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New genetics #24

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wants to merge 60 commits into from
Closed

New genetics #24

wants to merge 60 commits into from

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TheoPannetier
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TheoPannetier and others added 30 commits January 14, 2024 11:56
@TheoPannetier
fix indentation and spacing
13dda18
@TheoPannetier
import new_genetics to BatchMode
c332474
@TheoPannetier
fix indentation and spacing
9a693ca
@TheoPannetier
merging @RoslynHenry's new genetics module to main RS code
90b8292
@TheoPannetier
switch to RScore new_genetics branch
28e456a
@TheoPannetier
Add 'src/RScore/' from commit '90b82921bb8e82b92e022688ea51f2a87778b461'
8da22cd 
git-subtree-dir: src/RScore
git-subtree-mainline: 28e456a
git-subtree-split: 90b8292
@TheoPannetier
renaming variables and classes
bfd833b
@TheoPannetier
Merge commit 'bfd833b27d938f1b6cb028c587cc2d816135a553' into new_gene…
6a3ca27 
…tics
@TheoPannetier
update names with RScore
0710e3c
@TheoPannetier
fix merge conflict
59b7fbc
@TheoPannetier
fix merge conflict
0aaf5db
@TheoPannetier
does git subtree not track CMakeLists?
825a643
@TheoPannetier
why would you delete CMakeLists?
720b857
@TheoPannetier
add new genetics file to CMake target + drop unused Distribution classes
606f371
@TheoPannetier
Merge commit '606f3714753e67f83c073c8a758df4506e60b935' into new_gene…
b0f89c6 
…tics
@TheoPannetier
fix merge conflict
1ce2fdb
@TheoPannetier
ranges in new_genetics require cpp20
41ff240
@TheoPannetier
fix merge conflict
1fb0c0c
@JetteReeg
Update CONTRIBUTING.md
6b0a6c3 
Updated referenced links
@TheoPannetier
fix link to logo
ab90761
@TheoPannetier
update CMake
239a795
@TheoPannetier
rm DEBUGLOG blobs
3a02aab
@TheoPannetier
fix missing argument
10ecad7
@TheoPannetier
tediously mergeing develop into new_genetics
ae31119
@TheoPannetier
fix default constructor
f1a6378
@TheoPannetier
fix a few warnings
3fedb66
@TheoPannetier
fix undefined function call
6ec8a76
@TheoPannetier
define undefined stringToSex functiono
3c7f153
@TheoPannetier
add definition for undefined function convertStringToChromosomeEnds
d8c910f
@TheoPannetier
change input of chromosomeEnds and nbPatches to match RScore d8c910f
50ecaa6
TheoPannetier and others added 28 commits February 13, 2024 12:47
@TheoPannetier
rm iequals()
fc7c3f4
@TheoPannetier
fwd declaration to fix circular dependency issue
c7c95da
@TheoPannetier
clarify chromosome switch; compiler mistakes it for bitwise operation
ce60603
@TheoPannetier
fix set iterators
d6aba0d
@TheoPannetier
fix a bunch of warnings and messages
bf735cc
@TheoPannetier
more warnings and messages fixes
ab4dc2c
@TheoPannetier
Merge commit 'ab4dc2cb0b2d165d439415271d01d798ae72afea' into new_gene…
a6cc181 
…tics
@TheoPannetier
rm iequals
f3bbe73
@TheoPannetier
trigger cmakelist change
df3563b
@TheoPannetier
Merge commit 'df3563b2254756b7329dfc8c2db10c7cbb1291ab' into new_gene…
682a558 
…tics
@TheoPannetier
switching subtree branch
0e47a9a
@TheoPannetier
Add 'src/RScore/' from commit 'df3563b2254756b7329dfc8c2db10c7cbb1291ab'
c989e9c 
git-subtree-dir: src/RScore
git-subtree-mainline: 0e47a9a
git-subtree-split: df3563b
@TheoPannetier
merge develop into new_genetics
5d1c2fd
@TheoPannetier
drop unused variables
a99eb7a
@TheoPannetier
rm fiona options from batchMode
608ba2c
@TheoPannetier
Merge branch 'develop' into new_genetics
8aacd42
@TheoPannetier
errors in unix build
6c1a8c7
@TheoPannetier
gcc dislikes switch missing a default
71839b9
@TheoPannetier
oops misplaced default
037ea02
@TheoPannetier
break was not the issue, switch cases must be fenced
8f21329
@TheoPannetier
missing include for ranges
521ed05
@TheoPannetier
fix input handling and input files
1063083
@TheoPannetier
would this be better, xcode?
4f4bb07
@TheoPannetier
like this?
0825983
@TheoPannetier
switch to macOS 13 to hopefully get access to xcode15 and support for…
41cf786 
… cpp20 ranges
@TheoPannetier
oopsie daisy
326ba21
@TheoPannetier
update expected output files for test scenario
6e75cdf
@TheoPannetier
Merge branch 'new_genetics' of https://github.com/RangeShifter/RangeS…
6f0244f 
…hifter_batch_dev into new_genetics
TheoPannetier pushed a commit that referenced this pull request Apr 22, 2024
@JetteReeg
Merge pull request #24 from RangeShifter/translocation
0b36338 
Translocation
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2 participants
@TheoPannetier @JetteReeg