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Release 1.2.3 #48

Merged
merged 24 commits into from
Oct 19, 2024
Merged

Release 1.2.3 #48

merged 24 commits into from
Oct 19, 2024

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helrick
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@helrick helrick commented Oct 17, 2024 •
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  • New approach for allele-counting, improving speed and performance
  • Improved copy number output
  • Added additional copy number parameters
  • Improved documentation for copy number
  • Added --overwrite flag to force continue even if files present in outdir
  • Coverage bins bugfix

cmsauer and others added 24 commits October 16, 2024 11:26
@cmsauer
remove 'default' conda channel from environment.yml
3f0794e
@cmsauer
update python version
f57bf7e
@cmsauer
remove importing of unnecessary packages
a9440a1
@cmsauer
commit new updated allele_counter for improved speed and performance.
969949c
@cmsauer
allele counter version update to v1.2.3
8963cf2
@cmsauer
implement new allele counter into savana workflow and add tmpdir func…
d83ebb5 
…tion to helper
@cmsauer
add and improve various parameters and functions for allele counting …
a908901 
…and cn fitting
@cmsauer
minor parameter fix
616e3dd
@cmsauer
minor parameter fix
5421498
@cmsauer
minor parameter fix
6fc8e6d
@cmsauer
fix minor bug in allele counter ref base
8709991
@cmsauer
add cna_threads parameter
a9f0af8
@cmsauer
add mean BAF and number of used hetSNPs to main output
215a7aa
@cmsauer
clean CN output to main output files and add headers.
f6674dd
@cmsauer
addition of parameters and improvement of parameter documentation
8cd6f7d
@cmsauer
addition of parameters and improvement of parameter documentation
d1acdff
@cmsauer
addition of parameters and improvement of parameter documentation
b336f85
@cmsauer
addition of parameters and improvement of parameter documentation
58bce95
@cmsauer
fix output file headers
8d421ff
@cmsauer
fix output file headers
c9d26d2
@cmsauer
minor bug fix
dc667ff
@helrick
fix for coverage in t2t 🏄‍♀️
9d8b7a6
@helrick
adding --overwrite flag, cleaning up tmpdir
1429ace
@helrick
Merge branch 't2t-coverage-fixes' into csauer/allele_count_dev
a762648
@helrick helrick requested a review from cmsauer October 17, 2024 20:58
cmsauer
cmsauer approved these changes Oct 18, 2024
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Looks great

@helrick helrick merged commit bfd4337 into main Oct 19, 2024
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@cmsauer cmsauer cmsauer approved these changes

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@helrick @cmsauer