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

Building Samtools

See INSTALL for complete details. Release tarballs contain generated files that have not been committed to this repository, so building the code from a Git repository requires an extra step:

autoconf -Wno-syntax  # Generate the configure script, if needed
./configure           # Optional, needed for choosing optional functionality
make
make install

By default, this will build against an HTSlib source tree in ../htslib. You can alter this to a source tree elsewhere or to a previously-installed HTSlib by configuring with --with-htslib=DIR.

Name	Name	Last commit date
.travis	.travis
examples	examples
m4	m4
misc	misc
test	test
win32	win32
.gitattributes	.gitattributes
.gitignore	.gitignore
.travis.yml	.travis.yml
AUTHORS	AUTHORS
ChangeLog.old	ChangeLog.old	< 10000 /div>
INSTALL	INSTALL
LICENSE	LICENSE
Makefile	Makefile
Makefile.mingw	Makefile.mingw
NEWS	NEWS
README	README
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_addrprg.c	bam_addrprg.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< 10000 /a>
bam_quickcheck.c	bam_quickcheck.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
config.h.in	config.h.in
config.mk.in	config.mk.in
configure.ac	configure.ac
cut_target.c	cut_target.c
dict.c	dict.c
faidx.c	faidx.c
install-sh	install-sh
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_opts.c	sam_opts.c
sam_opts.h	sam_opts.h
sam_utils.c	sam_utils.c
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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