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ChangeLog
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------------------------------------------------------------------------
r925 | lh3lh3 | 2011-02-28 15:45:17 -0500 (Mon, 28 Feb 2011) | 2 lines
Changed paths:
M /trunk/samtools/phase.c
minor changes to a heuristic rule
------------------------------------------------------------------------
r924 | lh3lh3 | 2011-02-28 15:24:04 -0500 (Mon, 28 Feb 2011) | 4 lines
Changed paths:
M /trunk/samtools/bam.h
M /trunk/samtools/bcftools/vcfutils.pl
M /trunk/samtools/phase.c
* 0.1.12-r924:126
* fixed a bug in phase (due to recent changes)
* fixed a bug in vcf2fq
------------------------------------------------------------------------
r923 | lh3lh3 | 2011-02-28 12:57:39 -0500 (Mon, 28 Feb 2011) | 5 lines
Changed paths:
M /trunk/samtools/Makefile
M /trunk/samtools/bam.h
M /trunk/samtools/bam_plcmd.c
M /trunk/samtools/bamtk.c
M /trunk/samtools/phase.c
* put version number in bam.h
* write version to BCF
* in phase, change the default -q to 37
* output a little more information during phasing
------------------------------------------------------------------------
r922 | lh3lh3 | 2011-02-25 16:40:09 -0500 (Fri, 25 Feb 2011) | 3 lines
Changed paths:
M /trunk/samtools/bam2bcf.c
M /trunk/samtools/bamtk.c
M /trunk/samtools/bcftools/bcf.c
M /trunk/samtools/bcftools/bcf.tex
M /trunk/samtools/bcftools/bcf2qcall.c
M /trunk/samtools/bcftools/bcfutils.c
M /trunk/samtools/bcftools/ld.c
M /trunk/samtools/bcftools/prob1.c
M /trunk/samtools/bcftools/vcf.c
M /trunk/samtools/cut_target.c
* change the order of PL/GL according to the latest VCF spec
* change the type of SP to int32_t
------------------------------------------------------------------------
r921 | lh3lh3 | 2011-02-25 14:40:56 -0500 (Fri, 25 Feb 2011) | 2 lines
Changed paths:
M /trunk/samtools/bcftools/bcf.tex
update the BCF spec
------------------------------------------------------------------------
r920 | lh3lh3 | 2011-02-25 00:59:27 -0500 (Fri, 25 Feb 2011) | 2 lines
Changed paths:
M /trunk/samtools/Makefile
M /trunk/samtools/bam_md.c
M /trunk/samtools/bam_plcmd.c
M /trunk/samtools/bam_sort.c
M /trunk/samtools/bamtk.c
A /trunk/samtools/cut_target.c
M /trunk/samtools/errmod.h
M /trunk/samtools/faidx.c
M /trunk/samtools/khash.h
M /trunk/samtools/kstring.c
M /trunk/samtools/kstring.h
A /trunk/samtools/phase.c
M /trunk/samtools/samtools.1
added the phase command
------------------------------------------------------------------------
r918 | lh3lh3 | 2011-02-24 10:05:54 -0500 (Thu, 24 Feb 2011) | 2 lines
Changed paths:
M /trunk/samtools/bcftools/prob1.c
M /trunk/samtools/bcftools/prob1.h
added "const" to bcf_p1_cal()
------------------------------------------------------------------------
r917 | lh3lh3 | 2011-02-24 09:36:30 -0500 (Thu, 24 Feb 2011) | 2 lines
Changed paths:
M /trunk/samtools/bam.c
more meaningful BAM truncation message
------------------------------------------------------------------------
r916 | lh3lh3 | 2011-02-24 09:35:06 -0500 (Thu, 24 Feb 2011) | 3 lines
Changed paths:
M /trunk/samtools/bcftools/bcf.c
M /trunk/samtools/bcftools/vcf.c
* automatically fix errors in GL
* output unrecognized FORMAT as "."
------------------------------------------------------------------------
r913 | lh3lh3 | 2011-02-10 22:59:47 -0500 (Thu, 10 Feb 2011) | 2 lines
Changed paths:
M /trunk/samtools/bcftools/bcf.h
M /trunk/samtools/bcftools/call1.c
M /trunk/samtools/bcftools/vcf.c
finished VCF->BCF conversion
------------------------------------------------------------------------
r910 | petulda | 2011-02-03 03:13:48 -0500 (Thu, 03 Feb 2011) | 1 line
Changed paths:
M /trunk/samtools/bcftools/vcfutils.pl
Prevent division by zero
------------------------------------------------------------------------
r909 | lh3lh3 | 2011-02-02 11:29:20 -0500 (Wed, 02 Feb 2011) | 2 lines
Changed paths:
M /trunk/samtools/bcftools/call1.c
fixed a typo in the VCF header
------------------------------------------------------------------------
r908 | lh3lh3 | 2011-02-02 11:28:24 -0500 (Wed, 02 Feb 2011) | 3 lines
Changed paths:
M /trunk/samtools/bam2bcf.c
M /trunk/samtools/bam_index.c
* fixed an out-of-boundary bug
* improved sorting order checking in index
------------------------------------------------------------------------
r907 | lh3lh3 | 2011-01-29 22:59:20 -0500 (Sat, 29 Jan 2011) | 4 lines
Changed paths:
M /trunk/samtools/INSTALL
M /trunk/samtools/bam_tview.c
M /trunk/samtools/knetfile.c
* avoid a segfault when network connect fails
* update INSTALL
* fixed a bug in tview on big-endian by Nathan Weeks
------------------------------------------------------------------------
r903 | lh3lh3 | 2011-01-27 14:50:02 -0500 (Thu, 27 Jan 2011) | 3 lines
Changed paths:
M /trunk/samtools/bam2bcf_indel.c
M /trunk/samtools/bam_md.c
* fixed a rare memory issue in bam_md.c
* fixed a bug in indel calling related to unmapped and refskip reads
------------------------------------------------------------------------
r902 | lh3lh3 | 2011-01-23 21:46:18 -0500 (Sun, 23 Jan 2011) | 2 lines
Changed paths:
M /trunk/samtools/bcftools/fet.c
fixed two minor bugs in Fisher's exact test
------------------------------------------------------------------------
r899 | petulda | 2011-01-19 09:28:02 -0500 (Wed, 19 Jan 2011) | 1 line
Changed paths:
M /trunk/samtools/bcftools/vcfutils.pl
Skip sites with unknown ref
------------------------------------------------------------------------
r898 | lh3lh3 | 2011-01-15 12:56:05 -0500 (Sat, 15 Jan 2011) | 2 lines
Changed paths:
M /trunk/samtools/ChangeLog
M /trunk/samtools/bam_maqcns.c
M /trunk/samtools/bam_md.c
move bam_nt16_nt4_table[] from bam_maqcns.c to bam_md.c
------------------------------------------------------------------------
r896 | lh3lh3 | 2011-01-06 10:52:15 -0500 (Thu, 06 Jan 2011) | 3 lines
Changed paths:
M /trunk/samtools/bam_plcmd.c
M /trunk/samtools/bamtk.c
M /trunk/samtools/bcftools/bcf.h
M /trunk/samtools/bcftools/bcfutils.c
M /trunk/samtools/bcftools/call1.c
* samtools-0.1.12-10 (r896)
* allow to exclude read groups in mpileup
------------------------------------------------------------------------
r895 | lh3lh3 | 2011-01-04 11:31:29 -0500 (Tue, 04 Jan 2011) | 2 lines
Changed paths:
M /trunk/samtools/bcftools/bcf.tex
sorry. It is SP not ST
------------------------------------------------------------------------
r894 | lh3lh3 | 2011-01-04 11:29:06 -0500 (Tue, 04 Jan 2011) | 2 lines
Changed paths:
M /trunk/samtools/bcftools/bcf.tex
added ST
------------------------------------------------------------------------
r893 | petulda | 2011-01-04 06:55:56 -0500 (Tue, 04 Jan 2011) | 1 line
Changed paths:
M /trunk/samtools/bcftools/call1.c
Fixed a typo in read_samples
------------------------------------------------------------------------
r892 | jmarshall | 2010-12-28 08:06:49 -0500 (Tue, 28 Dec 2010) | 9 lines
Changed paths:
M /trunk/samtools/Makefile
M /trunk/samtools/bcftools/Makefile
M /trunk/samtools/examples/Makefile
System libraries go *after* user libraries in link commands, because
the user libraries may themselves have dependencies that are satisfied
by the system libraries. It's not rocket science!
This makes a difference with some linkers; or with -static or --as-needed.
The examples/Makefile fix is from Charles Plessy.
See also http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=606004
------------------------------------------------------------------------
r891 | lh3lh3 | 2010-12-21 12:16:33 -0500 (Tue, 21 Dec 2010) | 3 lines
Changed paths:
M /trunk/samtools/bamtk.c
M /trunk/samtools/bcftools/bcf.h
M /trunk/samtools/bcftools/bcfutils.c
M /trunk/samtools/bcftools/call1.c
* samtools-0.1.12-9 (r891)
* allow to call SNPs from a subset of samples
------------------------------------------------------------------------
r889 | lh3lh3 | 2010-12-15 11:28:16 -0500 (Wed, 15 Dec 2010) | 3 lines
Changed paths:
M /trunk/samtools/bam2bcf.c
M /trunk/samtools/bamtk.c
* samtools-0.1.12-12 (r889)
* set mapQ as 20 if it equals 255
------------------------------------------------------------------------
r888 | lh3lh3 | 2010-12-14 22:41:09 -0500 (Tue, 14 Dec 2010) | 2 lines
Changed paths:
M /trunk/samtools/bam_plcmd.c
M /trunk/samtools/bamtk.c
When -B is applied to mpileup, still use paired reads only unless -A is flagged.
------------------------------------------------------------------------
r887 | lh3lh3 | 2010-12-14 22:37:05 -0500 (Tue, 14 Dec 2010) | 3 lines
Changed paths:
M /trunk/samtools/bam_md.c
M /trunk/samtools/bam_plcmd.c
M /trunk/samtools/bamtk.c
* samtools-0.1.12-6 (r887)
* added a hidden option -E to mpileup/calmd. -E triggers an alternative way to apply BAQ.
------------------------------------------------------------------------
r886 | lh3lh3 | 2010-12-14 12:51:03 -0500 (Tue, 14 Dec 2010) | 2 lines
Changed paths:
M /trunk/samtools/bam2bcf_indel.c
M /trunk/samtools/bamtk.c
(Arguably) improved the indel caller a tiny bit for lowCov data.
------------------------------------------------------------------------
r885 | petulda | 2010-12-14 04:55:46 -0500 (Tue, 14 Dec 2010) | 1 line
Changed paths:
M /trunk/samtools/bcftools/call1.c
Fixed the VCF header to pass validation
------------------------------------------------------------------------
r884 | lh3lh3 | 2010-12-12 23:02:19 -0500 (Sun, 12 Dec 2010) | 3 lines
Changed paths:
M /trunk/samtools/bam2bcf_indel.c
M /trunk/samtools/bamtk.c
M /trunk/samtools/bcftools/vcfutils.pl
* samtools-0.1.12-4 (r884)
* fixed a long-existing flaw in the INDEL calling model
------------------------------------------------------------------------
r883 | lh3lh3 | 2010-12-11 20:05:42 -0500 (Sat, 11 Dec 2010) | 2 lines
Changed paths:
M /trunk/samtools/bcftools/bcfutils.c
M /trunk/samtools/bcftools/call1.c
M /trunk/samtools/bcftools/vcfutils.pl
compute max SP and max GQ from sample genotypes
------------------------------------------------------------------------
r880 | lh3lh3 | 2010-12-10 10:50:54 -0500 (Fri, 10 Dec 2010) | 2 lines
Changed paths:
D /trunk/samtools/bcftools/bcf-fix.pl
drop bcf-fix.pl as it is redundant by the latest changes
------------------------------------------------------------------------
r879 | lh3lh3 | 2010-12-10 10:50:29 -0500 (Fri, 10 Dec 2010) | 3 lines
Changed paths:
M /trunk/samtools/bcftools/call1.c
M /trunk/samtools/bcftools/vcf.c
* fixed a minor issue in printing VCFs
* write bcftools specific INFO and FORMAT in the header
------------------------------------------------------------------------
r878 | lh3lh3 | 2010-12-10 10:09:14 -0500 (Fri, 10 Dec 2010) | 2 lines
Changed paths:
M /trunk/samtools/bamtk.c
M /trunk/samtools/bcftools/bcfutils.c
M /trunk/samtools/bcftools/call1.c
Make sure that the GT genotype field is the first
------------------------------------------------------------------------
r877 | lh3lh3 | 2010-12-08 17:27:05 -0500 (Wed, 08 Dec 2010) | 7 lines
Changed paths:
M /trunk/samtools/bam2bcf.c
M /trunk/samtools/bam2bcf.h
M /trunk/samtools/bam2bcf_indel.c
M /trunk/samtools/bam_plcmd.c
M /trunk/samtools/bamtk.c
* samtools-0.1.12-2 (r877)
* allow to fine control the selection of indel candidates. The current
setting is okay for lowCov and highCov with ~100 samples, but it
skips too many indels for highCov with >250 samples.
------------------------------------------------------------------------
r874 | lh3lh3 | 2010-12-07 22:40:35 -0500 (Tue, 07 Dec 2010) | 2 lines
Changed paths:
M /trunk/samtools/bam_plcmd.c
a spelling error..
------------------------------------------------------------------------
r873 | lh3lh3 | 2010-12-07 22:39:57 -0500 (Tue, 07 Dec 2010) | 3 lines
Changed paths:
M /trunk/samtools/bam_plcmd.c
M /trunk/samtools/bamtk.c
* samtools-0.1.12-1 (r873)
* added a switch to allow anomalous read pairs in calling
------------------------------------------------------------------------
r872 | lh3lh3 | 2010-12-07 14:43:54 -0500 (Tue, 07 Dec 2010) | 2 lines
Changed paths:
M /trunk/samtools/bcftools/vcfutils.pl
fixed a bug in vcf2fq
------------------------------------------------------------------------
r869 | lh3lh3 | 2010-12-05 01:18:06 -0500 (Sun, 05 Dec 2010) | 2 lines
Changed paths:
M /trunk/samtools/bamtk.c
added a warning for the Windows version
------------------------------------------------------------------------
r868 | lh3lh3 | 2010-12-05 01:05:51 -0500 (Sun, 05 Dec 2010) | 4 lines
Changed paths:
M /trunk/samtools/bcftools/call1.c
In ksprintf(), change "%lf" and "%lg" to "%f" and "%g", respectively.
According to the manual page, this change is valid. However, MinGW seems
to interpret "%lf" as "%Lf".
------------------------------------------------------------------------
r867 | lh3lh3 | 2010-12-05 00:35:43 -0500 (Sun, 05 Dec 2010) | 2 lines
Changed paths:
M /trunk/samtools/Makefile.mingw
M /trunk/samtools/bam_aux.c
bring back the windows support
------------------------------------------------------------------------
r866 | lh3lh3 | 2010-12-04 23:33:51 -0500 (Sat, 04 Dec 2010) | 2 lines
Changed paths:
M /trunk/samtools/bam_reheader.c
M /trunk/samtools/bcftools/vcfutils.pl
Fixed a compiling error when knetfile is not used.
------------------------------------------------------------------------
r865 | lh3lh3 | 2010-12-04 00:13:22 -0500 (Sat, 04 Dec 2010) | 2 lines
Changed paths:
M /trunk/samtools/bcftools/vcfutils.pl
vcf->fastq
------------------------------------------------------------------------
r864 | lh3lh3 | 2010-12-03 17:12:30 -0500 (Fri, 03 Dec 2010) | 3 lines
Changed paths:
M /trunk/samtools/bcftools/call1.c
M /trunk/samtools/bcftools/prob1.c
M /trunk/samtools/bcftools/prob1.h
* remove "-f". Instead always compute consensus quality
* increase the upper limit of quality
------------------------------------------------------------------------
r863 | lh3lh3 | 2010-12-03 15:28:15 -0500 (Fri, 03 Dec 2010) | 2 lines
Changed paths:
M /trunk/samtools/bcftools/bcf.c
more informative error message
------------------------------------------------------------------------
r862 | lh3lh3 | 2010-12-02 16:16:08 -0500 (Thu, 02 Dec 2010) | 2 lines
Changed paths:
M /trunk/samtools/NEWS
M /trunk/samtools/bamtk.c
Release samtools-0.1.12a
------------------------------------------------------------------------
r861 | lh3lh3 | 2010-12-02 15:55:06 -0500 (Thu, 02 Dec 2010) | 2 lines
Changed paths:
M /trunk/samtools/bcftools/call1.c
a possible fix to DP4=0,0,0,0; have not tested, but should have no side-effect
------------------------------------------------------------------------
r859 | lh3lh3 | 2010-12-02 11:39:57 -0500 (Thu, 02 Dec 2010) | 2 lines
Changed paths:
M /trunk/samtools/NEWS
M /trunk/samtools/bam_index.c
M /trunk/samtools/bamtk.c
M /trunk/samtools/samtools.1
Release samtools-0.1.12
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r858 | lh3lh3 | 2010-12-02 11:24:41 -0500 (Thu, 02 Dec 2010) | 4 lines
Changed paths:
M /trunk/samtools/bam_plcmd.c
M /trunk/samtools/bamtk.c
M /trunk/samtools/bcftools/bcf.c
* samtools-0.1.11-1 (r858)
* fixed a bug in mpileup which causes segfaults
* bcftools: do not segfault when BCF contains errors
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r857 | lh3lh3 | 2010-11-30 23:52:50 -0500 (Tue, 30 Nov 2010) | 2 lines
Changed paths:
M /trunk/samtools/bam_index.c
fixed a memory leak in bam_fetch()
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r856 | lh3lh3 | 2010-11-26 00:07:31 -0500 (Fri, 26 Nov 2010) | 3 lines
Changed paths:
M /trunk/samtools/bam2bcf_indel.c
M /trunk/samtools/bcftools/vcfutils.pl
* fixed a memory violation
* added splitchr to vcfutils.pl
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r854 | lh3lh3 | 2010-11-23 09:05:08 -0500 (Tue, 23 Nov 2010) | 2 lines
Changed paths:
M /trunk/samtools/bcftools/ld.c
fixed a typo/bug in r^2 computation
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r852 | lh3lh3 | 2010-11-21 22:20:20 -0500 (Sun, 21 Nov 2010) | 2 lines
Changed paths:
M /trunk/samtools/bamtk.c
forget to change the version information
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r851 | lh3lh3 | 2010-11-21 22:16:52 -0500 (Sun, 21 Nov 2010) | 2 lines
Changed paths:
M /trunk/samtools/ChangeLog
M /trunk/samtools/NEWS
M /trunk/samtools/bcftools/bcftools.1
M /trunk/samtools/samtools.1
Release samtools-0.1.11
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r844 | lh3lh3 | 2010-11-19 23:16:08 -0500 (Fri, 19 Nov 2010) | 3 lines
Changed paths:
M /trunk/samtools/bamtk.c
M /trunk/samtools/bcftools/call1.c
M /trunk/samtools/bcftools/prob1.c
M /trunk/samtools/bcftools/prob1.h
* samtools-0.1.10-9 (r844)
* added the "folded" or reference-free mode for variant calling
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r843 | lh3lh3 | 2010-11-19 22:26:36 -0500 (Fri, 19 Nov 2010) | 2 lines
Changed paths:
M /trunk/samtools/NEWS
M /trunk/samtools/bam_sort.c
In merging, if -R is specified, do not abort if the sequence dictionary is different.
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r842 | jmarshall | 2010-11-19 21:24:28 -0500 (Fri, 19 Nov 2010) | 5 lines
Changed paths:
M /trunk/samtools/bam_sort.c
When merging BAM headers, compare the list of target reference sequences
strictly (and fail/abort if there is a mismatch), but allow one list to be a
prefix of the other. (i.e., check that the lists are identical up until the
shorter runs out, and add the excess targets from the longer to the output.)
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r841 | lh3lh3 | 2010-11-19 14:49:27 -0500 (Fri, 19 Nov 2010) | 4 lines
Changed paths:
M /trunk/samtools/bam_index.c
M /trunk/samtools/bam_pileup.c
M /trunk/samtools/bamtk.c
* samtools-0.1.10 (r841)
* fixed a bug in pileup when the first CIGAR operation is D
* fixed a bug in view with range query
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r840 | lh3lh3 | 2010-11-19 13:45:51 -0500 (Fri, 19 Nov 2010) | 10 lines
Changed paths:
M /trunk/samtools/ChangeLog
M /trunk/samtools/bam2bcf.c
M /trunk/samtools/bam2bcf.h
M /trunk/samtools/bam2bcf_indel.c
M /trunk/samtools/bam_plcmd.c
M /trunk/samtools/bamtk.c
* samtools-0.1.10-4 (r840)
* drop the MNP caller. It is slow while does not diliver too much
benefit. Possibly I will work on it in future given more time.
* there is a segfault in pileup
* someone has reported segfault from view/index/sort
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r839 | lh3lh3 | 2010-11-18 17:30:11 -0500 (Thu, 18 Nov 2010) | 9 lines
Changed paths:
M /trunk/samtools/bam2bcf.h
M /trunk/samtools/bam2bcf_indel.c
M /trunk/samtools/bamtk.c
* samtools-0.1.10-6 (r839)
* call MNPs without realignment because it seems to me that it is not
worthwhile to significantly slow down SNP calling.
* the result looks quite different from the previous version. I have
work to do...
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r838 | lh3lh3 | 2010-11-18 11:26:09 -0500 (Thu, 18 Nov 2010) | 2 lines
Changed paths:
M /trunk/samtools/knetfile.c
Apply a patch by Rob Davis, which improves fault detection.
------------------------------------------------------------------------
r836 | lh3lh3 | 2010-11-18 11:09:23 -0500 (Thu, 18 Nov 2010) | 3 lines
Changed paths:
M /trunk/samtools/bam2bcf_indel.c
M /trunk/samtools/bamtk.c
* samtools-r836
* initiate MNP realignment when the MNP has at least 0.2% frequency (otherwise too slow)
------------------------------------------------------------------------
r835 | lh3lh3 | 2010-11-18 00:25:13 -0500 (Thu, 18 Nov 2010) | 3 lines
Changed paths:
M /trunk/samtools/bcftools/vcfutils.pl
* modify the filtering rule: also filter SNPs around filtered indels
* added MNP filter
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r834 | lh3lh3 | 2010-11-17 23:13:52 -0500 (Wed, 17 Nov 2010) | 4 lines
Changed paths:
M /trunk/samtools/bam2bcf.c
M /trunk/samtools/bam2bcf_indel.c
M /trunk/samtools/bamtk.c
* samtools-0.1.10-4 (r834)
* fixed a silly bug in printing MNP
* restrict to at most 1 alternative allele
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r833 | lh3lh3 | 2010-11-17 21:58:58 -0500 (Wed, 17 Nov 2010) | 2 lines
Changed paths:
M /trunk/samtools/bam2bcf.c
M /trunk/samtools/bamtk.c
fixed a bug in printing MNPs
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r832 | lh3lh3 | 2010-11-17 21:47:20 -0500 (Wed, 17 Nov 2010) | 2 lines
Changed paths:
M /trunk/samtools/bam2bcf_indel.c
M /trunk/samtools/bamtk.c
minor change to how seqQ is applied
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r831 | lh3lh3 | 2010-11-17 21:41:12 -0500 (Wed, 17 Nov 2010) | 3 lines
Changed paths:
M /trunk/samtools/bam2bcf.c
M /trunk/samtools/bam2bcf.h
M /trunk/samtools/bam2bcf_indel.c
M /trunk/samtools/bam_plcmd.c
M /trunk/samtools/bamtk.c
* samtools-0.1.10 (r831)
* initial MNP caller
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r829 | lh3lh3 | 2010-11-16 23:14:15 -0500 (Tue, 16 Nov 2010) | 2 lines
Changed paths:
M /trunk/samtools/ChangeLog
M /trunk/samtools/NEWS
M /trunk/samtools/bamtk.c
Release samtools-0.1.10 (r829)
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r828 | lh3lh3 | 2010-11-16 20:48:49 -0500 (Tue, 16 Nov 2010) | 2 lines
Changed paths:
M /trunk/samtools/bamtk.c
update version information: samtools-0.1.9-20 (r828)
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r827 | lh3lh3 | 2010-11-16 15:32:50 -0500 (Tue, 16 Nov 2010) | 2 lines
Changed paths:
M /trunk/samtools/bcftools/call1.c
bcftools: allow to skip indels
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r826 | lh3lh3 | 2010-11-16 14:11:58 -0500 (Tue, 16 Nov 2010) | 2 lines
Changed paths:
M /trunk/samtools/bam_md.c
remove ZQ if both BQ and ZQ are present
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r825 | lh3lh3 | 2010-11-16 13:51:33 -0500 (Tue, 16 Nov 2010) | 3 lines
Changed paths:
M /trunk/samtools/bam2bcf_indel.c
M /trunk/samtools/bam_md.c
M /trunk/samtools/bamtk.c
M /trunk/samtools/samtools.1
* samtools-0.1.9-18 (r825)
* change the behaviour of calmd such that by default it does not change the base quality
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r824 | lh3lh3 | 2010-11-15 23:31:53 -0500 (Mon, 15 Nov 2010) | 4 lines
Changed paths:
M /trunk/samtools/bam_plcmd.c
M /trunk/samtools/bamtk.c
M /trunk/samtools/bcftools/call1.c
M /trunk/samtools/samtools.1
* samtools-0.1.9-17 (r824)
* added command line options to change the default parameters in indel calling
* update the manual
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r823 | lh3lh3 | 2010-11-15 12:20:13 -0500 (Mon, 15 Nov 2010) | 3 lines
Changed paths:
M /trunk/samtools/bam2bcf_indel.c
M /trunk/samtools/bam_md.c
M /trunk/samtools/bamtk.c
* samtools-0.1.9-r823
* the BQ tag is now 64 shifted, not 33 shifted
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r822 | lh3lh3 | 2010-11-15 00:30:18 -0500 (Mon, 15 Nov 2010) | 3 lines
Changed paths:
M /trunk/samtools/bam2bcf.c
M /trunk/samtools/bam2bcf.h
M /trunk/samtools/bamtk.c
M /trunk/samtools/bcftools/vcfutils.pl
M /trunk/samtools/misc/samtools.pl
* samtools-0.1.9-16 (r822)
* keep the raw depth because in indel calling, DP4 may be way off the true depth
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r821 | lh3lh3 | 2010-11-13 01:18:31 -0500 (Sat, 13 Nov 2010) | 4 lines
Changed paths:
M /trunk/samtools/bam_md.c
M /trunk/samtools/bamtk.c
* samtools-0.1.9-15 (r821)
* calmd: write BQ
* skip realignment if BQ is present
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r820 | lh3lh3 | 2010-11-13 01:08:26 -0500 (Sat, 13 Nov 2010) | 3 lines
Changed paths:
M /trunk/samtools/bam2bcf_indel.c
M /trunk/samtools/bamtk.c
* samtools-0.1.9-14 (r820)
* penalize reads with excessive differences in indel calling
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r819 | lh3lh3 | 2010-11-12 21:36:27 -0500 (Fri, 12 Nov 2010) | 3 lines
Changed paths:
M /trunk/samtools/bam_maqcns.c
M /trunk/samtools/bamtk.c
* samtools-0.1.9-13 (r819)
* fixed a bug in pileup given refskip
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r818 | lh3lh3 | 2010-11-12 13:04:53 -0500 (Fri, 12 Nov 2010) | 3 lines
Changed paths:
M /trunk/samtools/bam2bcf_indel.c
M /trunk/samtools/bamtk.c
* samtools-r818
* for indel calling, do two rounds of probabilistic realignments
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r817 | lh3lh3 | 2010-11-11 20:04:07 -0500 (Thu, 11 Nov 2010) | 3 lines
Changed paths:
M /trunk/samtools/bam2bcf_indel.c
M /trunk/samtools/bamtk.c
M /trunk/samtools/bcftools/vcfutils.pl
* samtools-0.1.19-11 (r817)
* only initiate indel calling when 0.2% of reads contain a gap
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r816 | lh3lh3 | 2010-11-11 01:22:59 -0500 (Thu, 11 Nov 2010) | 7 lines
Changed paths:
M /trunk/samtools/bam2bcf_indel.c
M /trunk/samtools/bamtk.c
* samtools-0.1.9-10 (r816)
* I know why the forward method fails. it is because of zero base
qualities. when that is fixed, the forward method seems to give
better results than Viterbi, as it should be. I am tired...
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r815 | lh3lh3 | 2010-11-11 00:57:15 -0500 (Thu, 11 Nov 2010) | 2 lines
Changed paths:
M /trunk/samtools/ChangeLog
M /trunk/samtools/bam2bcf_indel.c
effectively revert to the viterbi version. The forward realignment gives too many false positives.
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r814 | lh3lh3 | 2010-11-11 00:18:02 -0500 (Thu, 11 Nov 2010) | 4 lines
Changed paths:
M /trunk/samtools/bam2bcf_indel.c
M /trunk/samtools/bam_md.c
M /trunk/samtools/bam_plcmd.c
M /trunk/samtools/bamtk.c
* samtools-0.1.9-9 (r810)
* use forward, instead of viterbi, for realignment
* realignment is now quality aware
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r813 | lh3lh3 | 2010-11-10 22:45:24 -0500 (Wed, 10 Nov 2010) | 2 lines
Changed paths:
M /trunk/samtools/bam2bcf_indel.c
M /trunk/samtools/kprobaln.c
M /trunk/samtools/kprobaln.h
* prepare to replace kaln with kprobaln in realignment
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r812 | lh3lh3 | 2010-11-10 17:28:50 -0500 (Wed, 10 Nov 2010) | 2 lines
Changed paths:
M /trunk/samtools/bcftools/bcf.c
fixed a typo
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r811 | lh3lh3 | 2010-11-10 16:54:46 -0500 (Wed, 10 Nov 2010) | 2 lines
Changed paths:
M /trunk/samtools/bcftools/bcf.c
M /trunk/samtools/bcftools/bcf.h
use zlib for direct reading when BCF_LITE is in use
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r810 | lh3lh3 | 2010-11-10 16:32:13 -0500 (Wed, 10 Nov 2010) | 3 lines
Changed paths:
M /trunk/samtools/bam2bcf_indel.c
* do not use reads containing too many mismatches for indel calling
* fixed a trivial bug in case of multi-allelic indels
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r809 | lh3lh3 | 2010-11-10 13:23:02 -0500 (Wed, 10 Nov 2010) | 3 lines
Changed paths:
M /trunk/samtools/bam2bcf.c
M /trunk/samtools/bam2bcf_indel.c
M /trunk/samtools/bam_plcmd.c
M /trunk/samtools/bamtk.c
* samtools-0.1.9-8 (r809)
* fixed a bug in the indel caller
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r808 | lh3lh3 | 2010-11-10 12:24:10 -0500 (Wed, 10 Nov 2010) | 2 lines
Changed paths:
M /trunk/samtools/Makefile
minor change to makefile
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r807 | lh3lh3 | 2010-11-10 12:10:21 -0500 (Wed, 10 Nov 2010) | 4 lines
Changed paths:
M /trunk/samtools/Makefile
M /trunk/samtools/bam2bcf.h
M /trunk/samtools/bam2bcf_indel.c
M /trunk/samtools/bam_plcmd.c
M /trunk/samtools/bamtk.c
M /trunk/samtools/bcftools/vcfutils.pl
* samtools-0.1.9-8 (r807)
* collect indel candidates only from specified platforms (@RG-PL)
* merge varFilter and filter4vcf in vcfutils.pl
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r806 | lh3lh3 | 2010-11-09 22:05:46 -0500 (Tue, 09 Nov 2010) | 2 lines
Changed paths:
M /trunk/samtools/bcftools/call1.c
M /trunk/samtools/bcftools/prob1.c
M /trunk/samtools/bcftools/prob1.h
bcftools: compute equal-tail (Bayesian) credible interval
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r805 | lh3lh3 | 2010-11-09 16:28:39 -0500 (Tue, 09 Nov 2010) | 2 lines
Changed paths:
M /trunk/samtools/bcftools/vcfutils.pl
added a double-hit filter to avoid overestimated indel likelihood
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r804 | lh3lh3 | 2010-11-09 14:12:06 -0500 (Tue, 09 Nov 2010) | 3 lines
Changed paths:
M /trunk/samtools/bam2bcf_indel.c
M /trunk/samtools/bamtk.c
* samtools-0.1.9-7 (r804)
* fixed a bug in the gap caller
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r803 | lh3lh3 | 2010-11-09 10:45:33 -0500 (Tue, 09 Nov 2010) | 4 lines
Changed paths:
M /trunk/samtools/bam2bcf.c
M /trunk/samtools/bam2bcf_indel.c
M /trunk/samtools/bamtk.c
M /trunk/samtools/bcftools/bcf.c
M /trunk/samtools/bcftools/bcf.h
M /trunk/samtools/bcftools/prob1.c
* samtools-0.1.9-6 (r803)
* mpileup: apply homopolymer correction when calculating GL, instead of before
* bcftools: apply a different prior to indels
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r802 | lh3lh3 | 2010-11-08 23:53:15 -0500 (Mon, 08 Nov 2010) | 3 lines
Changed paths:
M /trunk/samtools/bam2bcf.c
M /trunk/samtools/bamtk.c
* samtools-0.1.9-5 (r802)
* relax tandem penalty. this will be made a command-line option in future.
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r801 | lh3lh3 | 2010-11-08 23:35:52 -0500 (Mon, 08 Nov 2010) | 3 lines
Changed paths:
M /trunk/samtools/bam2bcf.c
M /trunk/samtools/bamtk.c
* samtools-0.1.9-4 (r801)
* fixed a minor issue in printing indel VCF
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r800 | lh3lh3 | 2010-11-08 15:28:14 -0500 (Mon, 08 Nov 2010) | 2 lines
Changed paths:
M /trunk/samtools/bam2bcf_indel.c
M /trunk/samtools/bcftools/vcfutils.pl
fixed another silly bug in mpileup's indel caller
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r799 | lh3lh3 | 2010-11-08 14:28:27 -0500 (Mon, 08 Nov 2010) | 2 lines
Changed paths:
M /trunk/samtools/bam2bcf.c
fixed a silly bug in the indel caller
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r798 | lh3lh3 | 2010-11-08 14:07:33 -0500 (Mon, 08 Nov 2010) | 2 lines
Changed paths:
M /trunk/samtools/ChangeLog
M /trunk/samtools/sam_view.c
M /trunk/samtools/samtools.1
Incorporate patches by Marcel Martin for read counting.
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r797 | lh3lh3 | 2010-11-08 13:39:52 -0500 (Mon, 08 Nov 2010) | 3 lines
Changed paths:
M /trunk/samtools/bam2bcf.c
M /trunk/samtools/bam2bcf.h
M /trunk/samtools/bam2bcf_indel.c
M /trunk/samtools/bam_plcmd.c
M /trunk/samtools/bamtk.c
* samtools-0.1.9-2 (r797)
* mpileup: indel calling seems to be working
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r796 | lh3lh3 | 2010-11-08 10:54:46 -0500 (Mon, 08 Nov 2010) | 2 lines
Changed paths:
M /trunk/samtools/bam2bcf.c
M /trunk/samtools/bam2bcf.h
M /trunk/samtools/bam2bcf_indel.c
M /trunk/samtools/bam_plcmd.c
M /trunk/samtools/kaln.c
indel calling is apparently working, but more information needs to be collected
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r795 | lh3lh3 | 2010-11-08 00:39:18 -0500 (Mon, 08 Nov 2010) | 2 lines
Changed paths:
M /trunk/samtools/bam2bcf.c
M /trunk/samtools/bam2bcf_indel.c
fixed a few bugs in the indel caller. Probably there are more.
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r794 | lh3lh3 | 2010-11-07 22:23:16 -0500 (Sun, 07 Nov 2010) | 2 lines
Changed paths:
M /trunk/samtools/Makefile
M /trunk/samtools/bam.h
M /trunk/samtools/bam2bcf.c
M /trunk/samtools/bam2bcf.h
A /trunk/samtools/bam2bcf_indel.c
M /trunk/samtools/bam_plcmd.c
M /trunk/samtools/kaln.c
M /trunk/samtools/kaln.h
prepare for the indel caller. It is not ready yet.
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r793 | lh3lh3 | 2010-11-05 11:28:23 -0400 (Fri, 05 Nov 2010) | 2 lines
Changed paths:
M /trunk/samtools/bam2bcf.c
M /trunk/samtools/bam2bcf.h
M /trunk/samtools/bam_plcmd.c
Revert to r790. The recent changes are not good...
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r792 | lh3lh3 | 2010-11-05 00:19:14 -0400 (Fri, 05 Nov 2010) | 6 lines
Changed paths:
M /trunk/samtools/bam2bcf.c
M /trunk/samtools/bam2bcf.h
M /trunk/samtools/bam_plcmd.c
* this revision is UNSTABLE
* indel caller seems working, but it is very insensitive and has
several things I do not quite understand.
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r791 | lh3lh3 | 2010-11-04 22:58:43 -0400 (Thu, 04 Nov 2010) | 2 lines
Changed paths:
M /trunk/samtools/bam2bcf.c
M /trunk/samtools/bam2bcf.h
M /trunk/samtools/bam_plcmd.c