GitHub - valeriuo/bcftools: This is the official development repository for BCFtools. To compile, the develop branch of htslib is needed: git clone --branch=develop git://github.com/samtools/htslib.git htslib

This is the official development repository for BCFtools. It contains all the vcf* commands which previously lived in the htslib repository (such as vcfcheck, vcfmerge, vcfisec, etc.) and the samtools BCF calling from bcftools subdirectory of samtools.

For a full documentation, see bcftools GitHub page.

Name	Name	Last commit message	Last commit date
Latest commit valeriuo Merge version number bump and NEWS file from master Dec 20, 2019 1f9449d · Dec 20, 2019 History 2,146 Commits
.travis	.travis	Travis builds clone corresponding htslib branch	Feb 19, 2015
doc	doc	Release 1.10.2	Dec 19, 2019
m4	m4	Add configure options to enable warnings and optionally Werror. See a…	May 16, 2018
misc	misc	Update print statements to be both Python 2 and 3 compatible	Nov 5, 2019
plugins	plugins	Rename --force to --force-AD for possible future additions	Dec 12, 2019
test	test	Add tests for samtools#1123	Dec 16, 2019
.appveyor.yml	.appveyor.yml	Fix some test paths.	Apr 15, 2019
.gitattributes	.gitattributes	Travis builds clone corresponding htslib branch	Feb 19, 2015
.gitignore	.gitignore	Add support for Cygwin plugins.	Nov 18, 2019
.travis.yml	.travis.yml	Make .travis.yml more readable with YAML block "\|" syntax.	Nov 10, 2019
AUTHORS	AUTHORS	Added missing contributors	Feb 4, 2015
HMM.c	HMM.c	Fix HMM initilization in ROH when snapshots are used in multiple chro…	May 10, 2017
HMM.h	HMM.h	Fix HMM initilization in ROH when snapshots are used in multiple chro…	May 10, 2017
INSTALL	INSTALL	Add package install suggestions to INSTALL	Jul 12, 2018
LICENSE	LICENSE	Add license title	Jul 19, 2018
Makefile	Makefile	Release 1.10.2	Dec 19, 2019
NEWS	NEWS	Merge version number bump and NEWS file from master	Dec 20, 2019
README	README	Add basic INSTALL and README files	Aug 15, 2014
README.md	README.md	Add Travis build status badge to README.md.	Nov 10, 2019
bam2bcf.c	bam2bcf.c	New `mpileup -a SCR` annotation which gives the number of soft-clippe…	Sep 23, 2019
bam2bcf.h	bam2bcf.h	Minor: add explanatory comment	Dec 20, 2019
bam2bcf_indel.c	bam2bcf_indel.c	Fix Makefile dependencies	Sep 20, 2019
bam_sample.c	bam_sample.c	Fix warnings identified with -fsanitize=address	Jul 17, 2018
bam_sample.h	bam_sample.h	mpileup: include reads with unlisted or missing RG ID to match previo…	Aug 5, 2016
bcftools.h	bcftools.h	Fix warnings due to function attributes added in htslib	Jan 21, 2019
bin.c	bin.c	Finally fix samtools#801	Jul 18, 2018
bin.h	bin.h	stats: make the AF binning code reusable	Aug 2, 2016
call.h	call.h	Add new `bcftools call -G, --group-samples` option	May 6, 2019
ccall.c	ccall.c	Fix samtools#599	Apr 28, 2017
cols.c	cols.c	Add calloc()/etc casts to suppress -Wc++-compat warnings	Nov 26, 2019
cols.h	cols.h	Proof of principle implementation of the split-vep plugin.	Mar 25, 2019
config.mk.in	config.mk.in	Fix test/test.pl command line when $(HTSDIR) is unset	Dec 5, 2019
configure.ac	configure.ac	Fix back to front language for --enable-perl-filters help	Nov 26, 2019
consensus.c	consensus.c	Prepare for 64-bit positions	Sep 9, 2019
convert.c	convert.c	Prepare for 64-bit positions	Sep 9, 2019
convert.h	convert.h	Make query output only matching genotype fields	Nov 12, 2017
csq.c	csq.c	More 64 bit preparations	Sep 25, 2019
em.c	em.c	Canonicalise whitespace -- USE -b/-w TO DIFF/BLAME ACROSS THIS COMMIT	Aug 14, 2014
filter.c	filter.c	Prepare for 64-bit positions	Sep 9, 2019
filter.h	filter.h	Speedup of `bcftools query` when FORMAT fields are not printed	Jun 12, 2015
gvcf.c	gvcf.c	Check return status of all write() and close() calls	Jul 19, 2018
gvcf.h	gvcf.h	Bringing "call --gvcf" from experimental to main repo.	Sep 30, 2015
hclust.c	hclust.c	gtcheck: prevent segfault with positive values of `-c max`	Aug 3, 2016
hclust.h	hclust.h	gtcheck: improved cross-check mode	Aug 3, 2016
hex.h	hex.h	Update variantkey with the new header-only version	Sep 6, 2018
install-sh	install-sh	bring over autoconf etc files from samtools unchanged	Jun 9, 2017
khash_str2str.h	khash_str2str.h	reheader: support spaces in sample names	Jan 14, 2016
kheap.h	kheap.h	New sort command	Jul 6, 2017
kmin.c	kmin.c	call: Original bcftools' -c calling now functional	Oct 1, 2013
kmin.h	kmin.h	call: Original bcftools' -c calling now functional	Oct 1, 2013
main.c	main.c	Update copyright date printed by --version option	Nov 28, 2019
mcall.c	mcall.c	Prepare for 64-bit positions	Sep 9, 2019
mpileup.c	mpileup.c	Merge pull request samtools#1083 from daviesrob/bigness	Sep 25, 2019
mw.h	mw.h	Added copyright/license boilerplate to mw.h.	Sep 15, 2016
peakfit.c	peakfit.c	peakfit build with GSLv2, resolves samtools#378	Feb 12, 2016
peakfit.h	peakfit.h	update copyright dates for peakfit	Jul 6, 2015
ploidy.c	ploidy.c	New bcftools/csq command, regidx overhaul and new %TBCSQ query format.	Sep 2, 2016
ploidy.h	ploidy.h	regidx: import regidx api from htslib into bcftools	Aug 5, 2016
polysomy.c	polysomy.c	Fix warning about using fabs() on integers.	May 30, 2019
prob1.c	prob1.c	Fix samtools#599	Apr 28, 2017
prob1.h	prob1.h	Fix samtools#599	Apr 28, 2017
rbuf.h	rbuf.h	New +prune plugin	May 17, 2017
regidx.c	regidx.c	Fix a bug in regidx	Jul 26, 2018
regidx.h	regidx.h	Minor documentation update	Jul 26, 2018
reheader.c	reheader.c	Merge pull request samtools#1057 from jmarshall/diagnostics	Aug 1, 2019
smpl_ilist.c	smpl_ilist.c	Make "roh --estimate-AF" complain if non-existent samples (e.g. wrong…	Oct 23, 2019
smpl_ilist.h	smpl_ilist.h	Make "roh --estimate-AF" complain if non-existent samples (e.g. wrong…	Oct 23, 2019
tabix.c	tabix.c	Improve support for MSYS environment.	Nov 22, 2019
tsv2vcf.c	tsv2vcf.c	Tidy upsfor C99 / _XOPEN_SOURCE=700 compliance.	Apr 5, 2017
tsv2vcf.h	tsv2vcf.h	convert: New --gensample2vcf option; change in --gensample output,	Sep 20, 2014
variantkey.h	variantkey.h	Update variantkey with the new header-only version	Sep 6, 2018
vcfannotate.c	vcfannotate.c	Add --single-overlaps option to invoke the pre-af6f0c9 behavior. Reso…	Sep 25, 2019
vcfbuf.c	vcfbuf.c	Allow duplicate positions in both VCF and the TAB file with `call -C …	Apr 18, 2019
vcfbuf.h	vcfbuf.h	Allow duplicate positions in both VCF and the TAB file with `call -C …	Apr 18, 2019
vcfcall.c	vcfcall.c	Fix Makefile dependencies	Sep 20, 2019
vcfcnv.c	vcfcnv.c	Prepare for 64-bit positions	Sep 9, 2019
vcfconcat.c	vcfconcat.c	Add calloc()/etc casts to suppress -Wc++-compat warnings	Nov 26, 2019
vcfconvert.c	vcfconvert.c	Add new --keep-duplicates option	Dec 20, 2019
vcffilter.c	vcffilter.c	Merge pull request samtools#1057 from jmarshall/diagnostics	Aug 1, 2019
vcfgtcheck.c	vcfgtcheck.c	Prepare for 64-bit positions	Sep 9, 2019
vcfindex.c	vcfindex.c	Clarify the meaning of the --threads option.	Jul 21, 2019
vcfisec.c	vcfisec.c	Minor usage page update to give a `-n~` example	Dec 7, 2019
vcfmerge.c	vcfmerge.c	More 64 bit preparations	Sep 25, 2019
vcfnorm.c	vcfnorm.c	New `norm --force` option	Dec 7, 2019
vcfplugin.c	vcfplugin.c	Fix a silly typo. And indentation	Nov 28, 2019
vcfquery.c	vcfquery.c	Add vcfsort error message; suppress various compiler warnings	Jul 31, 2019
vcfroh.c	vcfroh.c	Make "roh --estimate-AF" complain if non-existent samples (e.g. wrong…	Oct 23, 2019
vcfsom.c	vcfsom.c	Add vcfsort error message; suppress various compiler warnings	Jul 31, 2019
vcfsort.c	vcfsort.c	Improve support for MSYS environment.	Nov 22, 2019
vcfstats.c	vcfstats.c	Prepare for 64-bit positions	Sep 9, 2019
vcfview.c	vcfview.c	Prepare for 64-bit positions	Sep 9, 2019
vcmp.c	vcmp.c	Correctly transfer Number=G annotations,	Mar 15, 2018
vcmp.h	vcmp.h	Correctly transfer Number=G annotations,	Mar 15, 2018
version.c	version.c	Grab errno earlier in error_errno()	Jan 21, 2019
version.sh	version.sh	Release 1.10.2	Dec 19, 2019

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