Name		Name	Last commit message	Last commit date
examples		examples
misc		misc
test		test
win32		win32
.gitattributes		.gitattributes
.gitignore		.gitignore
.travis.yml		.travis.yml
AUTHORS		AUTHORS
COPYING		COPYING
ChangeLog.old		ChangeLog.old
INSTALL		INSTALL
Makefile		Makefile
Makefile.mingw		Makefile.mingw
NEWS		NEWS
README.md		README.md
bam.c		bam.c
bam.h		bam.h
bam2bcf.c		bam2bcf.c
bam2bcf.h		bam2bcf.h
bam2bcf_indel.c		bam2bcf_indel.c
bam2depth.c		bam2depth.c
bam_aux.c		bam_aux.c
bam_cat.c		bam_cat.c
bam_color.c		bam_color.c
bam_endian.h		bam_endian.h
bam_flags.c		bam_flags.c
bam_import.c		bam_import.c
bam_index.c		bam_index.c
bam_lpileup.c		bam_lpileup.c
bam_lpileup.h		bam_lpileup.h
bam_mate.c		bam_mate.c
bam_md.c		bam_md.c
bam_plbuf.c		bam_plbuf.c
bam_plbuf.h		bam_plbuf.h
bam_plcmd.c		bam_plcmd.c
bam_reheader.c		bam_reheader.c
bam_rmdup.c		bam_rmdup.c
bam_rmdupse.c		bam_rmdupse.c
bam_sort.c		bam_sort.c
bam_split.c		bam_split.c
bam_stat.c		bam_stat.c
bam_tview.c		bam_tview.c
bam_tview.h		bam_tview.h
bam_tview_curses.c		bam_tview_curses.c
bam_tview_html.c		bam_tview_html.c
bamshuf.c		bamshuf.c
bamtk.c		bamtk.c
bedcov.c		bedcov.c
bedidx.c		bedidx.c
cut_target.c		cut_target.c
errmod.c		errmod.c
errmod.h		errmod.h
faidx.c		faidx.c
kaln.c		kaln.c
kaln.h		kaln.h
kprobaln.c		kprobaln.c
kprobaln.h		kprobaln.h
padding.c		padding.c
phase.c		phase.c
sam.c		sam.c
sam.h		sam.h
sam_header.c		sam_header.c
sam_header.h		sam_header.h
sam_view.c		sam_view.c
sample.c		sample.c
sample.h		sample.h
samtools.1		samtools.1
samtools.h		samtools.h
stats.c		stats.c
stats_isize.c		stats_isize.c
stats_isize.h		stats_isize.h

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samtools

This is the official development repository for samtools.

The original samtools package has been split into three separate but tightly coordinated projects:

htslib: C-library for handling high-throughput sequencing data
samtools: mpileup and other tools for handling SAM, BAM, CRAM
bcftools: calling and other tools for handling VCF, BCF

See also https://github.com/samtools/

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