_averaged}
 
-        zcat {input.data_call} | java -cp software/LepMap3 OrderMarkers2 data=- evaluateOrder={input.lg} {params.dist_method} numThreads={threads} calculateIntervals={output.intervals} > {log.intervals} 2>&1
+        zcat {input.data_call} | java -cp $CONDA_PREFIX/bin/ OrderMarkers2 evaluateOrder={input.lg} data=- {params.dist_method} numThreads={threads} calculateIntervals={output.intervals} > {log.intervals} 2>&1
         """
\ No newline at end of file
diff --git a/rules/LepMap3/generate_map.smk b/rules/LepMap3/generate_map.smk
index 5612f06..092e4bf 100644
--- a/rules/LepMap3/generate_map.smk
+++ b/rules/LepMap3/generate_map.smk
@@ -9,7 +9,7 @@ rule separate_chromosomes:
         extra = sepchrom_extra,
     shell:
         """
-        zcat {input} | java -cp software/LepMap3 SeparateChromosomes2 data=- {params.extra} {informative} lodLimit={params.lod} numThreads={threads} > {output} 2> {log}
+        zcat {input} | java -cp $CONDA_PREFIX/bin/ SeparateChromosomes2 lodLimit={params.lod} data=- {params.extra} {informative} numThreads={threads} > {output} 2> {log}
         """
 
 
@@ -17,7 +17,7 @@ rule map_summary:
     input: expand("3_SeparateChromosomes/LOD.{LOD}", LOD = lod_range)
     output: "3_SeparateChromosomes/all.LOD.summary"
     message: "Summarizing SeperateChromosomes2 maps >> {output}"
-    shell: "scripts/MapSummary.r 3_SeparateChromosomes"
+    shell: "MapSummary.r 3_SeparateChromosomes"
 
 
 rule choose_map:
@@ -51,7 +51,7 @@ rule join_singles:
         JS2A=$(echo {params.run_js2all} | tr '[:upper:]' '[:lower:]')
         THEMAP=$(tail -1 {input.map_choice})
         if [ $JS2A == "true" ]; then
-            zcat {input.datacall} | java -cp software/LepMap3 JoinSingles2All map=$THEMAP data=- {params.extra} {params.lod_limit} {params.lod_diff} numThreads={threads} > {output}
+            zcat {input.datacall} | java -cp $CONDA_PREFIX/bin/ JoinSingles2All map=$THEMAP data=- {params.extra} {params.lod_limit} {params.lod_diff} numThreads={threads} > {output}
         else
             echo -e "\nSkipping JoinSingles2All and creating a symlink to $THEMAP instead"
             ln -sr $THEMAP {output}
diff --git a/rules/LepMap3/order.smk b/rules/LepMap3/order.smk
index 4d36f46..d0a5c52 100644
--- a/rules/LepMap3/order.smk
+++ b/rules/LepMap3/order.smk
@@ -15,7 +15,7 @@ rule order_markers:
     threads: 2
     shell:
         """
-        zcat {input.datacall} | java -cp software/LepMap3 OrderMarkers2 map={input.filt_map} {params.extra} data=- numThreads={threads} chromosome={params.chrom} &> {output.runlog}
+        zcat {input.datacall} | java -cp $CONDA_PREFIX/bin/ OrderMarkers2 chromosome={params.chrom} map={input.filt_map} {params.extra} data=- numThreads={threads} &> {output.runlog}
         sed -n '/\*\*\* LG \=/,$p' {output.runlog} > {output.lg}
         grep "recombin" {output.runlog} > {log.recomb}
         awk '/#java/{{flag=1}} flag; /logL/{{flag=0}}' {output.runlog} > {log.run}
@@ -25,7 +25,4 @@ rule recomb_summary:
     input: expand("4_OrderMarkers/ordered.{lg}", lg = lg_range)
     output: "4_OrderMarkers/recombination/recombination.summary"
     message: "Recombination summary: {output}"
-    shell:
-        """
-        Rscript scripts/RecombinationSummary.r 4_OrderMarkers/recombination > {output}
-        """
+    shell: "RecombinationSummary.r 4_OrderMarkers/recombination > {output}"
diff --git a/rules/LepMap3/prepare_data.smk b/rules/LepMap3/prepare_data.smk
index fa7b5b9..bbcac5e 100644
--- a/rules/LepMap3/prepare_data.smk
+++ b/rules/LepMap3/prepare_data.smk
@@ -6,7 +6,7 @@ rule parent_call:
     message: "Creating Lep-Map3 data file from {input.vcf} and {input.pedigree}"
     params:
         extra = parentcall_extra
-    shell: "java -cp software/LepMap3 ParentCall2 data={input.pedigree} vcfFile={input.vcf} {params} | gzip > {output}"
+    shell: "java -cp $CONDA_PREFIX/bin/ ParentCall2 data={input.pedigree} vcfFile={input.vcf} {params} | gzip > {output}"
 
 rule filtering:
     input: "1_ParentCall/data.lepmap3.gz"
@@ -21,6 +21,6 @@ rule filtering:
             echo "Skipping Filtering2 and creating symlink {output} instead"
             ln -sr {input} {output}
         else
-            zcat {input} | java -cp software/LepMap3 Filtering2 data=- dataTolerance={params.data_tolerance} {params.extra} | gzip > {output}
+            zcat {input} | java -cp $CONDA_PREFIX/bin/ Filtering2 data=- dataTolerance={params.data_tolerance} {params.extra} | gzip > {output}
         fi
         """
diff --git a/rules/LepMap3/reorder.smk b/rules/LepMap3/reorder.smk
index 18e570a..f5654b2 100644
--- a/rules/LepMap3/reorder.smk
+++ b/rules/LepMap3/reorder.smk
@@ -16,7 +16,7 @@ rule reorder_markers:
     threads: 2
     shell:
         """
-        zcat {input.datacall} | java -cp software/LepMap3 OrderMarkers2 {params.extra} map={input.filt_map} data=- numThreads={threads} evaluateOrder={input.lg_order} &> {output.runlog}
+        zcat {input.datacall} | java -cp $CONDA_PREFIX/bin/ OrderMarkers2 evaluateOrder={input.lg_order} {params.extra} map={input.filt_map} data=- numThreads={threads} &> {output.runlog}
         sed -n '/\*\*\* LG \=/,$p' {output.runlog} > {output.lg}
         grep "recombin" {output.runlog} > {log.recomb}
         awk '/#java/{{flag=1}} flag; /logL/{{flag=0}}' {output.runlog} > {log.run}
@@ -28,5 +28,5 @@ rule reorder_summary:
     message: "Recombination summary of reordering: {output}"
     shell:
         """
-        Rscript scripts/RecombinationSummary.r 6_OrderMarkers/recombination > {output}
+        RecombinationSummary.r 6_OrderMarkers/recombination > {output}
         """
diff --git a/rules/LepMap3/trim.smk b/rules/LepMap3/trim.smk
index 7f122c1..2021782 100644
--- a/rules/LepMap3/trim.smk
+++ b/rules/LepMap3/trim.smk
@@ -10,7 +10,7 @@ rule trim_edge_clusters:
     message: "Removing edge clusters >{params.trim_threshold}%cM apart from the other markers at the ends of {input}"
     shell:
         """
-        Rscript scripts/LepWrapTrim.r {input} {params.trim_threshold} {params.edge_length} 5_Trim
+        LepWrapTrim.r {input} {params.trim_threshold} {params.edge_length} 5_Trim
         """
 
 rule trim_summary:
@@ -33,8 +33,8 @@ rule trim_summary:
             BASE=$(basename $each | cut -d "." -f1,2)
             sed -e "s/^/$BASE /" $each
         done | sort -V > {output.detailed}
-        scripts/TrimCounts.r {output.detailed} {params.lg} > {output.summary}
-        scripts/TrimSummaryPlot.r {output.summary}
+        TrimCounts.r {output.detailed} {params.lg} > {output.summary}
+        TrimSummaryPlot.r {output.summary}
         echo "Merging QC plots for all linkage groups"
         convert -density 300 {input.plots} {output.mergeplots}
         """
diff --git a/scripts/FilterLinkageMap.r b/scripts/FilterLinkageMap.r
index 31fa7ff..c7c995b 100755
--- a/scripts/FilterLinkageMap.r
+++ b/scripts/FilterLinkageMap.r
@@ -1,3 +1,5 @@
+#! /usr/bin/env Rscript
+
 # This R file performs an adaptive method of filtering a linkage map
 # It works by creating a spline on the linkage map, then performing
 # a sliding window analysis on the residuals of the spline, calculating
diff --git a/scripts/RecombinationSummary.r b/scripts/RecombinationSummary.r
index e792bf4..fb37bbd 100755
--- a/scripts/RecombinationSummary.r
+++ b/scripts/RecombinationSummary.r
@@ -1,4 +1,5 @@
 #! /usr/bin/env Rscript
+
 # This script will parse all the recombination logs of LepWrap
 suppressMessages(library(tidyverse))
 suppressMessages(library("stringr"))
diff --git a/scripts/generate_config.sh b/scripts/generate_config.sh
new file mode 100755
index 0000000..232b018
--- /dev/null
+++ b/scripts/generate_config.sh
@@ -0,0 +1,151 @@
+#! /usr/bin/env bash
+
+cat <<EOF
+# Configuration file for LepWrap
+#=======================================================#
+#                       Lep-Map 3                       #
+#=======================================================#
+# Change this to false if you want to skip Lep-Map3
+run_lepmap: true
+
+  #----- ParentCall2 ------#
+# The filtered VCF file with your genotype likelihoods:
+vcf: "mydata.vcf"
+
+# Instructions to create pedigree file: https://sourceforge.net/p/lep-map3/wiki/software/LepMap3 Home/#parentcall2
+# the pedigree file associated with your data
+pedigree: "pedigree.txt"
+
+# Additional parameters for ParentCall2 (e.g. halfSibs=1), if any
+extra_params_ParentCall: "removeNonInformative=1"
+
+
+  #----- Filtering2 -----#
+# Data tolerance value-- set this to 0 if you want to skip the Filtering2 module
+data_tol: 0
+
+# Additional parameters for Filtering2 (e.g. convert2Biallelic=1), if any
+extra_params_Filtering: ""
+
+
+  #----- SeperateChromosomes2 -----#
+# LepWrap will iteratively perform SeperateChromosomes2 for each
+# LOD score in the range of lod_min to lod_max
+
+# The minimum LOD for SeperateChromosomes2
+lod_min: 10
+
+# The maximum LOD for SeperateChromosomes2
+lod_max: 50
+
+# Use only markers with informative father (1), mother(2), both parents(3) or neither parent(0)
+informative: "informativeMask=3"
+
+# Additional parameters for SeparateChromosomes2 (e.g. distrotionLOD=1), if any
+extra_params_SeparateChromosomes: "sizeLimit=5 distortionLod=1"
+
+
+  #----- JoinSingles2ALL -----#
+# Set this to false if you want to skip joining singles (0) to linkage groups
+run_joinsingles2all: false
+
+# These are the parameters for JoinSingles2ALL, and are highly data-dependent
+# Start with lower values for lod_limit and increase as necessary
+lod_limit: "lodLimit=2"
+
+# Start with lower values for lod_limit and increase as necessary
+lod_difference: "lodDifference=2"
+
+# Additional parameters for JoinSingles2All (e.g. iterate=1), if any
+extra_params_JoinSingles: "iterate=1 distortionLod=1"
+ 
+
+  #----- OrderMarkers2 -----#
+# Set exp_lg to your expected number of chromosomes for iterative ordering
+exp_lg: 24
+
+# Additional parameters for OrderMarkers2 (e.g. hyperPhaser=1), if any
+# I recommend setting numMergeIterations to ~100 (Lep-Map3 default is 6)
+extra_params_OrderMarkers: "useKosambi=1 phasingIterations=2 numMergeIterations=100"
+
+
+  #----- Edge Trimming -----#
+# Edge trimming will examine the first and last X% of markers in a linkage group
+# and remove clusters that are N% centimorgans (of the total cM span) away from 
+# the next marker. You can "skip" trimming by setting trim_cutoff really high (e.g. 80-100).
+
+# Set edge_length to the percent number of markers you would like to examine from either end of the linkage group
+# Value can be an integer or decimal, i.e. 15 is the same as 0.15, which both mean "15%" (10-20 is reasonable)
+edge_length: 20
+
+# Set trim_cuttoff to the centiMorgan distance cutoff (5-10 is reasonable)
+trim_cutoff: 100 
+
+
+  #----- Re-OrderMarkers2 -----#
+# The second round of OrderMarkers will use the same basic parameters as the first round (but not the extra params)
+# If there are additional parameters you would like to use, add them here:
+extra_params_reOrderMarkers: "improveOrder=1 useKosambi=1 numMergeIterations=75"
+
+  #----- Calculate Distances -----#
+# If you used useKosambi=1 or useMorgan=1 for Ordering/reOrdering, add that same
+# parameter to distance_method, otherwise leave it as a blank string
+distance_method: "useKosambi=1"
+
+
+#=======================================================#
+#                       Lep-Anchor                      #
+#=======================================================#
+  #---- global settings ----#
+# Change this to false if you want to skip Lep-Anchor
+run_lepanchor: true
+
+# The path to the genome assembly you are trying to anchor 
+assembly: "assembly.fasta"
+
+# The number of linkage groups you have
+lg_count: 24
+
+# If you have a PAF file of long reads mapped to your genome, add it here, otherwise leave the text as "/dev/null"
+PAF_file: "/dev/null"
+
+# If you have a proximity file add it here, otherwise leave the text as "/dev/null".
+# This isn't yet implemented in Lep-Anchor.
+proximity_file: "/dev/null"
+
+
+  #----- CleanMap -----#
+# Additional parameters for CleanMap (e.g. chimericDistance=500), if any
+extra_params_CleanMap: ""
+
+
+  #----- Map2Bed -----#
+# Additional parameters for Map2Bed (e.g. markerSupport=4), if any
+extra_params_Map2Bed: ""
+
+
+  #----- PlaceAndOrientContigs -----#
+# Choose which of the input types you want to generate by leaving it uncommented. Intervals are the default, but either works.
+#lepanchor_input: "noIntervals=0"  # data is intervals
+lepanchor_input: "noIntervals=1"  # data is distances
+
+# The size limit for detecting potential haplotype contigs (LepAnchor default: 2000)
+# Set this value really high (50000+) to ignore haplotype removal in between PlaceOrient iterations
+haplotype_limit: 2000
+
+# Additional parameters you would like to use for PlaceAndOrientContigs, if any (e.g. randomOrder=1)
+extra_params_PlaceOrient: "keepEmptyIntervals=1 numRuns=10"
+
+
+  #----- Edge Trimming -----#
+# Edge trimming will examine the first and last X% of markers in a linkage group
+# and remove clusters that are N% centimorgans (of the total cM span) away from 
+# the next marker. You can "skip" trimming by setting  LA_trim_cutoff really high (e.g. 80-100) 
+
+# Set edge_length to the percent number of markers you would like to examine from either end of the linkage group
+# Value can be an integer or decimal, i.e. 15 is the same as 0.15, which both mean "15%" (10-15 is reasonable)
+LA_edge_length: 15
+
+# Set trim_cuttoff to the centiMorgan distance cutoff (5-10 is reasonable)
+LA_trim_cutoff: 5
+EOF
\ No newline at end of file
diff --git a/scripts/generate_lastzctl.sh b/scripts/generate_lastzctl.sh
new file mode 100755
index 0000000..2b7765e
--- /dev/null
+++ b/scripts/generate_lastzctl.sh
@@ -0,0 +1,48 @@
+#! /usr/bin/env bash
+
+cat <<EOF
+### This file is MY default parameter setting file for all_lastz.pl!
+
+##(!!!actually this section is never useful)if want to infer score matrix, uncomment the following two line 
+#--inferonly				 	# when infering score, lastz_D is used instead of lastz, gap penalty should not be inferred in present. 
+#--infscores[=<output_file>], 	# inferred score output to this file. 
+
+##dynamic masking
+# equivalent to the BLASTZ_M, default is 0, when required, set to 50 normally, some set to 254
+--masking=254					
+# --notrivial is required for haploMerger, should not changed!
+--notrivial
+
+##scoring parameters for tuning
+#--scores=<scoring_file>       	# should not specify when using scoreMatrix inference procedure, i.e. --infer
+#--inner=2000					# equivalent to the BLASTZ_H, normally H=2000
+--hspthresh=3000				# equivalent to the BLASTZ_K, 3000 by default
+--ydrop=3400					# equivalent to the BLASTZ_Y, O+300E by default
+--gappedthresh=3000				# equivalent to the BLASTZ_L, L=K by default
+
+##################################################
+##scoring parameters usually don't need change
+
+# equivalent to BLASTZ_O and BLASTZ_E, 400 and 30, by default
+--gap=400,30					
+#--nogapped
+
+#Offset between the starting positions of successive target words considered for potential seeds. 
+#(But this does not apply to the query words, which always use a step size of 1.) 
+# equivalent to the BLASTZ_Z, z=1 by default
+# set to 20 can reduce the memory consumtion by a factor of 3
+--step=20
+
+# by default --seed=12of19	, or --seed=14of22					
+--seed=12of19					
+
+# default setting=--transition, alternative --notransition
+# set to --notranstion can shorten the time by a factor of 10
+--notransition					
+
+################################################## 
+##non scoring parameters usually don't need change
+--format=axt					# lav (default), axt, maf, and so on
+--markend						# Just before normal completion, write "# lastz end-of-file" to the output file.
+--verbosity=1					# logfile details
+EOF
\ No newline at end of file
diff --git a/scripts/generate_qscoremtx.sh b/scripts/generate_qscoremtx.sh
new file mode 100755
index 0000000..7385953
--- /dev/null
+++ b/scripts/generate_qscoremtx.sh
@@ -0,0 +1,9 @@
+#! /usr/bin/env bash
+
+cat <<EOF
+    A     C     G     T
+   84  -213  -144  -212
+ -213   100  -203  -144
+ -144  -203   100  -213
+ -212  -144  -213    84
+EOF
\ No newline at end of file
diff --git a/scripts/iterate_js2all.sh b/scripts/iterate_js2all.sh
index 8a7642b..dec5dac 100755
--- a/scripts/iterate_js2all.sh
+++ b/scripts/iterate_js2all.sh
@@ -32,7 +32,7 @@ else
 fi
 
 for i in $(seq $LODMIN $LODMAX); do
-    zcat 2_Filtering/data.filtered.lepmap3.gz | java -cp software/LepMap3 JoinSingles2All map=$TARGETMAP data=- lodLimit=$i lodDifference=4 iterate=1 distortionLod=1 numThreads=10 informativeMask=$INFMASK > JoinSingles2All_iter/logs/map.$i.$4.js2all
+    zcat 2_Filtering/data.filtered.lepmap3.gz | java -cp $CONDA_PREFIX/bin/ JoinSingles2All map=$TARGETMAP data=- lodLimit=$i lodDifference=4 iterate=1 distortionLod=1 numThreads=10 informativeMask=$INFMASK > JoinSingles2All_iter/logs/map.$i.$4.js2all
     cut -f1 JoinSingles2All_iter/logs/map.$i.$4.js2all > JoinSingles2All_iter/LOD.$i.$4.js2all
 done
 
diff --git a/scripts/refinemap.sh b/scripts/refinemap.sh
index 092f0b2..fd60344 100755
--- a/scripts/refinemap.sh
+++ b/scripts/refinemap.sh
@@ -31,7 +31,7 @@ LODMAX=$4
 SIZELIM=$5
 
 for i in $(seq $LODMIN $LODMAX); do
-    zcat 2_Filtering/data.filtered.lepmap3.gz | java -cp software/LepMap3 SeparateChromosomes2 data=- map=$TARGETMAP lg=$TARGETLG sizeLimit=$SIZELIM lodLimit=$i distortionLod=1 numThreads=4 > $1.refine/map.$i
+    zcat 2_Filtering/data.filtered.lepmap3.gz | java -cp $CONDA_PREFIX/bin/ SeparateChromosomes2 data=- map=$TARGETMAP lg=$TARGETLG sizeLimit=$SIZELIM lodLimit=$i distortionLod=1 numThreads=4 > $1.refine/map.$i
 done
 
 # generate a summary of the results
diff --git a/scripts/usage b/scripts/usage
index ab95740..d7a1411 100755
--- a/scripts/usage
+++ b/scripts/usage
@@ -27,7 +27,7 @@ EOF
 fi
 
 if [[ $1 == "Map2Bed" || $1 == "CleanMap" || $1 == "PlaceAndOrientContigs" ]]; then
-  java -cp software/LepAnchor $1 2>&1
+  java -cp $CONDA_PREFIX/bin/ $1 2>&1
 else
-  java -cp software/LepMap3 $1 2>&1 |  tail -n +2
+  java -cp $CONDA_PREFIX/bin/ $1 2>&1 |  tail -n +2
 fi
diff --git a/thingsx.seq b/thingsx.seq
new file mode 120000
index 0000000..9fedc8c
--- /dev/null
+++ b/thingsx.seq
@@ -0,0 +1 @@
+things.seq
\ No newline at end of file
diff --git a/thingsx.sizes b/thingsx.sizes
new file mode 120000
index 0000000..df0fce3
--- /dev/null
+++ b/thingsx.sizes
@@ -0,0 +1 @@
+things.sizes
\ No newline at end of file
diff --git a/x.seq b/x.seq
new file mode 120000
index 0000000..0fc2021
--- /dev/null
+++ b/x.seq
@@ -0,0 +1 @@
+.seq
\ No newline at end of file
diff --git a/x.sizes b/x.sizes
new file mode 120000
index 0000000..4e9432d
--- /dev/null
+++ b/x.sizes
@@ -0,0 +1 @@
+.sizes
\ No newline at end of file

From 0f91a76fb8984eb1cf3488e2faef1b6830f2a2cd Mon Sep 17 00:00:00 2001
From: Pavel Dimens <pdimens@live.com>
Date: Mon, 14 Feb 2022 12:49:10 -0500
Subject: [PATCH 35/46] update paths and error text

---
 .misc/install.sh                  |  20 --
 HM.all_lastz.log                  |   0
 HM.axtChainRecipBestNet.log       |   1 -
 HM.initiation.log                 |   1 -
 HM2.all_lastz.log                 |   3 -
 LepWrap                           |  24 +-
 conda_setup.yml                   | 363 ------------------------------
 rules/LepAnchor/place_orient3.smk |  87 -------
 software/LepAnchor/deps/step1.HM2 |   4 +-
 software/LepAnchor/deps/step2.HM2 |   2 +-
 thingsx.seq                       |   1 -
 thingsx.sizes                     |   1 -
 x.seq                             |   1 -
 x.sizes                           |   1 -
 14 files changed, 21 insertions(+), 488 deletions(-)
 delete mode 100644 .misc/install.sh
 delete mode 100644 HM.all_lastz.log
 delete mode 100644 HM.axtChainRecipBestNet.log
 delete mode 100644 HM.initiation.log
 delete mode 100644 HM2.all_lastz.log
 delete mode 100644 conda_setup.yml
 delete mode 100644 rules/LepAnchor/place_orient3.smk
 delete mode 120000 thingsx.seq
 delete mode 120000 thingsx.sizes
 delete mode 120000 x.seq
 delete mode 120000 x.sizes

diff --git a/.misc/install.sh b/.misc/install.sh
deleted file mode 100644
index d87f015..0000000
--- a/.misc/install.sh
+++ /dev/null
@@ -1,20 +0,0 @@
-#! /usr/bin/env bash
-
-# install LepWrap into conda PATH
-mkdir -p $CONDA_PREFIX/bin
-# LepWrap executable
-cp LepWrap $CONDA_PREFIX/bin/
-chmod +x $CONDA_PREFIX/bin/LepWrap
-# associated scripts
-chmod +x scripts/*
-cp scripts/* $CONDA_PREFIX/bin/
-# LepMap3 modules and scripts
-cp software/LepMap3/*.class $CONDA_PREFIX/bin
-cp software/LepMap3/scripts/* $CONDA_PREFIX/bin
-# LepAnchor modules and scripts
-cp software/LepAnchor/*.class software/LepAnchor/lepanchor_wrapper.sh $CONDA_PREFIX/bin
-cp $CONDA_PREFIX/bin/* $CONDA_PREFIX/bin
-cp software/LepAnchor/deps/ucsc_binaries/* $CONDA_PREFIX/bin
-cp software/LepAnchor/deps/*.pl software/LepAnchor/deps/Red software/LepAnchor/deps/all_lastz.ctl software/LepAnchor/deps/scoreMatrix.q software/LepAnchor/deps/step* $CONDA_PREFIX/bin
-# Snakemake rules
-cp rules/LepAnchor/*.smk rules/LepMap3/*.smk $CONDA_PREFIX/bin
diff --git a/HM.all_lastz.log b/HM.all_lastz.log
deleted file mode 100644
index e69de29..0000000
diff --git a/HM.axtChainRecipBestNet.log b/HM.axtChainRecipBestNet.log
deleted file mode 100644
index 9efda7c..0000000
--- a/HM.axtChainRecipBestNet.log
+++ /dev/null
@@ -1 +0,0 @@
-Can't open perl script "../software/LepAnchor/deps/HM_axtChainRecipBestNet.pl": No such file or directory
diff --git a/HM.initiation.log b/HM.initiation.log
deleted file mode 100644
index 1134612..0000000
--- a/HM.initiation.log
+++ /dev/null
@@ -1 +0,0 @@
-Can't open perl script "../software/LepAnchor/deps/initiation.pl": No such file or directory
diff --git a/HM2.all_lastz.log b/HM2.all_lastz.log
deleted file mode 100644
index 7b3c223..0000000
--- a/HM2.all_lastz.log
+++ /dev/null
@@ -1,3 +0,0 @@
-Can't open perl script "../software/LepAnchor/deps/HM_all_lastz_mThreads.pl": No such file or directory
-Can't open perl script "../software/LepAnchor/deps/HM_all_lastz_mThreads.pl": No such file or directory
-Can't open perl script "../software/LepAnchor/deps/HM_all_lastz_mThreads.pl": No such file or directory
diff --git a/LepWrap b/LepWrap
index 2b78c49..2921105 100755
--- a/LepWrap
+++ b/LepWrap
@@ -20,12 +20,29 @@ if [[ -z "$1" ]]; then
   exit 1
 fi
 
+if [ -z "$CONDA_PREFIX" ]; then
+  echo -e "No active conda environment detected and one is required for the pipeline to work. If you cloned the repository rather than installing the conda package, you may install the environment using:\n"
+  printf "\033[01;32m"
+  printf "conda env create -f conda_setup.yml\n\n"
+  printf "\033[0m"
+  echo -e "Then, activate it using:\n"
+  printf "\033[01;32m"
+  printf "conda activate lepwrap\n"
+  printf "\033[0m"
+  exit 1
+fi
+
 # Check for snakemake
 if which snakemake &>/dev/null; then
   foo=1
 else
   echo -e "ERROR:\nSnakemake installation is required to run LepWrap, but not found in the current environment."
-  echo -e "If [ana|mini]conda are installed, created a pre-configred environment with:\n"
+  echo -e "It is likely LepWrap was not installed using [ana|mini]conda, which bundles all the dependencies."
+  echo -e "Please install LepWrap using conda: "
+  printf "\033[01;32m"
+  printf "conda install -c bioconda lepwrap\n\n"
+  printf "\033[0m"
+  echo -e "Alternatively, if you cloned the repository, you may install the environment using:\n"
   printf "\033[01;32m"
   printf "conda env create -f conda_setup.yml\n"
   printf "\033[0m"
@@ -85,11 +102,6 @@ lepanchor(){
   snakemake --cores $1 --snakefile $CONDA_PREFIX/bin/LepAnchor.smk --configfile $CONF --directory .
 }
 
-if [ -z "$CONDA_PREFIX" ]; then
-  echo "No active conda environment detected. The LepWrap conda environment is required for the pipeline to work."
-  exit 1
-fi
-
 LM=$(grep "run_lepmap" config.yml | cut -d":" -f2 | xargs | tr '[:upper:]' '[:lower:]')
 LA=$(grep "run_lepanchor" config.yml | cut -d":" -f2 | xargs | tr '[:upper:]' '[:lower:]')
 
diff --git a/conda_setup.yml b/conda_setup.yml
deleted file mode 100644
index c81b970..0000000
--- a/conda_setup.yml
+++ /dev/null
@@ -1,363 +0,0 @@
-name: lepwrap
-channels:
-  - conda-forge/label/main
-  - bioconda
-  - conda-forge
-  - defaults
-  - r
-dependencies:
-  - _libgcc_mutex=0.1=conda_forge
-  - _openmp_mutex=4.5=1_gnu
-  - _r-mutex=1.0.1=anacondar_1
-  - aioeasywebdav=2.4.0=py39hf3d152e_1001
-  - aiohttp=3.7.4=py39h3811e60_0
-  - amply=0.1.4=py_0
-  - appdirs=1.4.4=pyh9f0ad1d_0
-  - async-timeout=3.0.1=py_1000
-  - atk-1.0=2.36.0=h3371d22_4
-  - attmap=0.13.0=pyhd8ed1ab_0
-  - attrs=21.2.0=pyhd8ed1ab_0
-  - azure-common=1.1.27=pyhd8ed1ab_0
-  - azure-core=1.14.0=pyhd8ed1ab_0
-  - azure-storage-blob=12.8.1=pyhd8ed1ab_0
-  - backports=1.0=py_2
-  - backports.functools_lru_cache=1.6.4=pyhd8ed1ab_0
-  - bcrypt=3.2.0=py39h3811e60_1
-  - binutils_impl_linux-64=2.35.1=h193b22a_2
-  - binutils_linux-64=2.35=h67ddf6f_30
-  - blinker=1.4=py_1
-  - boto=2.49.0=py_0
-  - boto3=1.17.76=pyhd8ed1ab_0
-  - botocore=1.20.76=pyhd8ed1ab_0
-  - brotlipy=0.7.0=py39h3811e60_1001
-  - bwidget=1.9.14=ha770c72_0
-  - bzip2=1.0.8=h7f98852_4
-  - c-ares=1.17.1=h7f98852_1
-  - ca-certificates=2020.12.5=ha878542_0
-  - cachetools=4.2.2=pyhd8ed1ab_0
-  - cairo=1.16.0=h6cf1ce9_1008
-  - certifi=2020.12.5=py39hf3d152e_1
-  - cffi=1.14.5=py39he32792d_0
-  - chardet=4.0.0=py39hf3d152e_1
-  - coincbc=2.10.5=hcee13e7_1
-  - configargparse=1.4.1=pyhd8ed1ab_0
-  - connection_pool=0.0.3=pyhd3deb0d_0
-  - cryptography=3.4.7=py39hbca0aa6_0
-  - curl=7.76.1=hea6ffbf_2
-  - datrie=0.8.2=py39h3811e60_2
-  - decorator=5.0.9=pyhd8ed1ab_0
-  - docutils=0.17.1=py39hf3d152e_0
-  - dropbox=11.9.0=pyhd8ed1ab_0
-  - expat=2.3.0=h9c3ff4c_0
-  - fftw=3.3.9=nompi_h74d3f13_101
-  - filechunkio=1.8=py_2
-  - filelock=3.0.12=pyh9f0ad1d_0
-  - font-ttf-dejavu-sans-mono=2.37=hab24e00_0
-  - font-ttf-inconsolata=3.000=h77eed37_0
-  - font-ttf-source-code-pro=2.038=h77eed37_0
-  - font-ttf-ubuntu=0.83=hab24e00_0
-  - fontconfig=2.13.1=hba837de_1005
-  - fonts-conda-ecosystem=1=0
-  - fonts-conda-forge=1=0
-  - freetype=2.10.4=h0708190_1
-  - fribidi=1.0.10=h36c2ea0_0
-  - ftputil=5.0.1=pyhd8ed1ab_0
-  - gcc_impl_linux-64=9.3.0=h70c0ae5_19
-  - gcc_linux-64=9.3.0=hf25ea35_30
-  - gdk-pixbuf=2.42.6=h04a7f16_0
-  - gettext=0.19.8.1=h0b5b191_1005
-  - gfortran_impl_linux-64=9.3.0=hc4a2995_19
-  - gfortran_linux-64=9.3.0=hdc58fab_30
-  - ghostscript=9.18=1
-  - giflib=5.2.1=h36c2ea0_2
-  - gitdb=4.0.7=pyhd8ed1ab_0
-  - gitpython=3.1.17=pyhd8ed1ab_0
-  - google-api-core=1.26.3=pyhd8ed1ab_0
-  - google-api-python-client=2.5.0=pyhd8ed1ab_0
-  - google-auth=1.30.0=pyh44b312d_0
-  - google-auth-httplib2=0.1.0=pyhd8ed1ab_0
-  - google-cloud-core=1.5.0=pyhd3deb0d_0
-  - google-cloud-storage=1.19.0=py_0
-  - google-crc32c=1.1.2=py39hb81f231_0
-  - google-resumable-media=1.2.0=pyhd3deb0d_0
-  - googleapis-common-protos=1.53.0=py39hf3d152e_0
-  - graphite2=1.3.13=h58526e2_1001
-  - graphviz=2.47.1=h85b4f2f_1
-  - grpcio=1.37.1=py39hff7568b_0
-  - gsl=2.6=he838d99_2
-  - gtk2=2.24.33=h539f30e_1
-  - gts=0.7.6=h64030ff_2
-  - gxx_impl_linux-64=9.3.0=hd87eabc_19
-  - gxx_linux-64=9.3.0=h3fbe746_30
-  - harfbuzz=2.8.1=h83ec7ef_0
-  - httplib2=0.19.1=pyhd8ed1ab_0
-  - icu=68.1=h58526e2_0
-  - idna=2.10=pyh9f0ad1d_0
-  - imagemagick=7.0.11_13=pl5320hb118871_0
-  - importlib-metadata=4.0.1=py39hf3d152e_0
-  - iniconfig=1.1.1=pyh9f0ad1d_0
-  - ipython_genutils=0.2.0=py_1
-  - isodate=0.6.0=py_1
-  - jbig=2.1=h7f98852_2003
-  - jinja2=3.0.1=pyhd8ed1ab_0
-  - jmespath=0.10.0=pyh9f0ad1d_0
-  - jpeg=9d=h36c2ea0_0
-  - jsonschema=3.2.0=pyhd8ed1ab_3
-  - jupyter_core=4.7.1=py39hf3d152e_0
-  - kernel-headers_linux-64=2.6.32=h77966d4_13
-  - krb5=1.19.1=hcc1bbae_0
-  - ld_impl_linux-64=2.35.1=hea4e1c9_2
-  - libblas=3.9.0=9_openblas
-  - libcblas=3.9.0=9_openblas
-  - libcrc32c=1.1.1=h9c3ff4c_2
-  - libcurl=7.76.1=h2574ce0_2
-  - libedit=3.1.20191231=he28a2e2_2
-  - libev=4.33=h516909a_1
-  - libffi=3.3=h58526e2_2
-  - libgcc=7.2.0=h69d50b8_2
-  - libgcc-devel_linux-64=9.3.0=h7864c58_19
-  - libgcc-ng=9.3.0=h2828fa1_19
-  - libgd=2.3.2=h78a0170_0
-  - libgfortran-ng=9.3.0=hff62375_19
-  - libgfortran5=9.3.0=hff62375_19
-  - libglib=2.68.2=h3e27bee_0
-  - libgomp=9.3.0=h2828fa1_19
-  - libiconv=1.16=h516909a_0
-  - liblapack=3.9.0=9_openblas
-  - libnghttp2=1.43.0=h812cca2_0
-  - libopenblas=0.3.15=pthreads_h8fe5266_1
-  - libpng=1.6.37=h21135ba_2
-  - libprotobuf=3.17.0=h780b84a_0
-  - librsvg=2.50.5=hc3c00ef_0
-  - libsodium=1.0.18=h36c2ea0_1
-  - libssh2=1.9.0=ha56f1ee_6
-  - libstdcxx-devel_linux-64=9.3.0=hb016644_19
-  - libstdcxx-ng=9.3.0=h6de172a_19
-  - libtiff=4.3.0=hf544144_0
-  - libtool=2.4.6=h58526e2_1007
-  - libuuid=2.32.1=h7f98852_1000
-  - libwebp=1.2.0=h3452ae3_0
-  - libwebp-base=1.2.0=h7f98852_2
-  - libxcb=1.13=h7f98852_1003
-  - libxml2=2.9.12=h72842e0_0
-  - logmuse=0.2.6=pyh8c360ce_0
-  - lz4-c=1.9.3=h9c3ff4c_0
-  - make=4.3=hd18ef5c_1
-  - markupsafe=2.0.1=py39h3811e60_0
-  - more-itertools=8.7.0=pyhd8ed1ab_1
-  - msrest=0.6.21=pyh44b312d_0
-  - multidict=5.1.0=py39h3811e60_1
-  - nbformat=5.1.3=pyhd8ed1ab_0
-  - ncurses=6.2=h58526e2_4
-  - networkx=2.5=py_0
-  - numpy=1.20.3=py39hdbf815f_0
-  - oauth2client=4.1.3=py_0
-  - oauthlib=3.0.1=py_0
-  - openjpeg=2.4.0=hb52868f_1
-  - openssl=1.1.1k=h7f98852_0
-  - packaging=20.9=pyh44b312d_0
-  - pandas=1.2.4=py39hde0f152_0
-  - pandoc=2.13=h7f98852_0
-  - pango=1.48.5=hb8ff022_0
-  - paramiko=2.7.2=pyh9f0ad1d_0
-  - pcre=8.44=he1b5a44_0
-  - pcre2=10.36=h032f7d1_1
-  - peppy=0.31.1=pyhd8ed1ab_0
-  - perl=5.32.0=h36c2ea0_0
-  - pip=21.1.1=pyhd8ed1ab_0
-  - pixman=0.40.0=h36c2ea0_0
-  - pkg-config=0.29.2=h36c2ea0_1008
-  - pluggy=0.13.1=py39hf3d152e_4
-  - ply=3.11=py_1
-  - prettytable=2.1.0=pyhd8ed1ab_0
-  - protobuf=3.17.0=py39he80948d_0
-  - psutil=5.8.0=py39h3811e60_1
-  - pthread-stubs=0.4=h36c2ea0_1001
-  - pulp=2.4=py39hf3d152e_0
-  - py=1.10.0=pyhd3deb0d_0
-  - pyasn1=0.4.8=py_0
-  - pyasn1-modules=0.2.7=py_0
-  - pycparser=2.20=pyh9f0ad1d_2
-  - pygments=2.9.0=pyhd8ed1ab_0
-  - pygraphviz=1.7=py39h78163bd_0
-  - pyjwt=2.1.0=pyhd8ed1ab_0
-  - pynacl=1.4.0=py39h3811e60_2
-  - pyopenssl=20.0.1=pyhd8ed1ab_0
-  - pyparsing=2.4.7=pyh9f0ad1d_0
-  - pyrsistent=0.17.3=py39h3811e60_2
-  - pysftp=0.2.9=py_1
-  - pysocks=1.7.1=py39hf3d152e_3
-  - pytest=6.2.4=py39hf3d152e_0
-  - python=3.9.4=hffdb5ce_0_cpython
-  - python-dateutil=2.8.1=py_0
-  - python-irodsclient=0.9.0=pyhd8ed1ab_0
-  - python_abi=3.9=1_cp39
-  - pytz=2021.1=pyhd8ed1ab_0
-  - pyyaml=5.4.1=py39h3811e60_0
-  - r-askpass=1.1=r40hcdcec82_2
-  - r-assertthat=0.2.1=r40h6115d3f_2
-  - r-backports=1.2.1=r40hcfec24a_0
-  - r-base=4.0.5=h9e01966_1
-  - r-base64enc=0.1_3=r40hcdcec82_1004
-  - r-blob=1.2.1=r40h6115d3f_1
-  - r-brio=1.1.2=r40hcfec24a_0
-  - r-broom=0.7.6=r40hc72bb7e_0
-  - r-callr=3.7.0=r40hc72bb7e_0
-  - r-cellranger=1.1.0=r40h6115d3f_1003
-  - r-cli=2.5.0=r40hc72bb7e_0
-  - r-clipr=0.7.1=r40h142f84f_0
-  - r-colorspace=2.0_1=r40hcfec24a_0
-  - r-cowplot=1.1.1=r40hc72bb7e_0
-  - r-cpp11=0.2.7=r40hc72bb7e_0
-  - r-crayon=1.4.1=r40hc72bb7e_0
-  - r-curl=4.3.1=r40hcfec24a_0
-  - r-data.table=1.14.0=r40hcfec24a_0
-  - r-dbi=1.1.1=r40hc72bb7e_0
-  - r-dbplyr=2.1.1=r40hc72bb7e_0
-  - r-desc=1.3.0=r40hc72bb7e_0
-  - r-diffobj=0.3.4=r40hcfec24a_0
-  - r-digest=0.6.27=r40h03ef668_0
-  - r-dplyr=1.0.6=r40h03ef668_1
-  - r-dtplyr=1.1.0=r40hc72bb7e_0
-  - r-ellipsis=0.3.2=r40hcfec24a_0
-  - r-evaluate=0.14=r40h6115d3f_2
-  - r-fansi=0.4.2=r40hcfec24a_0
-  - r-farver=2.1.0=r40h03ef668_0
-  - r-forcats=0.5.1=r40hc72bb7e_0
-  - r-fs=1.5.0=r40h0357c0b_0
-  - r-fuzzyjoin=0.1.6=r40_0
-  - r-gargle=1.1.0=r40hc72bb7e_0
-  - r-gdtools=0.2.2=r40h36050f4_1
-  - r-generics=0.1.0=r40hc72bb7e_0
-  - r-geosphere=1.5_10=r40hcfec24a_2
-  - r-ggplot2=3.3.3=r40hc72bb7e_0
-  - r-glue=1.4.2=r40hcfec24a_0
-  - r-googledrive=1.0.1=r40h6115d3f_1
-  - r-googlesheets4=0.3.0=r40hc72bb7e_0
-  - r-gtable=0.3.0=r40h6115d3f_3
-  - r-haven=2.4.1=r40h2713e49_0
-  - r-highr=0.9=r40hc72bb7e_0
-  - r-hms=1.1.0=r40hc72bb7e_0
-  - r-htmltools=0.5.1.1=r40h03ef668_0
-  - r-httr=1.4.2=r40h6115d3f_0
-  - r-ids=1.0.1=r40h6115d3f_1
-  - r-isoband=0.2.4=r40h03ef668_0
-  - r-jsonlite=1.7.2=r40hcfec24a_0
-  - r-knitr=1.33=r40hc72bb7e_0
-  - r-labeling=0.4.2=r40h142f84f_0
-  - r-lattice=0.20_44=r40hcfec24a_0
-  - r-lifecycle=1.0.0=r40hc72bb7e_0
-  - r-lubridate=1.7.10=r40h03ef668_0
-  - r-magrittr=2.0.1=r40hcfec24a_1
-  - r-markdown=1.1=r40hcfec24a_1
-  - r-mass=7.3_54=r40hcfec24a_0
-  - r-matrix=1.3_3=r40he454529_0
-  - r-mgcv=1.8_35=r40he454529_0
-  - r-mime=0.10=r40hcfec24a_0
-  - r-modelr=0.1.8=r40h6115d3f_0
-  - r-munsell=0.5.0=r40h6115d3f_1003
-  - r-nlme=3.1_152=r40h859d828_0
-  - r-openssl=1.4.4=r40he36bf35_0
-  - r-pillar=1.6.1=r40hc72bb7e_0
-  - r-pkgconfig=2.0.3=r40h6115d3f_1
-  - r-pkgload=1.2.1=r40h03ef668_0
-  - r-plyr=1.8.6=r40h0357c0b_1
-  - r-praise=1.0.0=r40h6115d3f_1004
-  - r-prettyunits=1.1.1=r40h6115d3f_1
-  - r-processx=3.5.2=r40hcfec24a_0
-  - r-progress=1.2.2=r40h6115d3f_2
-  - r-ps=1.6.0=r40hcfec24a_0
-  - r-purrr=0.3.4=r40hcfec24a_1
-  - r-r6=2.5.0=r40hc72bb7e_0
-  - r-rappdirs=0.3.3=r40hcfec24a_0
-  - r-rcolorbrewer=1.1_2=r40h6115d3f_1003
-  - r-rcpp=1.0.6=r40h03ef668_0
-  - r-readr=1.4.0=r40h1b71b39_0
-  - r-readxl=1.3.1=r40hde08347_4
-  - r-rematch=1.0.1=r40h6115d3f_1003
-  - r-rematch2=2.1.2=r40h6115d3f_1
-  - r-reprex=2.0.0=r40hc72bb7e_0
-  - r-reshape2=1.4.4=r40h0357c0b_1
-  - r-rlang=0.4.11=r40hcfec24a_0
-  - r-rmarkdown=2.8=r40hc72bb7e_0
-  - r-rprojroot=2.0.2=r40hc72bb7e_0
-  - r-rstudioapi=0.13=r40hc72bb7e_0
-  - r-rvest=1.0.0=r40hc72bb7e_0
-  - r-scales=1.1.1=r40h6115d3f_0
-  - r-selectr=0.4_2=r40h6115d3f_1
-  - r-sp=1.4_5=r40hcfec24a_0
-  - r-stringdist=0.9.6.3=r40hcfec24a_0
-  - r-stringi=1.6.2=r40hcabe038_0
-  - r-stringr=1.4.0=r40h6115d3f_2
-  - r-svglite=2.0.0=r40h03ef668_0
-  - r-sys=3.4=r40hcdcec82_0
-  - r-systemfonts=1.0.2=r40hef9c87a_0
-  - r-testthat=3.0.2=r40h03ef668_0
-  - r-tibble=3.1.2=r40hcfec24a_0
-  - r-tidyr=1.1.3=r40h03ef668_0
-  - r-tidyselect=1.1.1=r40hc72bb7e_0
-  - r-tidyverse=1.3.1=r40hc72bb7e_0
-  - r-tinytex=0.31=r40hc72bb7e_0
-  - r-utf8=1.2.1=r40hcfec24a_0
-  - r-uuid=0.1_4=r40hcdcec82_1
-  - r-vctrs=0.3.8=r40hcfec24a_0
-  - r-viridislite=0.4.0=r40hc72bb7e_0
-  - r-waldo=0.2.5=r40hc72bb7e_0
-  - r-withr=2.4.2=r40hc72bb7e_0
-  - r-xfun=0.23=r40hcfec24a_0
-  - r-xml2=1.3.2=r40h0357c0b_1
-  - r-yaml=2.2.1=r40hcfec24a_1
-  - r-zeallot=0.1.0=r40h6115d3f_1002
-  - ratelimiter=1.2.0=py_1002
-  - readline=8.1=h46c0cb4_0
-  - requests=2.25.1=pyhd3deb0d_0
-  - requests-oauthlib=1.3.0=pyh9f0ad1d_0
-  - rsa=4.7.2=pyh44b312d_0
-  - s3transfer=0.4.2=pyhd8ed1ab_0
-  - sed=4.8=he412f7d_0
-  - setuptools=49.6.0=py39hf3d152e_3
-  - simplejson=3.17.2=py39h3811e60_2
-  - six=1.16.0=pyh6c4a22f_0
-  - slacker=0.14.0=py_0
-  - smart_open=5.0.0=pyhd8ed1ab_0
-  - smmap=3.0.5=pyh44b312d_0
-  - snakemake=6.4.0=hdfd78af_0
-  - snakemake-minimal=6.4.0=pyhdfd78af_0
-  - sqlite=3.35.5=h74cdb3f_0
-  - stone=3.2.1=pyhd8ed1ab_0
-  - stopit=1.1.2=py_0
-  - sysroot_linux-64=2.12=h77966d4_13
-  - tk=8.6.10=h21135ba_1
-  - tktable=2.10=hb7b940f_3
-  - toml=0.10.2=pyhd8ed1ab_0
-  - toposort=1.6=pyhd8ed1ab_0
-  - traitlets=5.0.5=py_0
-  - typing-extensions=3.7.4.3=0
-  - typing_extensions=3.7.4.3=py_0
-  - tzdata=2021a=he74cb21_0
-  - ubiquerg=0.6.1=pyh9f0ad1d_0
-  - uritemplate=3.0.1=py_0
-  - urllib3=1.26.4=pyhd8ed1ab_0
-  - veracitools=0.1.3=py_0
-  - wcwidth=0.2.5=pyh9f0ad1d_2
-  - wheel=0.36.2=pyhd3deb0d_0
-  - wrapt=1.12.1=py39h3811e60_3
-  - xmlrunner=1.7.7=py_0
-  - xorg-kbproto=1.0.7=h7f98852_1002
-  - xorg-libice=1.0.10=h7f98852_0
-  - xorg-libsm=1.2.3=hd9c2040_1000
-  - xorg-libx11=1.7.1=h7f98852_0
-  - xorg-libxau=1.0.9=h7f98852_0
-  - xorg-libxdmcp=1.1.3=h7f98852_0
-  - xorg-libxext=1.3.4=h7f98852_1
-  - xorg-libxrender=0.9.10=h7f98852_1003
-  - xorg-libxt=1.2.1=h7f98852_2
-  - xorg-renderproto=0.11.1=h7f98852_1002
-  - xorg-xextproto=7.3.0=h7f98852_1002
-  - xorg-xproto=7.0.31=h7f98852_1007
-  - xz=5.2.5=h516909a_1
-  - yaml=0.2.5=h516909a_0
-  - yarl=1.6.3=py39h3811e60_1
-  - zipp=3.4.1=pyhd8ed1ab_0
-  - zlib=1.2.11=h516909a_1010
-  - zstd=1.5.0=ha95c52a_0
diff --git a/rules/LepAnchor/place_orient3.smk b/rules/LepAnchor/place_orient3.smk
deleted file mode 100644
index 57f7651..0000000
--- a/rules/LepAnchor/place_orient3.smk
+++ /dev/null
@@ -1,87 +0,0 @@
-rule place_orient3:
-  input:
-    chain = "9_Chain/chainfile.gz",
-    bedfile = "10_PlaceAndOrientContigs/map.propogated2.bed",
-    paf = paf,
-    prox = proximity,
-    lift = "10_PlaceAndOrientContigs/liftover.la",
-    chrom = "10_PlaceAndOrientContigs/1_orient/chr.{lg_range}.la",
-    propogated = "10_PlaceAndOrientContigs/propogate/propogated.{lg_range}.la"
-  output:
-    chrom = "10_PlaceAndOrientContigs/3_orient/chr.{lg_range}.la",
-    errors = "10_PlaceAndOrientContigs/3_orient/errors/chr.{lg_range}.err"
-  params:
-    chrom = "{lg_range}",
-    extras = place_orient_extra,
-    datatype = data_type
-  message: "Running 3rd round of PlaceAndOrientContigs for linkage group {params.chrom}"
-  threads: 2
-  shell:
-    """
-    gunzip -fc {input.chain} | java -cp $CONDA_PREFIX/bin PlaceAndOrientContigs chromosome={params.chrom} numThreads={threads} $(awk -f $CONDA_PREFIX/bin/pickorientation.awk {input.chrom}) bed={input.bedfile} map={input.lift} chain=- paf={input.paf} proximity={input.prox} evaluateAnchoring={input.propogated} improveAnchoring=1 {params.datatype} {params.extras} > {output.chrom} 2> {output.errors}
-    """
-    
-rule prune_contigblocks:
-  input: "10_PlaceAndOrientContigs/3_orient/chr.{lg_range}.la"
-  output: 
-    chrom = "10_PlaceAndOrientContigs/pruned/chr.{lg_range}.pruned.la",
-    err = "10_PlaceAndOrientContigs/pruned/err/chr.{lg_range}.pruned.err"
-  message: "Pruning contig blocks without map support and removing overlaps"
-  params:
-    chrom = lg
-  shell: "awk -f $CONDA_PREFIX/bin/prune.awk {input} > {output.chrom} 2> {output.err}"
-
-rule prune_post:
-  input:
-    bedfile = "10_PlaceAndOrientContigs/map.propogated2.bed",
-    prunedchrom = expand("10_PlaceAndOrientContigs/pruned/chr.{lgs}.pruned.la", lgs = lg_range),
-    prunederr = expand("10_PlaceAndOrientContigs/pruned/err/chr.{lgs}.pruned.err", lgs = lg_range)
-  output: 
-    overlaps = "10_PlaceAndOrientContigs/overlaps.removed.la",
-    pruned = "10_PlaceAndOrientContigs/pruned.la"
-  message: "Removing overlaps"
-  threads: 1
-  shell:
-    """
-    cat {input.prunederr} > {output.pruned}
-    awk -f $CONDA_PREFIX/bin/removeOverlaps.awk {input.bedfile} {input.prunedchrom} > {output.overlaps}
-    """
-
-#rule find_haplotypes2:
-#  input:
-#    errors = expand("10_PlaceAndOrientContigs/3_orient/errors/chr.{lgs}.err", lgs = lg_range)
-#  output:
-#    haplos = "10_PlaceAndOrientContigs/suspected.haplotypes"
-#  message: "Finding full haplotypes"
-#  params:
-#    haplo = haplo_limit
-#  shell:
-#    """
-#    awk '($NF=="haplotype")' {input.errors} | 
-#      sort -n -r | 
-#      awk -vlimit={params.haplo} '($NF=="haplotype" && ($1>=($4-$3+1-limit)/limit) && (!(($5 SUBSEP $6 SUBSEP $7) in h))){{h[$2,$3,$4]; print}}' > {output.haplos}
-#    """
-#
-#rule liftoverHaplotypes:
-#  input:
-#    chain = "9_Chain/chainfile.gz",
-#    chrom = "10_PlaceAndOrientContigs/1_orient/chr.{lg_range}.la",
-#    haplos = "10_PlaceAndOrientContigs/suspected.haplotypes"
-#  output: "10_PlaceAndOrientContigs/liftover/chr.{lg_range}.liftover"
-#  message: "Running liftoverHaplotypes for {input.chrom}"
-#  threads: 1
-#  shell:
-#    """
-#    gunzip -fc {input.chain} | java -cp $CONDA_PREFIX/bin/ LiftoverHaplotypes map={input.chrom} haplotypes={input.haplos} chain=- > {output}
-#    """
-#
-#rule removehaplotypes:
-#  input:
-#    mapfile = "10_PlaceAndOrientContigs/map.propogated2.bed", 
-#    haplos = "10_PlaceAndOrientContigs/suspected.haplotypes"
-#  output:
-#    bedfile = "10_PlaceAndOrientContigs/map.propogated2.nohaplo.bed"
-#  message: "Removing haplotypes from the map"
-#  threads: 1
-#  shell: "awk -f $CONDA_PREFIX/bin/removeHaplotypes.awk {input} > {output}"
-#
\ No newline at end of file
diff --git a/software/LepAnchor/deps/step1.HM2 b/software/LepAnchor/deps/step1.HM2
index 0849458..29fd6c1 100755
--- a/software/LepAnchor/deps/step1.HM2
+++ b/software/LepAnchor/deps/step1.HM2
@@ -38,7 +38,7 @@ querySize=1600000000  # split query fasta file by size N bp (default=1600000000)
 #### ===========================================================
 
 rm -f -r $name.seq ${name}x.seq $name.sizes ${name}x.sizes ${name}x.fa.gz
-perl ../software/LepAnchor/deps/initiation.pl \
+perl $CONDA_PREFIX/bin/initiation.pl \
   --faSplit \
   --faToNib \
   --faSize \
@@ -58,7 +58,7 @@ ln -s $name.seq ${name}x.seq
 
 rm -f -r $name.${name}x.result/raw.axt
 
-perl ../software/LepAnchor/deps/HM_all_lastz_mThreads.pl \
+perl $CONDA_PREFIX/bin/HM_all_lastz_mThreads.pl \
   --Species $name ${name}x \
   --noself \
   --threads=$threads \
diff --git a/software/LepAnchor/deps/step2.HM2 b/software/LepAnchor/deps/step2.HM2
index 1598e4b..bd764c8 100755
--- a/software/LepAnchor/deps/step2.HM2
+++ b/software/LepAnchor/deps/step2.HM2
@@ -33,7 +33,7 @@ threads=$2						# the number of cpu cores to use (default=1)
 #### run axtChainRecipBestNet
 #### ===========================================================
 
-perl ../software/LepAnchor/deps/HM_axtChainRecipBestNet.pl \
+perl $CONDA_PREFIX/bin/HM_axtChainRecipBestNet.pl \
   --rbestNet \
   --axtChain \
   --tbest \
diff --git a/thingsx.seq b/thingsx.seq
deleted file mode 120000
index 9fedc8c..0000000
--- a/thingsx.seq
+++ /dev/null
@@ -1 +0,0 @@
-things.seq
\ No newline at end of file
diff --git a/thingsx.sizes b/thingsx.sizes
deleted file mode 120000
index df0fce3..0000000
--- a/thingsx.sizes
+++ /dev/null
@@ -1 +0,0 @@
-things.sizes
\ No newline at end of file
diff --git a/x.seq b/x.seq
deleted file mode 120000
index 0fc2021..0000000
--- a/x.seq
+++ /dev/null
@@ -1 +0,0 @@
-.seq
\ No newline at end of file
diff --git a/x.sizes b/x.sizes
deleted file mode 120000
index 4e9432d..0000000
--- a/x.sizes
+++ /dev/null
@@ -1 +0,0 @@
-.sizes
\ No newline at end of file

From 87769ef0afbb14000f83844d5c9fcf1ebbb27dd0 Mon Sep 17 00:00:00 2001
From: Pavel Dimens <pdimens@live.com>
Date: Mon, 14 Feb 2022 12:50:34 -0500
Subject: [PATCH 36/46] restore the conda env

---
 conda_setup.yml | 362 ++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 362 insertions(+)
 create mode 100644 conda_setup.yml

diff --git a/conda_setup.yml b/conda_setup.yml
new file mode 100644
index 0000000..8457238
--- /dev/null
+++ b/conda_setup.yml
@@ -0,0 +1,362 @@
+name: lepwrap
+channels:
+  - conda-forge/label/main
+  - bioconda
+  - conda-forge
+  - defaults
+  - r
+dependencies:
+  - _libgcc_mutex=0.1=conda_forge
+  - _openmp_mutex=4.5=1_gnu
+  - _r-mutex=1.0.1=anacondar_1
+  - aioeasywebdav=2.4.0=py39hf3d152e_1001
+  - aiohttp=3.7.4=py39h3811e60_0
+  - amply=0.1.4=py_0
+  - appdirs=1.4.4=pyh9f0ad1d_0
+  - async-timeout=3.0.1=py_1000
+  - atk-1.0=2.36.0=h3371d22_4
+  - attmap=0.13.0=pyhd8ed1ab_0
+  - attrs=21.2.0=pyhd8ed1ab_0
+  - azure-common=1.1.27=pyhd8ed1ab_0
+  - azure-core=1.14.0=pyhd8ed1ab_0
+  - azure-storage-blob=12.8.1=pyhd8ed1ab_0
+  - backports=1.0=py_2
+  - backports.functools_lru_cache=1.6.4=pyhd8ed1ab_0
+  - bcrypt=3.2.0=py39h3811e60_1
+  - binutils_impl_linux-64=2.35.1=h193b22a_2
+  - binutils_linux-64=2.35=h67ddf6f_30
+  - blinker=1.4=py_1
+  - boto=2.49.0=py_0
+  - boto3=1.17.76=pyhd8ed1ab_0
+  - botocore=1.20.76=pyhd8ed1ab_0
+  - brotlipy=0.7.0=py39h3811e60_1001
+  - bwidget=1.9.14=ha770c72_0
+  - bzip2=1.0.8=h7f98852_4
+  - c-ares=1.17.1=h7f98852_1
+  - ca-certificates=2020.12.5=ha878542_0
+  - cachetools=4.2.2=pyhd8ed1ab_0
+  - cairo=1.16.0=h6cf1ce9_1008
+  - certifi=2020.12.5=py39hf3d152e_1
+  - cffi=1.14.5=py39he32792d_0
+  - chardet=4.0.0=py39hf3d152e_1
+  - coincbc=2.10.5=hcee13e7_1
+  - configargparse=1.4.1=pyhd8ed1ab_0
+  - connection_pool=0.0.3=pyhd3deb0d_0
+  - cryptography=3.4.7=py39hbca0aa6_0
+  - curl=7.76.1=hea6ffbf_2
+  - datrie=0.8.2=py39h3811e60_2
+  - decorator=5.0.9=pyhd8ed1ab_0
+  - docutils=0.17.1=py39hf3d152e_0
+  - dropbox=11.9.0=pyhd8ed1ab_0
+  - expat=2.3.0=h9c3ff4c_0
+  - fftw=3.3.9=nompi_h74d3f13_101
+  - filechunkio=1.8=py_2
+  - filelock=3.0.12=pyh9f0ad1d_0
+  - font-ttf-dejavu-sans-mono=2.37=hab24e00_0
+  - font-ttf-inconsolata=3.000=h77eed37_0
+  - font-ttf-source-code-pro=2.038=h77eed37_0
+  - font-ttf-ubuntu=0.83=hab24e00_0
+  - fontconfig=2.13.1=hba837de_1005
+  - fonts-conda-ecosystem=1=0
+  - fonts-conda-forge=1=0
+  - freetype=2.10.4=h0708190_1
+  - fribidi=1.0.10=h36c2ea0_0
+  - ftputil=5.0.1=pyhd8ed1ab_0
+  - gcc_impl_linux-64=9.3.0=h70c0ae5_19
+  - gcc_linux-64=9.3.0=hf25ea35_30
+  - gdk-pixbuf=2.42.6=h04a7f16_0
+  - gettext=0.19.8.1=h0b5b191_1005
+  - gfortran_impl_linux-64=9.3.0=hc4a2995_19
+  - gfortran_linux-64=9.3.0=hdc58fab_30
+  - ghostscript=9.18=1
+  - giflib=5.2.1=h36c2ea0_2
+  - gitdb=4.0.7=pyhd8ed1ab_0
+  - gitpython=3.1.17=pyhd8ed1ab_0
+  - google-api-core=1.26.3=pyhd8ed1ab_0
+  - google-api-python-client=2.5.0=pyhd8ed1ab_0
+  - google-auth=1.30.0=pyh44b312d_0
+  - google-auth-httplib2=0.1.0=pyhd8ed1ab_0
+  - google-cloud-core=1.5.0=pyhd3deb0d_0
+  - google-cloud-storage=1.19.0=py_0
+  - google-crc32c=1.1.2=py39hb81f231_0
+  - google-resumable-media=1.2.0=pyhd3deb0d_0
+  - googleapis-common-protos=1.53.0=py39hf3d152e_0
+  - graphite2=1.3.13=h58526e2_1001
+  - graphviz=2.47.1=h85b4f2f_1
+  - grpcio=1.37.1=py39hff7568b_0
+  - gsl=2.6=he838d99_2
+  - gtk2=2.24.33=h539f30e_1
+  - gts=0.7.6=h64030ff_2
+  - gxx_impl_linux-64=9.3.0=hd87eabc_19
+  - gxx_linux-64=9.3.0=h3fbe746_30
+  - harfbuzz=2.8.1=h83ec7ef_0
+  - httplib2=0.19.1=pyhd8ed1ab_0
+  - icu=68.1=h58526e2_0
+  - idna=2.10=pyh9f0ad1d_0
+  - imagemagick=7.0.11_13=pl5320hb118871_0
+  - importlib-metadata=4.0.1=py39hf3d152e_0
+  - iniconfig=1.1.1=pyh9f0ad1d_0
+  - ipython_genutils=0.2.0=py_1
+  - isodate=0.6.0=py_1
+  - jbig=2.1=h7f98852_2003
+  - jinja2=3.0.1=pyhd8ed1ab_0
+  - jmespath=0.10.0=pyh9f0ad1d_0
+  - jpeg=9d=h36c2ea0_0
+  - jsonschema=3.2.0=pyhd8ed1ab_3
+  - jupyter_core=4.7.1=py39hf3d152e_0
+  - kernel-headers_linux-64=2.6.32=h77966d4_13
+  - krb5=1.19.1=hcc1bbae_0
+  - ld_impl_linux-64=2.35.1=hea4e1c9_2
+  - libblas=3.9.0=9_openblas
+  - libcblas=3.9.0=9_openblas
+  - libcrc32c=1.1.1=h9c3ff4c_2
+  - libcurl=7.76.1=h2574ce0_2
+  - libedit=3.1.20191231=he28a2e2_2
+  - libev=4.33=h516909a_1
+  - libffi=3.3=h58526e2_2
+  - libgcc=7.2.0=h69d50b8_2
+  - libgcc-devel_linux-64=9.3.0=h7864c58_19
+  - libgcc-ng=9.3.0=h2828fa1_19
+  - libgd=2.3.2=h78a0170_0
+  - libgfortran-ng=9.3.0=hff62375_19
+  - libgfortran5=9.3.0=hff62375_19
+  - libglib=2.68.2=h3e27bee_0
+  - libgomp=9.3.0=h2828fa1_19
+  - libiconv=1.16=h516909a_0
+  - liblapack=3.9.0=9_openblas
+  - libnghttp2=1.43.0=h812cca2_0
+  - libopenblas=0.3.15=pthreads_h8fe5266_1
+  - libpng=1.6.37=h21135ba_2
+  - libprotobuf=3.17.0=h780b84a_0
+  - librsvg=2.50.5=hc3c00ef_0
+  - libsodium=1.0.18=h36c2ea0_1
+  - libssh2=1.9.0=ha56f1ee_6
+  - libstdcxx-devel_linux-64=9.3.0=hb016644_19
+  - libstdcxx-ng=9.3.0=h6de172a_19
+  - libtiff=4.3.0=hf544144_0
+  - libtool=2.4.6=h58526e2_1007
+  - libuuid=2.32.1=h7f98852_1000
+  - libwebp=1.2.0=h3452ae3_0
+  - libwebp-base=1.2.0=h7f98852_2
+  - libxcb=1.13=h7f98852_1003
+  - libxml2=2.9.12=h72842e0_0
+  - logmuse=0.2.6=pyh8c360ce_0
+  - lz4-c=1.9.3=h9c3ff4c_0
+  - make=4.3=hd18ef5c_1
+  - markupsafe=2.0.1=py39h3811e60_0
+  - more-itertools=8.7.0=pyhd8ed1ab_1
+  - msrest=0.6.21=pyh44b312d_0
+  - multidict=5.1.0=py39h3811e60_1
+  - nbformat=5.1.3=pyhd8ed1ab_0
+  - ncurses=6.2=h58526e2_4
+  - networkx=2.5=py_0
+  - numpy=1.20.3=py39hdbf815f_0
+  - oauth2client=4.1.3=py_0
+  - oauthlib=3.0.1=py_0
+  - openjpeg=2.4.0=hb52868f_1
+  - openssl=1.1.1k=h7f98852_0
+  - packaging=20.9=pyh44b312d_0
+  - pandas=1.2.4=py39hde0f152_0
+  - pandoc=2.13=h7f98852_0
+  - pango=1.48.5=hb8ff022_0
+  - paramiko=2.7.2=pyh9f0ad1d_0
+  - pcre=8.44=he1b5a44_0
+  - pcre2=10.36=h032f7d1_1
+  - peppy=0.31.1=pyhd8ed1ab_0
+  - perl=5.32.0=h36c2ea0_0
+  - pip=21.1.1=pyhd8ed1ab_0
+  - pixman=0.40.0=h36c2ea0_0
+  - pkg-config=0.29.2=h36c2ea0_1008
+  - pluggy=0.13.1=py39hf3d152e_4
+  - ply=3.11=py_1
+  - prettytable=2.1.0=pyhd8ed1ab_0
+  - protobuf=3.17.0=py39he80948d_0
+  - psutil=5.8.0=py39h3811e60_1
+  - pthread-stubs=0.4=h36c2ea0_1001
+  - pulp=2.4=py39hf3d152e_0
+  - py=1.10.0=pyhd3deb0d_0
+  - pyasn1=0.4.8=py_0
+  - pyasn1-modules=0.2.7=py_0
+  - pycparser=2.20=pyh9f0ad1d_2
+  - pygments=2.9.0=pyhd8ed1ab_0
+  - pygraphviz=1.7=py39h78163bd_0
+  - pyjwt=2.1.0=pyhd8ed1ab_0
+  - pynacl=1.4.0=py39h3811e60_2
+  - pyopenssl=20.0.1=pyhd8ed1ab_0
+  - pyparsing=2.4.7=pyh9f0ad1d_0
+  - pyrsistent=0.17.3=py39h3811e60_2
+  - pysftp=0.2.9=py_1
+  - pysocks=1.7.1=py39hf3d152e_3
+  - pytest=6.2.4=py39hf3d152e_0
+  - python=3.9.4=hffdb5ce_0_cpython
+  - python-dateutil=2.8.1=py_0
+  - python-irodsclient=0.9.0=pyhd8ed1ab_0
+  - python_abi=3.9=1_cp39
+  - pytz=2021.1=pyhd8ed1ab_0
+  - pyyaml=5.4.1=py39h3811e60_0
+  - r-askpass=1.1=r40hcdcec82_2
+  - r-assertthat=0.2.1=r40h6115d3f_2
+  - r-backports=1.2.1=r40hcfec24a_0
+  - r-base=4.0.5=h9e01966_1
+  - r-base64enc=0.1_3=r40hcdcec82_1004
+  - r-blob=1.2.1=r40h6115d3f_1
+  - r-brio=1.1.2=r40hcfec24a_0
+  - r-broom=0.7.6=r40hc72bb7e_0
+  - r-callr=3.7.0=r40hc72bb7e_0
+  - r-cellranger=1.1.0=r40h6115d3f_1003
+  - r-cli=2.5.0=r40hc72bb7e_0
+  - r-clipr=0.7.1=r40h142f84f_0
+  - r-colorspace=2.0_1=r40hcfec24a_0
+  - r-cpp11=0.2.7=r40hc72bb7e_0
+  - r-crayon=1.4.1=r40hc72bb7e_0
+  - r-curl=4.3.1=r40hcfec24a_0
+  - r-data.table=1.14.0=r40hcfec24a_0
+  - r-dbi=1.1.1=r40hc72bb7e_0
+  - r-dbplyr=2.1.1=r40hc72bb7e_0
+  - r-desc=1.3.0=r40hc72bb7e_0
+  - r-diffobj=0.3.4=r40hcfec24a_0
+  - r-digest=0.6.27=r40h03ef668_0
+  - r-dplyr=1.0.6=r40h03ef668_1
+  - r-dtplyr=1.1.0=r40hc72bb7e_0
+  - r-ellipsis=0.3.2=r40hcfec24a_0
+  - r-evaluate=0.14=r40h6115d3f_2
+  - r-fansi=0.4.2=r40hcfec24a_0
+  - r-farver=2.1.0=r40h03ef668_0
+  - r-forcats=0.5.1=r40hc72bb7e_0
+  - r-fs=1.5.0=r40h0357c0b_0
+  - r-fuzzyjoin=0.1.6=r40_0
+  - r-gargle=1.1.0=r40hc72bb7e_0
+  - r-gdtools=0.2.2=r40h36050f4_1
+  - r-generics=0.1.0=r40hc72bb7e_0
+  - r-geosphere=1.5_10=r40hcfec24a_2
+  - r-ggplot2=3.3.3=r40hc72bb7e_0
+  - r-glue=1.4.2=r40hcfec24a_0
+  - r-googledrive=1.0.1=r40h6115d3f_1
+  - r-googlesheets4=0.3.0=r40hc72bb7e_0
+  - r-gtable=0.3.0=r40h6115d3f_3
+  - r-haven=2.4.1=r40h2713e49_0
+  - r-highr=0.9=r40hc72bb7e_0
+  - r-hms=1.1.0=r40hc72bb7e_0
+  - r-htmltools=0.5.1.1=r40h03ef668_0
+  - r-httr=1.4.2=r40h6115d3f_0
+  - r-ids=1.0.1=r40h6115d3f_1
+  - r-isoband=0.2.4=r40h03ef668_0
+  - r-jsonlite=1.7.2=r40hcfec24a_0
+  - r-knitr=1.33=r40hc72bb7e_0
+  - r-labeling=0.4.2=r40h142f84f_0
+  - r-lattice=0.20_44=r40hcfec24a_0
+  - r-lifecycle=1.0.0=r40hc72bb7e_0
+  - r-lubridate=1.7.10=r40h03ef668_0
+  - r-magrittr=2.0.1=r40hcfec24a_1
+  - r-markdown=1.1=r40hcfec24a_1
+  - r-mass=7.3_54=r40hcfec24a_0
+  - r-matrix=1.3_3=r40he454529_0
+  - r-mgcv=1.8_35=r40he454529_0
+  - r-mime=0.10=r40hcfec24a_0
+  - r-modelr=0.1.8=r40h6115d3f_0
+  - r-munsell=0.5.0=r40h6115d3f_1003
+  - r-nlme=3.1_152=r40h859d828_0
+  - r-openssl=1.4.4=r40he36bf35_0
+  - r-pillar=1.6.1=r40hc72bb7e_0
+  - r-pkgconfig=2.0.3=r40h6115d3f_1
+  - r-pkgload=1.2.1=r40h03ef668_0
+  - r-plyr=1.8.6=r40h0357c0b_1
+  - r-praise=1.0.0=r40h6115d3f_1004
+  - r-prettyunits=1.1.1=r40h6115d3f_1
+  - r-processx=3.5.2=r40hcfec24a_0
+  - r-progress=1.2.2=r40h6115d3f_2
+  - r-ps=1.6.0=r40hcfec24a_0
+  - r-purrr=0.3.4=r40hcfec24a_1
+  - r-r6=2.5.0=r40hc72bb7e_0
+  - r-rappdirs=0.3.3=r40hcfec24a_0
+  - r-rcolorbrewer=1.1_2=r40h6115d3f_1003
+  - r-rcpp=1.0.6=r40h03ef668_0
+  - r-readr=1.4.0=r40h1b71b39_0
+  - r-readxl=1.3.1=r40hde08347_4
+  - r-rematch=1.0.1=r40h6115d3f_1003
+  - r-rematch2=2.1.2=r40h6115d3f_1
+  - r-reprex=2.0.0=r40hc72bb7e_0
+  - r-reshape2=1.4.4=r40h0357c0b_1
+  - r-rlang=0.4.11=r40hcfec24a_0
+  - r-rmarkdown=2.8=r40hc72bb7e_0
+  - r-rprojroot=2.0.2=r40hc72bb7e_0
+  - r-rstudioapi=0.13=r40hc72bb7e_0
+  - r-rvest=1.0.0=r40hc72bb7e_0
+  - r-scales=1.1.1=r40h6115d3f_0
+  - r-selectr=0.4_2=r40h6115d3f_1
+  - r-sp=1.4_5=r40hcfec24a_0
+  - r-stringdist=0.9.6.3=r40hcfec24a_0
+  - r-stringi=1.6.2=r40hcabe038_0
+  - r-stringr=1.4.0=r40h6115d3f_2
+  - r-svglite=2.0.0=r40h03ef668_0
+  - r-sys=3.4=r40hcdcec82_0
+  - r-systemfonts=1.0.2=r40hef9c87a_0
+  - r-testthat=3.0.2=r40h03ef668_0
+  - r-tibble=3.1.2=r40hcfec24a_0
+  - r-tidyr=1.1.3=r40h03ef668_0
+  - r-tidyselect=1.1.1=r40hc72bb7e_0
+  - r-tidyverse=1.3.1=r40hc72bb7e_0
+  - r-tinytex=0.31=r40hc72bb7e_0
+  - r-utf8=1.2.1=r40hcfec24a_0
+  - r-uuid=0.1_4=r40hcdcec82_1
+  - r-vctrs=0.3.8=r40hcfec24a_0
+  - r-viridislite=0.4.0=r40hc72bb7e_0
+  - r-waldo=0.2.5=r40hc72bb7e_0
+  - r-withr=2.4.2=r40hc72bb7e_0
+  - r-xfun=0.23=r40hcfec24a_0
+  - r-xml2=1.3.2=r40h0357c0b_1
+  - r-yaml=2.2.1=r40hcfec24a_1
+  - r-zeallot=0.1.0=r40h6115d3f_1002
+  - ratelimiter=1.2.0=py_1002
+  - readline=8.1=h46c0cb4_0
+  - requests=2.25.1=pyhd3deb0d_0
+  - requests-oauthlib=1.3.0=pyh9f0ad1d_0
+  - rsa=4.7.2=pyh44b312d_0
+  - s3transfer=0.4.2=pyhd8ed1ab_0
+  - sed=4.8=he412f7d_0
+  - setuptools=49.6.0=py39hf3d152e_3
+  - simplejson=3.17.2=py39h3811e60_2
+  - six=1.16.0=pyh6c4a22f_0
+  - slacker=0.14.0=py_0
+  - smart_open=5.0.0=pyhd8ed1ab_0
+  - smmap=3.0.5=pyh44b312d_0
+  - snakemake=6.4.0=hdfd78af_0
+  - snakemake-minimal=6.4.0=pyhdfd78af_0
+  - sqlite=3.35.5=h74cdb3f_0
+  - stone=3.2.1=pyhd8ed1ab_0
+  - stopit=1.1.2=py_0
+  - sysroot_linux-64=2.12=h77966d4_13
+  - tk=8.6.10=h21135ba_1
+  - tktable=2.10=hb7b940f_3
+  - toml=0.10.2=pyhd8ed1ab_0
+  - toposort=1.6=pyhd8ed1ab_0
+  - traitlets=5.0.5=py_0
+  - typing-extensions=3.7.4.3=0
+  - typing_extensions=3.7.4.3=py_0
+  - tzdata=2021a=he74cb21_0
+  - ubiquerg=0.6.1=pyh9f0ad1d_0
+  - uritemplate=3.0.1=py_0
+  - urllib3=1.26.4=pyhd8ed1ab_0
+  - veracitools=0.1.3=py_0
+  - wcwidth=0.2.5=pyh9f0ad1d_2
+  - wheel=0.36.2=pyhd3deb0d_0
+  - wrapt=1.12.1=py39h3811e60_3
+  - xmlrunner=1.7.7=py_0
+  - xorg-kbproto=1.0.7=h7f98852_1002
+  - xorg-libice=1.0.10=h7f98852_0
+  - xorg-libsm=1.2.3=hd9c2040_1000
+  - xorg-libx11=1.7.1=h7f98852_0
+  - xorg-libxau=1.0.9=h7f98852_0
+  - xorg-libxdmcp=1.1.3=h7f98852_0
+  - xorg-libxext=1.3.4=h7f98852_1
+  - xorg-libxrender=0.9.10=h7f98852_1003
+  - xorg-libxt=1.2.1=h7f98852_2
+  - xorg-renderproto=0.11.1=h7f98852_1002
+  - xorg-xextproto=7.3.0=h7f98852_1002
+  - xorg-xproto=7.0.31=h7f98852_1007
+  - xz=5.2.5=h516909a_1
+  - yaml=0.2.5=h516909a_0
+  - yarl=1.6.3=py39h3811e60_1
+  - zipp=3.4.1=pyhd8ed1ab_0
+  - zlib=1.2.11=h516909a_1010
+  - zstd=1.5.0=ha95c52a_0

From 01b8a7e3d9f1fe442b688cb5a1ede7b6338e6474 Mon Sep 17 00:00:00 2001
From: Pavel Dimens <pdimens@live.com>
Date: Mon, 14 Feb 2022 13:27:54 -0500
Subject: [PATCH 37/46] update readme

---
 .misc/install.sh | 25 +++++++++++++++++++++++++
 .misc/meta.yml   |  6 +++++-
 README.md        | 29 ++++++++++++++++++++++-------
 3 files changed, 52 insertions(+), 8 deletions(-)
 create mode 100644 .misc/install.sh

diff --git a/.misc/install.sh b/.misc/install.sh
new file mode 100644
index 0000000..c186161
--- /dev/null
+++ b/.misc/install.sh
@@ -0,0 +1,25 @@
+#! /usr/bin/env bash
+
+if [ -z "$CONDA_PREFIX" ]; then
+    echo "No active conda environment detected, will not install dependencies unless in an active environment"
+    exit 1
+fi
+
+# install LepWrap into conda PATH
+mkdir -p $CONDA_PREFIX/bin
+# LepWrap executable
+cp LepWrap $CONDA_PREFIX/bin/
+chmod +x $CONDA_PREFIX/bin/LepWrap
+# associated scripts
+chmod +x scripts/*
+cp scripts/* $CONDA_PREFIX/bin/
+# LepMap3 modules and scripts
+cp software/LepMap3/*.class $CONDA_PREFIX/bin
+cp software/LepMap3/scripts/* $CONDA_PREFIX/bin
+# LepAnchor modules and scripts
+cp software/LepAnchor/*.class $CONDA_PREFIX/bin
+cp software/LepAnchor/scripts/* $CONDA_PREFIX/bin
+cp software/LepAnchor/deps/ucsc_binaries/* $CONDA_PREFIX/bin
+cp software/LepAnchor/deps/*.pl software/LepAnchor/deps/Red software/LepAnchor/deps/all_lastz.ctl software/LepAnchor/deps/scoreMatrix.q software/LepAnchor/deps/step* $CONDA_PREFIX/bin
+# Snakemake rules
+cp rules/LepAnchor/*.smk rules/LepMap3/*.smk $CONDA_PREFIX/bin
\ No newline at end of file
diff --git a/.misc/meta.yml b/.misc/meta.yml
index 26e8868..15c625f 100644
--- a/.misc/meta.yml
+++ b/.misc/meta.yml
@@ -27,7 +27,11 @@ requirements:
     - pandoc
     - python >=3.9
     - r-base >=4
-    - r-tidyverse
+    - r-dplyr
+    - r-tidyr
+    - r-stringr
+    - r-ggplot2
+    - r-readr
     - sed
     - snakemake >=6.4
 
diff --git a/README.md b/README.md
index edc77ae..188acaf 100644
--- a/README.md
+++ b/README.md
@@ -4,6 +4,7 @@ _It's Lep-Map3 and Lep-Anchor, but with snakes 🐍🐍_
 
 [![alt text](https://img.shields.io/badge/docs-wiki-75ae6c?style=for-the-badge&logo=Read%20The%20Docs)](https://github.com/pdimens/LepWrap/wiki) 
 
+[![Cite](https://img.shields.io/badge/Cite-10.5281/zenodo.6055566-e1e1e1?style=for-the-badge)](https://zenodo.org/badge/latestdoi/260516189) 
 # LepWrap
 
 LepWrap is a reusable pipeline to use the linkage map software [Lep-Map3](https://sourceforge.net/projects/lep-map3/) and the genome assembly map-based anchoring and orienting software [Lep-Anchor](https://sourceforge.net/p/lep-anchor/wiki/Home/). It is the Snakemake-based successor to [LepMapp3r](https://github.com/pdimens/LepMapp3r). Check out [the wiki](https://github.com/pdimens/LepWrap/wiki) for detailed installation, usage, and workflow information.
@@ -11,15 +12,23 @@ LepWrap is a reusable pipeline to use the linkage map software [Lep-Map3](https:
 
 
 ### How to install
-You will need a `conda` installation ([Anaconda](https://docs.anaconda.com/anaconda/install/) or [Miniconda](https://docs.conda.io/en/latest/miniconda.html), I recommend Miniconda), along with downloading the latest release or cloning this repository locally. Using the latest release is a more stable solution.
+You will need a `conda` installation ([Anaconda](https://docs.anaconda.com/anaconda/install/) or [Miniconda](https://docs.conda.io/en/latest/miniconda.html), I recommend Miniconda). Alternatively, you can download latest release or clone this repository locally.
 
-#### 1. Cloning LepWrap
+#### 1. The Easy Way™️
+Create an environment called `lepwrap` and install `LepWrap` into it in a single command.
+```bash
+conda create -n lepwrap -c bioconda lepwrap
+```
+Activate the environment with `conda activate lepwrap`
+
+#### 2. The Other Way
+##### 2.1 Cloning LepWrap
 Download a zip of this repository using the "Code" button on the top-right and unzip it on your machine or:
 ```bash
 git clone https://github.com/pdimens/LepWrap.git
 ```
 
-#### 2. Installing other dependencies
+##### 2.2 Installing everything
 Assuming you have `anaconda` or `miniconda` installed:
 ```bash
 cd LepWrap
@@ -29,25 +38,31 @@ This will create an environment called `lepwrap` that can be activated with:
 ```bash
 conda activate lepwrap
 ```
+Then, install all the software dependencies into the environment's path with 
+```bash
+.misc/install.sh
+```
 
 ### How to run
 You will need to modify `config.yml` to suit your needs, then you can simply run the pipeline with the wrapper:
 ```bash
-./LepWrap <number_of_cores> <config.yml>
+LepWrap <number_of_cores> <config.yml>
 ```
 where `<number_of_cores>` is an integer of the maximum number of cores/threads you want the pipeline to use and `<config.yml>` (optional!) is the name of the config file, if it's different than `config.yml`. 
 
 **Examples**
 ```bash
-./LepWrap 15                    # assumes config.yml
-./LepWrap 32 nojoinsingles.yml  # specific config file
+LepWrap 15                    # assumes config.yml
+LepWrap 32 nojoinsingles.yml  # specific config file
 ```
 ### Something to keep in mind
 LepWrap does things a certain way, employing the most common/reasonable way of using Lep-Map3 (and LepAnchor more or less). Current versions are **a lot** more flexible that the predecessors, but might still lack something you need. Your study is unique, and I encourage you to clone/fork this repository and adapt LepWrap to it! All of the code in LepWrap is written in human-readable bash or aggressively annotated R, so give it a shot and adapt it to your workflow. PR's always welcome!
 
 
 ## Citation
-If using LepWrap in a publication, cite **Pasi Rastas** for their work on Lep-Map3/Lep-Anchor and please include a link to this repository. If you like using it, please Star the repository and/or give me (Pavel) a shout out on Twitter [@pvdimens](https://twitter.com/PVDimens) [![alt text](http://i.imgur.com/wWzX9uB.png)](https://twitter.com/PVDimens)  =)
+If using LepWrap in a publication, cite **Pasi Rastas** for their work on Lep-Map3/Lep-Anchor and cite this repository using the Zenodo citation. You are also encouraged to cite LepWrap if you just use the edge-trimming part of it. If you like LepWrap, please Star the repository and/or give me (Pavel) a shout out on Twitter [@pvdimens](https://twitter.com/PVDimens) [![alt text](http://i.imgur.com/wWzX9uB.png)](https://twitter.com/PVDimens)  =)
+
+> Pavel V. Dimens. (2022). pdimens/LepWrap: link with zenodo (3.6.2). Zenodo. https://doi.org/10.5281/zenodo.6055566
 
 > Pasi Rastas, Lep-MAP3: robust linkage mapping even for low-coverage whole genome sequencing data, Bioinformatics, Volume 33, Issue 23, 01 December 2017, Pages 3726–3732,https://doi.org/10.1093/bioinformatics/btx494
 

From 51310090a3c9af82498a771e00616392d1057bb5 Mon Sep 17 00:00:00 2001
From: Pavel Dimens <pdimens@live.com>
Date: Mon, 14 Feb 2022 13:29:04 -0500
Subject: [PATCH 38/46] move citation inline

---
 README.md | 1 -
 1 file changed, 1 deletion(-)

diff --git a/README.md b/README.md
index 188acaf..4cb519f 100644
--- a/README.md
+++ b/README.md
@@ -3,7 +3,6 @@
 _It's Lep-Map3 and Lep-Anchor, but with snakes 🐍🐍_
 
 [![alt text](https://img.shields.io/badge/docs-wiki-75ae6c?style=for-the-badge&logo=Read%20The%20Docs)](https://github.com/pdimens/LepWrap/wiki) 
-
 [![Cite](https://img.shields.io/badge/Cite-10.5281/zenodo.6055566-e1e1e1?style=for-the-badge)](https://zenodo.org/badge/latestdoi/260516189) 
 # LepWrap
 

From 18b015b031a444dce5104f52e3b214cb1308c3b0 Mon Sep 17 00:00:00 2001
From: Pavel Dimens <pdimens@live.com>
Date: Mon, 14 Feb 2022 14:45:13 -0500
Subject: [PATCH 39/46] split out java software b/c of overwriting

---
 .misc/build.sh                      | 8 +++++---
 .misc/install.sh                    | 7 +++++--
 rules/LepAnchor/generate_inputs.smk | 6 +++---
 rules/LepAnchor/place_orient1.smk   | 2 +-
 rules/LepAnchor/place_orient2.smk   | 2 +-
 rules/LepAnchor/place_orient4.smk   | 2 +-
 rules/LepMap3/distances.smk         | 4 ++--
 rules/LepMap3/generate_map.smk      | 4 ++--
 rules/LepMap3/order.smk             | 2 +-
 rules/LepMap3/prepare_data.smk      | 4 ++--
 rules/LepMap3/reorder.smk           | 2 +-
 scripts/iterate_js2all.sh           | 2 +-
 scripts/refinemap.sh                | 2 +-
 13 files changed, 26 insertions(+), 21 deletions(-)

diff --git a/.misc/build.sh b/.misc/build.sh
index 2ba015f..56ae559 100644
--- a/.misc/build.sh
+++ b/.misc/build.sh
@@ -2,6 +2,8 @@
 
 # for installing conda package
 mkdir -p $PREFIX/bin
+mkdir -p $PREFIX/bin/lepmap3
+mkdir -p $PREFIX/bin/lepanchor
 # LepWrap executable
 cp LepWrap $PREFIX/bin/
 chmod +x $PREFIX/bin/LepWrap
@@ -9,11 +11,11 @@ chmod +x $PREFIX/bin/LepWrap
 chmod +x scripts/*
 cp scripts/* $PREFIX/bin/
 # LepMap3 modules and scripts
-cp software/LepMap3/*.class $PREFIX/bin
+cp software/LepMap3/*.class $PREFIX/bin/lepmap3
 cp software/LepMap3/scripts/* $PREFIX/bin
 # LepAnchor modules and scripts
-cp software/LepAnchor/*.class software/LepAnchor/lepanchor_wrapper.sh $PREFIX/bin
-cp $CONDA_PREFIX/bin/* $PREFIX/bin
+cp software/LepAnchor/*.class $PREFIX/bin/lepanchor
+cp software/LepAnchor/scripts/* $PREFIX/bin
 cp software/LepAnchor/deps/ucsc_binaries/* $PREFIX/bin
 cp software/LepAnchor/deps/*.pl software/LepAnchor/deps/Red software/LepAnchor/deps/all_lastz.ctl software/LepAnchor/deps/scoreMatrix.q software/LepAnchor/deps/step* $PREFIX/bin
 # Snakemake rules
diff --git a/.misc/install.sh b/.misc/install.sh
index c186161..f791fdc 100644
--- a/.misc/install.sh
+++ b/.misc/install.sh
@@ -7,6 +7,8 @@ fi
 
 # install LepWrap into conda PATH
 mkdir -p $CONDA_PREFIX/bin
+mkdir -p $CONDA_PREFIX/bin/lepmap3
+mkdir -p $CONDA_PREFIX/bin/lepanchor
 # LepWrap executable
 cp LepWrap $CONDA_PREFIX/bin/
 chmod +x $CONDA_PREFIX/bin/LepWrap
@@ -14,11 +16,12 @@ chmod +x $CONDA_PREFIX/bin/LepWrap
 chmod +x scripts/*
 cp scripts/* $CONDA_PREFIX/bin/
 # LepMap3 modules and scripts
-cp software/LepMap3/*.class $CONDA_PREFIX/bin
+cp software/LepMap3/*.class $CONDA_PREFIX/bin/lepmap3
 cp software/LepMap3/scripts/* $CONDA_PREFIX/bin
 # LepAnchor modules and scripts
-cp software/LepAnchor/*.class $CONDA_PREFIX/bin
+cp software/LepAnchor/*.class $CONDA_PREFIX/bin/lepanchor
 cp software/LepAnchor/scripts/* $CONDA_PREFIX/bin
+ln -s $CONDA_PREFIX/bin/lepmap3/*.class $CONDA_PREFIX/bin/lepanchor/*.class $CONDA_PREFIX/bin/ 
 cp software/LepAnchor/deps/ucsc_binaries/* $CONDA_PREFIX/bin
 cp software/LepAnchor/deps/*.pl software/LepAnchor/deps/Red software/LepAnchor/deps/all_lastz.ctl software/LepAnchor/deps/scoreMatrix.q software/LepAnchor/deps/step* $CONDA_PREFIX/bin
 # Snakemake rules
diff --git a/rules/LepAnchor/generate_inputs.smk b/rules/LepAnchor/generate_inputs.smk
index f1e3aa8..96b3dd2 100644
--- a/rules/LepAnchor/generate_inputs.smk
+++ b/rules/LepAnchor/generate_inputs.smk
@@ -52,7 +52,7 @@ rule liftover:
   message: "Running liftoverHaplotypes for the input maps"
   shell: 
     """
-    gunzip -fc {input.chain} | java -cp $CONDA_PREFIX/bin/ LiftoverHaplotypes map={input.intervals} haplotypes={input.haplos} chain=- > {output.lift}
+    gunzip -fc {input.chain} | java -cp $CONDA_PREFIX/bin/lepanchor LiftoverHaplotypes map={input.intervals} haplotypes={input.haplos} chain=- > {output.lift}
     cat {output.lift} | sort -V -k 1,1 -k 2,2n > {output.sortedlift}
     """
 
@@ -64,7 +64,7 @@ rule cleanmap:
   message: "Running CleanMap"
   params:
     extras = cleanmap_extra
-  shell: "java -cp $CONDA_PREFIX/bin/ CleanMap map={input} {params.extras} > {output} 2> {log}"
+  shell: "java -cp $CONDA_PREFIX/bin/lepanchor CleanMap map={input} {params.extras} > {output} 2> {log}"
 
 
 rule map2bed:
@@ -76,7 +76,7 @@ rule map2bed:
   message: "Running Map2Bed"
   params:
     extras = map2bed_extra
-  shell: "java -cp $CONDA_PREFIX/bin/ Map2Bed map={input.cleanmap} contigLength={input.lengths} {params.extras} > {output} 2> {log}"
+  shell: "java -cp $CONDA_PREFIX/bin/lepanchor Map2Bed map={input.cleanmap} contigLength={input.lengths} {params.extras} > {output} 2> {log}"
 
 
 rule ungrouped:
diff --git a/rules/LepAnchor/place_orient1.smk b/rules/LepAnchor/place_orient1.smk
index 4b97cca..5f024aa 100644
--- a/rules/LepAnchor/place_orient1.smk
+++ b/rules/LepAnchor/place_orient1.smk
@@ -16,7 +16,7 @@ rule place_orient:
   message: "Running the 1st round of PlaceAndOrientContigs for linkage group {params.chrom}"
   shell:
     """
-    gunzip -fc {input.chain} | java -cp $CONDA_PREFIX/bin/ PlaceAndOrientContigs chromosome={params.chrom} numThreads={threads} bed={input.bedfile} map={input.lift} chain=- paf={input.paf} proximity={input.prox} {params.datatype} {params.extras} > {output.chrom} 2> {output.chromerr}
+    gunzip -fc {input.chain} | java -cp $CONDA_PREFIX/bin/lepanchor PlaceAndOrientContigs chromosome={params.chrom} numThreads={threads} bed={input.bedfile} map={input.lift} chain=- paf={input.paf} proximity={input.prox} {params.datatype} {params.extras} > {output.chrom} 2> {output.chromerr}
     """
 
 rule propogate1:
diff --git a/rules/LepAnchor/place_orient2.smk b/rules/LepAnchor/place_orient2.smk
index b6ad01d..243cef8 100644
--- a/rules/LepAnchor/place_orient2.smk
+++ b/rules/LepAnchor/place_orient2.smk
@@ -17,7 +17,7 @@ rule place_orient2:
   message: "Running 2nd round of PlaceAndOrientContigs for linkage group {params.chrom}"
   shell:
     """
-    gunzip -fc {input.chain} | java -cp $CONDA_PREFIX/bin/ PlaceAndOrientContigs chromosome={params.chrom} numThreads={threads} $(awk -f $CONDA_PREFIX/bin/pickorientation.awk {input.chrom}) bed={input.bedfile} map={input.lift} chain=- paf={input.paf} proximity={input.prox} {params.datatype} {params.extras} > {output.chrom} 2> {output.chromerr}
+    gunzip -fc {input.chain} | java -cp $CONDA_PREFIX/bin/lepanchor PlaceAndOrientContigs chromosome={params.chrom} numThreads={threads} $(awk -f $CONDA_PREFIX/bin/pickorientation.awk {input.chrom}) bed={input.bedfile} map={input.lift} chain=- paf={input.paf} proximity={input.prox} {params.datatype} {params.extras} > {output.chrom} 2> {output.chromerr}
     """
 
 rule propogate2:
diff --git a/rules/LepAnchor/place_orient4.smk b/rules/LepAnchor/place_orient4.smk
index 1640b17..e86a093 100644
--- a/rules/LepAnchor/place_orient4.smk
+++ b/rules/LepAnchor/place_orient4.smk
@@ -18,7 +18,7 @@ rule place_orient4:
     threads: 2
     shell:
         """
-        gunzip -fc {input.chain} | java -cp $CONDA_PREFIX/bin/ PlaceAndOrientContigs chromosome={params.chrom} numThreads={threads} $(awk -f $CONDA_PREFIX/bin/pickorientation.awk {input.chrom}) bed={input.bedfile} map={input.lift} chain=- paf={input.paf} proximity={input.prox} {params.datatype} {params.extras} evaluateAnchoring={input.chromlast} improveAnchoring=1 > {output.chrom} 2> {output.err}
+        gunzip -fc {input.chain} | java -cp $CONDA_PREFIX/bin/lepanchor PlaceAndOrientContigs chromosome={params.chrom} numThreads={threads} $(awk -f $CONDA_PREFIX/bin/pickorientation.awk {input.chrom}) bed={input.bedfile} map={input.lift} chain=- paf={input.paf} proximity={input.prox} {params.datatype} {params.extras} evaluateAnchoring={input.chromlast} improveAnchoring=1 > {output.chrom} 2> {output.err}
         """
 
 rule prune_contigblocks:
diff --git a/rules/LepMap3/distances.smk b/rules/LepMap3/distances.smk
index 65ce7f7..0807e7a 100644
--- a/rules/LepMap3/distances.smk
+++ b/rules/LepMap3/distances.smk
@@ -19,10 +19,10 @@ rule calculate_distances:
         """
         cp {input.lg} {output.distance}
         
-        zcat {input.data_call} | java -cp $CONDA_PREFIX/bin/ OrderMarkers2 evaluateOrder={input.lg} data=- {params.dist_method} numThreads={threads} improveOrder=0 sexAveraged=1 &> {output.sex_averagedtmp}
+        zcat {input.data_call} | java -cp $CONDA_PREFIX/bin/lepmap3 OrderMarkers2 evaluateOrder={input.lg} data=- {params.dist_method} numThreads={threads} improveOrder=0 sexAveraged=1 &> {output.sex_averagedtmp}
         sed -i -e 's/LG \= 0/LG \= {params.lg}/g' {output.sex_averagedtmp}
         sed -n '/\*\*\* LG \=/,$p' {output.sex_averagedtmp} > {output.sex_averaged} 
         awk '/#java/{{flag=1}} flag; /*** LG =/{{flag=0}}' {output.sex_averagedtmp} > {log.sex_averaged}
 
-        zcat {input.data_call} | java -cp $CONDA_PREFIX/bin/ OrderMarkers2 evaluateOrder={input.lg} data=- {params.dist_method} numThreads={threads} calculateIntervals={output.intervals} > {log.intervals} 2>&1
+        zcat {input.data_call} | java -cp $CONDA_PREFIX/bin/lepmap3 OrderMarkers2 evaluateOrder={input.lg} data=- {params.dist_method} numThreads={threads} calculateIntervals={output.intervals} > {log.intervals} 2>&1
         """
\ No newline at end of file
diff --git a/rules/LepMap3/generate_map.smk b/rules/LepMap3/generate_map.smk
index 092e4bf..3356fc8 100644
--- a/rules/LepMap3/generate_map.smk
+++ b/rules/LepMap3/generate_map.smk
@@ -9,7 +9,7 @@ rule separate_chromosomes:
         extra = sepchrom_extra,
     shell:
         """
-        zcat {input} | java -cp $CONDA_PREFIX/bin/ SeparateChromosomes2 lodLimit={params.lod} data=- {params.extra} {informative} numThreads={threads} > {output} 2> {log}
+        zcat {input} | java -cp $CONDA_PREFIX/bin/lepmap3 SeparateChromosomes2 lodLimit={params.lod} data=- {params.extra} {informative} numThreads={threads} > {output} 2> {log}
         """
 
 
@@ -51,7 +51,7 @@ rule join_singles:
         JS2A=$(echo {params.run_js2all} | tr '[:upper:]' '[:lower:]')
         THEMAP=$(tail -1 {input.map_choice})
         if [ $JS2A == "true" ]; then
-            zcat {input.datacall} | java -cp $CONDA_PREFIX/bin/ JoinSingles2All map=$THEMAP data=- {params.extra} {params.lod_limit} {params.lod_diff} numThreads={threads} > {output}
+            zcat {input.datacall} | java -cp $CONDA_PREFIX/bin/lepmap3 JoinSingles2All map=$THEMAP data=- {params.extra} {params.lod_limit} {params.lod_diff} numThreads={threads} > {output}
         else
             echo -e "\nSkipping JoinSingles2All and creating a symlink to $THEMAP instead"
             ln -sr $THEMAP {output}
diff --git a/rules/LepMap3/order.smk b/rules/LepMap3/order.smk
index d0a5c52..4643962 100644
--- a/rules/LepMap3/order.smk
+++ b/rules/LepMap3/order.smk
@@ -15,7 +15,7 @@ rule order_markers:
     threads: 2
     shell:
         """
-        zcat {input.datacall} | java -cp $CONDA_PREFIX/bin/ OrderMarkers2 chromosome={params.chrom} map={input.filt_map} {params.extra} data=- numThreads={threads} &> {output.runlog}
+        zcat {input.datacall} | java -cp $CONDA_PREFIX/bin/lepmap3 OrderMarkers2 chromosome={params.chrom} map={input.filt_map} {params.extra} data=- numThreads={threads} &> {output.runlog}
         sed -n '/\*\*\* LG \=/,$p' {output.runlog} > {output.lg}
         grep "recombin" {output.runlog} > {log.recomb}
         awk '/#java/{{flag=1}} flag; /logL/{{flag=0}}' {output.runlog} > {log.run}
diff --git a/rules/LepMap3/prepare_data.smk b/rules/LepMap3/prepare_data.smk
index bbcac5e..c066a77 100644
--- a/rules/LepMap3/prepare_data.smk
+++ b/rules/LepMap3/prepare_data.smk
@@ -6,7 +6,7 @@ rule parent_call:
     message: "Creating Lep-Map3 data file from {input.vcf} and {input.pedigree}"
     params:
         extra = parentcall_extra
-    shell: "java -cp $CONDA_PREFIX/bin/ ParentCall2 data={input.pedigree} vcfFile={input.vcf} {params} | gzip > {output}"
+    shell: "java -cp $CONDA_PREFIX/bin/lepmap3lepmap3lepmap3 ParentCall2 data={input.pedigree} vcfFile={input.vcf} {params} | gzip > {output}"
 
 rule filtering:
     input: "1_ParentCall/data.lepmap3.gz"
@@ -21,6 +21,6 @@ rule filtering:
             echo "Skipping Filtering2 and creating symlink {output} instead"
             ln -sr {input} {output}
         else
-            zcat {input} | java -cp $CONDA_PREFIX/bin/ Filtering2 data=- dataTolerance={params.data_tolerance} {params.extra} | gzip > {output}
+            zcat {input} | java -cp $CONDA_PREFIX/bin/lepmap3 Filtering2 data=- dataTolerance={params.data_tolerance} {params.extra} | gzip > {output}
         fi
         """
diff --git a/rules/LepMap3/reorder.smk b/rules/LepMap3/reorder.smk
index f5654b2..154ade2 100644
--- a/rules/LepMap3/reorder.smk
+++ b/rules/LepMap3/reorder.smk
@@ -16,7 +16,7 @@ rule reorder_markers:
     threads: 2
     shell:
         """
-        zcat {input.datacall} | java -cp $CONDA_PREFIX/bin/ OrderMarkers2 evaluateOrder={input.lg_order} {params.extra} map={input.filt_map} data=- numThreads={threads} &> {output.runlog}
+        zcat {input.datacall} | java -cp $CONDA_PREFIX/bin/lepmap3 OrderMarkers2 evaluateOrder={input.lg_order} {params.extra} map={input.filt_map} data=- numThreads={threads} &> {output.runlog}
         sed -n '/\*\*\* LG \=/,$p' {output.runlog} > {output.lg}
         grep "recombin" {output.runlog} > {log.recomb}
         awk '/#java/{{flag=1}} flag; /logL/{{flag=0}}' {output.runlog} > {log.run}
diff --git a/scripts/iterate_js2all.sh b/scripts/iterate_js2all.sh
index dec5dac..fee7cf3 100755
--- a/scripts/iterate_js2all.sh
+++ b/scripts/iterate_js2all.sh
@@ -32,7 +32,7 @@ else
 fi
 
 for i in $(seq $LODMIN $LODMAX); do
-    zcat 2_Filtering/data.filtered.lepmap3.gz | java -cp $CONDA_PREFIX/bin/ JoinSingles2All map=$TARGETMAP data=- lodLimit=$i lodDifference=4 iterate=1 distortionLod=1 numThreads=10 informativeMask=$INFMASK > JoinSingles2All_iter/logs/map.$i.$4.js2all
+    zcat 2_Filtering/data.filtered.lepmap3.gz | java -cp $CONDA_PREFIX/bin/lepmap3lepmap3 JoinSingles2All map=$TARGETMAP data=- lodLimit=$i lodDifference=4 iterate=1 distortionLod=1 numThreads=10 informativeMask=$INFMASK > JoinSingles2All_iter/logs/map.$i.$4.js2all
     cut -f1 JoinSingles2All_iter/logs/map.$i.$4.js2all > JoinSingles2All_iter/LOD.$i.$4.js2all
 done
 
diff --git a/scripts/refinemap.sh b/scripts/refinemap.sh
index fd60344..961558f 100755
--- a/scripts/refinemap.sh
+++ b/scripts/refinemap.sh
@@ -31,7 +31,7 @@ LODMAX=$4
 SIZELIM=$5
 
 for i in $(seq $LODMIN $LODMAX); do
-    zcat 2_Filtering/data.filtered.lepmap3.gz | java -cp $CONDA_PREFIX/bin/ SeparateChromosomes2 data=- map=$TARGETMAP lg=$TARGETLG sizeLimit=$SIZELIM lodLimit=$i distortionLod=1 numThreads=4 > $1.refine/map.$i
+    zcat 2_Filtering/data.filtered.lepmap3.gz | java -cp $CONDA_PREFIX/bin/lepmap3 SeparateChromosomes2 data=- map=$TARGETMAP lg=$TARGETLG sizeLimit=$SIZELIM lodLimit=$i distortionLod=1 numThreads=4 > $1.refine/map.$i
 done
 
 # generate a summary of the results

From 4005f99238741a484c47d8ed7d09be31ea488cbc Mon Sep 17 00:00:00 2001
From: Pavel Dimens <pdimens@live.com>
Date: Mon, 14 Feb 2022 14:48:10 -0500
Subject: [PATCH 40/46] fix grep target

---
 LepWrap | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/LepWrap b/LepWrap
index 2921105..f770c7a 100755
--- a/LepWrap
+++ b/LepWrap
@@ -102,8 +102,8 @@ lepanchor(){
   snakemake --cores $1 --snakefile $CONDA_PREFIX/bin/LepAnchor.smk --configfile $CONF --directory .
 }
 
-LM=$(grep "run_lepmap" config.yml | cut -d":" -f2 | xargs | tr '[:upper:]' '[:lower:]')
-LA=$(grep "run_lepanchor" config.yml | cut -d":" -f2 | xargs | tr '[:upper:]' '[:lower:]')
+LM=$(grep "run_lepmap" $CONF | cut -d":" -f2 | xargs | tr '[:upper:]' '[:lower:]')
+LA=$(grep "run_lepanchor" $CONF | cut -d":" -f2 | xargs | tr '[:upper:]' '[:lower:]')
 
 if [ $LM == "true" ]; then
   lepmap $1 $CONF

From bbf3adef6ccce7da3a9843441abad62f8e784eb3 Mon Sep 17 00:00:00 2001
From: Pavel Dimens <pdimens@live.com>
Date: Mon, 14 Feb 2022 15:02:48 -0500
Subject: [PATCH 41/46] update wrapper logic

---
 LepWrap | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/LepWrap b/LepWrap
index f770c7a..3c4f521 100755
--- a/LepWrap
+++ b/LepWrap
@@ -3,7 +3,11 @@
 # Help text
 if [[ -z "$1" ]]; then
   echo "Perform the modules of Lep-Map3 and/or Lep-Anchor" 
-  echo "The config file (default: config.yml) must be configured"
+  echo -n "A config file (default: config.yml) must be configured"
+  if [ ! -f config.yml ]; then
+    echo " (one was created for you)"
+    generate_config.sh > config.yml
+  fi
   echo -e "The second positional argument is optional if your config file is named config.yml\n"
   printf "\033[01;32m"
   printf "[usage]"

From 7a99d5deae75b1ae15bafaed1cf0fa0e574b9e02 Mon Sep 17 00:00:00 2001
From: Pavel Dimens <pdimens@live.com>
Date: Wed, 16 Feb 2022 16:33:07 -0500
Subject: [PATCH 42/46] fixes

---
 rules/LepAnchor/generate_inputs.smk |  2 +-
 rules/LepAnchor/place_orient3.smk   | 49 +++++++++++++++++++++++++++++
 scripts/LGcutoff.sh                 |  2 +-
 scripts/extract_markers.sh          |  2 +-
 scripts/iterate_js2all.sh           |  4 +--
 scripts/lepmap2anchor               |  4 +--
 scripts/refinemap.sh                |  4 +--
 scripts/usage                       |  2 +-
 8 files changed, 59 insertions(+), 10 deletions(-)
 create mode 100644 rules/LepAnchor/place_orient3.smk

diff --git a/rules/LepAnchor/generate_inputs.smk b/rules/LepAnchor/generate_inputs.smk
index 96b3dd2..1151398 100644
--- a/rules/LepAnchor/generate_inputs.smk
+++ b/rules/LepAnchor/generate_inputs.smk
@@ -2,7 +2,7 @@ rule extract_markers:
     input: "2_Filtering/data.filtered.lepmap3.gz"
     output: report("snps.txt", category = "Data")
     message: "Extracting marker information from Lep-Map3 data file {input}"
-    shell: "scripts/extract_markers.sh {input}"
+    shell: "extract_markers.sh {input}"
 
 
 rule generate_input_data:
diff --git a/rules/LepAnchor/place_orient3.smk b/rules/LepAnchor/place_orient3.smk
new file mode 100644
index 0000000..e72008d
--- /dev/null
+++ b/rules/LepAnchor/place_orient3.smk
@@ -0,0 +1,49 @@
+
+rule place_orient3:
+  input:
+    chain = "9_Chain/chainfile.gz",
+    bedfile = "10_PlaceAndOrientContigs/map.propogated2.bed",
+    paf = paf,
+    prox = proximity,
+    lift = "10_PlaceAndOrientContigs/liftover.la",
+    chrom = "10_PlaceAndOrientContigs/1_orient/chr.{lg_range}.la",
+    propogated = "10_PlaceAndOrientContigs/propogate/propogated.{lg_range}.la"
+  output:
+    chrom = "10_PlaceAndOrientContigs/3_orient/chr.{lg_range}.la",
+    errors = "10_PlaceAndOrientContigs/3_orient/errors/chr.{lg_range}.err"
+  params:
+    chrom = "{lg_range}",
+    extras = place_orient_extra,
+    datatype = data_type
+  message: "Running 3rd round of PlaceAndOrientContigs for linkage group {params.chrom}"
+  threads: 2
+  shell:
+    """
+    gunzip -fc {input.chain} | java -cp software/LepAnchor PlaceAndOrientContigs chromosome={params.chrom} numThreads={threads} $(awk -f software/LepAnchor/scripts/pickorientation.awk {input.chrom}) bed={input.bedfile} map={input.lift} chain=- paf={input.paf} proximity={input.prox} evaluateAnchoring={input.propogated} improveAnchoring=1 {params.datatype} {params.extras} > {output.chrom} 2> {output.errors}
+    """
+    
+rule prune_contigblocks:
+  input: "10_PlaceAndOrientContigs/3_orient/chr.{lg_range}.la"
+  output: 
+    chrom = "10_PlaceAndOrientContigs/pruned/chr.{lg_range}.pruned.la",
+    err = "10_PlaceAndOrientContigs/pruned/err/chr.{lg_range}.pruned.err"
+  message: "Pruning contig blocks without map support and removing overlaps"
+  params:
+    chrom = lg
+  shell: "awk -f software/LepAnchor/scripts/prune.awk {input} > {output.chrom} 2> {output.err}"
+
+rule prune_post:
+  input:
+    bedfile = "10_PlaceAndOrientContigs/map.propogated2.bed",
+    prunedchrom = expand("10_PlaceAndOrientContigs/pruned/chr.{lgs}.pruned.la", lgs = lg_range),
+    prunederr = expand("10_PlaceAndOrientContigs/pruned/err/chr.{lgs}.pruned.err", lgs = lg_range)
+  output: 
+    overlaps = "10_PlaceAndOrientContigs/overlaps.removed.la",
+    pruned = "10_PlaceAndOrientContigs/pruned.la"
+  message: "Removing overlaps"
+  threads: 1
+  shell:
+    """
+    cat {input.prunederr} > {output.pruned}
+    awk -f software/LepAnchor/scripts/removeOverlaps.awk {input.bedfile} {input.prunedchrom} > {output.overlaps}
+    """
\ No newline at end of file
diff --git a/scripts/LGcutoff.sh b/scripts/LGcutoff.sh
index 5224c44..5f189c8 100755
--- a/scripts/LGcutoff.sh
+++ b/scripts/LGcutoff.sh
@@ -8,7 +8,7 @@ Essentially, set an LG maximum, and markers above it will be assigned to group 0
 
 [usage]:	LGcutoff.sh <map.file> <LG max>
 # unassign all markers in LG's 25+
-[example]: 	scripts/LGcutoff.sh 3_SeparateChromosomes/map.13 24
+[example]: 	LGcutoff.sh 3_SeparateChromosomes/map.13 24
 
 EOF
   exit 1
diff --git a/scripts/extract_markers.sh b/scripts/extract_markers.sh
index acafdaa..4848635 100755
--- a/scripts/extract_markers.sh
+++ b/scripts/extract_markers.sh
@@ -6,7 +6,7 @@ cat <<EOF
 Extracts marker information (contig and position) from a Lep-Map3 data file.
 
 [usage]:	extract_markers.sh <data_file.gz>
-[example]: 	scripts/extract_markers.sh data.filtered.lepmap3.gz
+[example]: 	extract_markers.sh data.filtered.lepmap3.gz
 
 EOF
   exit 1
diff --git a/scripts/iterate_js2all.sh b/scripts/iterate_js2all.sh
index fee7cf3..fad7301 100755
--- a/scripts/iterate_js2all.sh
+++ b/scripts/iterate_js2all.sh
@@ -6,7 +6,7 @@ if [[ -z "$1" ]]; then
 cat <<EOF
 Iterate JoinSingles2All over a range of LODlimit values.
 [usage]:	iterate_js2all.sh <mapfile> <LOD start> <LOD end> <LOD difference> <informativemask OPTIONAL>
-[example]: 	scripts/iterate_js2all.sh 3_SeparateChromosomes/map.31 22 31 5 123
+[example]: 	iterate_js2all.sh 3_SeparateChromosomes/map.31 22 31 5 123
 EOF
   exit 1
 fi
@@ -39,5 +39,5 @@ done
 echo "The generated maps are named LOD.LODlim.LODdiff.js2all"
 
 # generate a summary of the results
-scripts/MapSummary.r JoinSingles2All_iter
+MapSummary.r JoinSingles2All_iter
 
diff --git a/scripts/lepmap2anchor b/scripts/lepmap2anchor
index d666ab3..a5c46f3 100755
--- a/scripts/lepmap2anchor
+++ b/scripts/lepmap2anchor
@@ -6,7 +6,7 @@ cat <<EOF
 Convert Lep-Map3 interval files into a single Lep-Anchor input file.
 
 [usage]:	lepmap2anchor <marker_file>
-[example]: 	scripts/lepmap2anchor snps.txt
+[example]: 	lepmap2anchor snps.txt
 
 EOF
   exit 1
@@ -15,7 +15,7 @@ fi
 LG=$(ls 7_Intervals/*.intervals | wc -l)
 
 if [ ! -f $1 ]; then
-    echo "Error: marker file $(echo $1) not found. It may be generated using scripts/extract_markers.sh"
+    echo "Error: marker file $(echo $1) not found. It may be generated using extract_markers.sh"
     exit 1
 fi
 
diff --git a/scripts/refinemap.sh b/scripts/refinemap.sh
index 961558f..d1fe0e4 100755
--- a/scripts/refinemap.sh
+++ b/scripts/refinemap.sh
@@ -9,7 +9,7 @@ Attempt to refine a map from SeparateChromosomes2 by splitting out markers from
 Uses 4 threads and distortionLod=1. Requires an input map, which linkage group to modify, LOD start:end values to iterate over, and a minimum size for new clusters.
 
 [usage]:	refinemap.sh <mapfile> <linkage group> <LOD start> <LOD end> <size limit>
-[example]: 	scripts/refinemap.sh 3_SeparateChromosomes/map.31 1 22 70 30
+[example]: 	refinemap.sh 3_SeparateChromosomes/map.31 1 22 70 30
 EOF
   exit 1
 fi
@@ -35,4 +35,4 @@ for i in $(seq $LODMIN $LODMAX); do
 done
 
 # generate a summary of the results
-scripts/MapSummary.r $1.refine
+MapSummary.r $1.refine
diff --git a/scripts/usage b/scripts/usage
index d7a1411..8e3daec 100755
--- a/scripts/usage
+++ b/scripts/usage
@@ -8,7 +8,7 @@ Should be used in main project directory.
 Module names are case-sensitive.
 
 [usage]:  params <module name>
-[example]:  scripts/usage OrderMarkers2
+[example]:  usage OrderMarkers2
 
 LepMap3 modules:
 - ParentCall2

From 88d6ee7f313b400b58fcd72d47f1f766bc1ca9e4 Mon Sep 17 00:00:00 2001
From: Pavel Dimens <pdimens@live.com>
Date: Wed, 16 Feb 2022 16:35:09 -0500
Subject: [PATCH 43/46] rm old paths

---
 rules/LepAnchor/mask_and_chain.smk | 2 +-
 rules/LepAnchor/place_orient3.smk  | 6 +++---
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/rules/LepAnchor/mask_and_chain.smk b/rules/LepAnchor/mask_and_chain.smk
index eaa763c..9e06d0e 100644
--- a/rules/LepAnchor/mask_and_chain.smk
+++ b/rules/LepAnchor/mask_and_chain.smk
@@ -23,7 +23,7 @@ rule repeatmask:
   threads: 30
   shell:
     """
-    software/LepAnchor/deps/Red -gnm 8_RepeatMask/inputgenome -msk 8_RepeatMask -sco 8_RepeatMask -cnd 8_RepeatMask -rpt 8_RepeatMask > {log} 2>> {log}
+    Red -gnm 8_RepeatMask/inputgenome -msk 8_RepeatMask -sco 8_RepeatMask -cnd 8_RepeatMask -rpt 8_RepeatMask > {log} 2>> {log}
     echo "- Compressing repeat-masked genome from Red"
     gzip --stdout 8_RepeatMask/*.msk > {output} && rm 8_RepeatMask/*.msk
     """
diff --git a/rules/LepAnchor/place_orient3.smk b/rules/LepAnchor/place_orient3.smk
index e72008d..bc89f6b 100644
--- a/rules/LepAnchor/place_orient3.smk
+++ b/rules/LepAnchor/place_orient3.smk
@@ -19,7 +19,7 @@ rule place_orient3:
   threads: 2
   shell:
     """
-    gunzip -fc {input.chain} | java -cp software/LepAnchor PlaceAndOrientContigs chromosome={params.chrom} numThreads={threads} $(awk -f software/LepAnchor/scripts/pickorientation.awk {input.chrom}) bed={input.bedfile} map={input.lift} chain=- paf={input.paf} proximity={input.prox} evaluateAnchoring={input.propogated} improveAnchoring=1 {params.datatype} {params.extras} > {output.chrom} 2> {output.errors}
+    gunzip -fc {input.chain} | java -cp software/LepAnchor PlaceAndOrientContigs chromosome={params.chrom} numThreads={threads} $(awk -f pickorientation.awk {input.chrom}) bed={input.bedfile} map={input.lift} chain=- paf={input.paf} proximity={input.prox} evaluateAnchoring={input.propogated} improveAnchoring=1 {params.datatype} {params.extras} > {output.chrom} 2> {output.errors}
     """
     
 rule prune_contigblocks:
@@ -30,7 +30,7 @@ rule prune_contigblocks:
   message: "Pruning contig blocks without map support and removing overlaps"
   params:
     chrom = lg
-  shell: "awk -f software/LepAnchor/scripts/prune.awk {input} > {output.chrom} 2> {output.err}"
+  shell: "awk -f prune.awk {input} > {output.chrom} 2> {output.err}"
 
 rule prune_post:
   input:
@@ -45,5 +45,5 @@ rule prune_post:
   shell:
     """
     cat {input.prunederr} > {output.pruned}
-    awk -f software/LepAnchor/scripts/removeOverlaps.awk {input.bedfile} {input.prunedchrom} > {output.overlaps}
+    awk -f removeOverlaps.awk {input.bedfile} {input.prunedchrom} > {output.overlaps}
     """
\ No newline at end of file

From 5193af6de8415b50be7eb37fbed441a7cf42120e Mon Sep 17 00:00:00 2001
From: Pavel Dimens <pdimens@live.com>
Date: Wed, 16 Feb 2022 22:34:03 -0500
Subject: [PATCH 44/46] update script paths

---
 rules/LepAnchor/place_orient3.smk | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/rules/LepAnchor/place_orient3.smk b/rules/LepAnchor/place_orient3.smk
index bc89f6b..90cd234 100644
--- a/rules/LepAnchor/place_orient3.smk
+++ b/rules/LepAnchor/place_orient3.smk
@@ -19,7 +19,7 @@ rule place_orient3:
   threads: 2
   shell:
     """
-    gunzip -fc {input.chain} | java -cp software/LepAnchor PlaceAndOrientContigs chromosome={params.chrom} numThreads={threads} $(awk -f pickorientation.awk {input.chrom}) bed={input.bedfile} map={input.lift} chain=- paf={input.paf} proximity={input.prox} evaluateAnchoring={input.propogated} improveAnchoring=1 {params.datatype} {params.extras} > {output.chrom} 2> {output.errors}
+    gunzip -fc {input.chain} | java -cp $CONDA_PREFIX/bin/lepanchor PlaceAndOrientContigs chromosome={params.chrom} numThreads={threads} $(awk -f $CONDA_PREFIX/bin/pickorientation.awk {input.chrom}) bed={input.bedfile} map={input.lift} chain=- paf={input.paf} proximity={input.prox} evaluateAnchoring={input.propogated} improveAnchoring=1 {params.datatype} {params.extras} > {output.chrom} 2> {output.errors}
     """
     
 rule prune_contigblocks:
@@ -45,5 +45,5 @@ rule prune_post:
   shell:
     """
     cat {input.prunederr} > {output.pruned}
-    awk -f removeOverlaps.awk {input.bedfile} {input.prunedchrom} > {output.overlaps}
+    awk -f $CONDA_PREFIX/bin/removeOverlaps.awk {input.bedfile} {input.prunedchrom} > {output.overlaps}
     """
\ No newline at end of file

From 589d2e538b82f1c61c54959c37d502c9cf3e4b9f Mon Sep 17 00:00:00 2001
From: Pavel Dimens <pdimens@live.com>
Date: Wed, 16 Feb 2022 22:36:12 -0500
Subject: [PATCH 45/46] missed one

---
 rules/LepAnchor/place_orient3.smk | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/rules/LepAnchor/place_orient3.smk b/rules/LepAnchor/place_orient3.smk
index 90cd234..342eeb1 100644
--- a/rules/LepAnchor/place_orient3.smk
+++ b/rules/LepAnchor/place_orient3.smk
@@ -30,7 +30,7 @@ rule prune_contigblocks:
   message: "Pruning contig blocks without map support and removing overlaps"
   params:
     chrom = lg
-  shell: "awk -f prune.awk {input} > {output.chrom} 2> {output.err}"
+  shell: "awk -f $CONDA_PREFIX/bin/prune.awk {input} > {output.chrom} 2> {output.err}"
 
 rule prune_post:
   input:

From 5a32c3bca2745c17f9f42cbb2eed02b9a3954697 Mon Sep 17 00:00:00 2001
From: "Pavel V. Dimens" <pdimens@live.com>
Date: Thu, 24 Feb 2022 11:02:31 -0500
Subject: [PATCH 46/46] Update build.sh

---
 .misc/build.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.misc/build.sh b/.misc/build.sh
index 56ae559..4ff9a13 100644
--- a/.misc/build.sh
+++ b/.misc/build.sh
@@ -5,8 +5,8 @@ mkdir -p $PREFIX/bin
 mkdir -p $PREFIX/bin/lepmap3
 mkdir -p $PREFIX/bin/lepanchor
 # LepWrap executable
+chmod +x LepWrap
 cp LepWrap $PREFIX/bin/
-chmod +x $PREFIX/bin/LepWrap
 # associated scripts
 chmod +x scripts/*
 cp scripts/* $PREFIX/bin/