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 some extra steps:

aclocal -I.../autoconf-archive/m4   # Cache configure subroutines
autoconf       # 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.

The configure script uses several macros from the autoconf-archive, so you will need to point aclocal at a copy of the archive in order to regenerate the script.

Name		Name	Last commit message	Last commit date
Latest commit History 1,711 Commits
.travis		.travis
examples		examples
misc		misc
test		test
win32		win32
.gitattributes		.gitattributes
.gitignore		.gitignore
.travis.yml		.travis.yml
AUTHORS		AUTHORS
ChangeLog.old		ChangeLog.old
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_decode.c		bam_decode.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_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
errmod.c		errmod.c
errmod.h		errmod.h
faidx.c		faidx.c
install-sh		install-sh
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_opts.c		sam_opts.c
sam_opts.h		sam_opts.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

License

dozy/samtools

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