Tools (written in C using htslib) for manipulating next-generation sequencing data
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valeriuo Fix the short options list, by removing the non-existent `-1`,
and the help message, by adding the `-g` required type.
Latest commit 74ecbcb Aug 15, 2018
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.github/ISSUE_TEMPLATE Add issue templates for bug reports and feature requests. May 4, 2018
.travis Fix travis to use owner/htslib <branch> or samtools/htslib HEAD Mar 16, 2018
examples Update 00README.txt Mar 9, 2015
lz4 Simplify lz4 build Dec 6, 2017
m4 Stop samtools configure from always trying to configure htslib Mar 9, 2017
misc Maintaing stats output format Aug 15, 2018
test Add option to quickcheck to allow unmapped data Aug 14, 2018
win32 * samtools-0.1.5-22 (r432) Aug 1, 2009
.appveyor.yml AppVeyor: remove limitation of develop branch only Dec 5, 2017
.gitattributes Prevent export of .appveyor.yml [minor] Mar 29, 2018
.gitignore Added Windows Mingw/MSYS support. Sep 25, 2017
.travis.yml Fix travis to use owner/htslib <branch> or samtools/htslib HEAD Mar 16, 2018
AUTHORS Remove razip source code and remaining vestiges May 28, 2014
ChangeLog.old Removed SVN ChangeLog; merged my private github Log to ChangeLog.old Mar 9, 2012
INSTALL Additional installation hints for dependencies. Jul 12, 2018
LICENSE Update date range in LICENSE file Jul 5, 2018
Makefile Add missing Makefile dependencies Jul 5, 2018
Makefile.mingw for WIN32 compatibility Jul 7, 2011
NEWS Merge version number bump and NEWS file from master Jul 18, 2018
README Release 1.9 Jul 18, 2018
README.md Added Windows Mingw/MSYS support. Sep 25, 2017
bam.c Fix warnings from adding HTS_RESULT_USED to htslib prototypes. Mar 8, 2016
bam.h Merge version number bump and NEWS file from master Jul 18, 2018
bam2bcf.c HTSlib now provides errmod_cal() etc Apr 25, 2016
bam2bcf.h HTSlib now provides errmod_cal() etc Apr 25, 2016
bam2bcf_indel.c Improvements for C99/XOPEN compliance. Apr 7, 2017
bam2depth.c Fix trivial buffer-read overrun in mpileup / depth. Jul 12, 2018
bam_addrprg.c Make addreplacerg choose output format by file extension Feb 1, 2018
bam_aux.c Add #include <config.h> to all *.c source files [minor] Jan 28, 2016
bam_cat.c Fix samtools cat error message. Jun 22, 2018
bam_color.c Add #include <config.h> to all *.c source files [minor] Jan 28, 2016
bam_endian.h Canonicalise whitespace -- USE -b/-w TO DIFF/BLAME ACROSS THIS COMMIT Aug 1, 2014
bam_flags.c Add #include <config.h> to all *.c source files [minor] Jan 28, 2016
bam_import.c Add #include <config.h> to all *.c source files [minor] Jan 28, 2016
bam_index.c Make samtools idxstats work on SAM and CRAM files. Apr 30, 2018
bam_lpileup.c Add missing Makefile dependencies Jul 5, 2018
bam_lpileup.h Canonicalise whitespace -- USE -b/-w TO DIFF/BLAME ACROSS THIS COMMIT Aug 1, 2014
bam_markdup.c Changed a memory check to catch buffer overflow. Aug 15, 2018
bam_mate.c Check return values in samtools fixmate. Mar 27, 2018
bam_md.c Add quiet mode to calmd Feb 12, 2018
bam_plbuf.c Add #include <config.h> to all *.c source files [minor] Jan 28, 2016
bam_plbuf.h Canonicalise whitespace -- USE -b/-w TO DIFF/BLAME ACROSS THIS COMMIT Aug 1, 2014
bam_plcmd.c Add checks on return value of bam_hdr_write, bam_write1 Jul 30, 2018
bam_quickcheck.c Add option to quickcheck to allow unmapped data Aug 14, 2018
bam_reheader.c Update inputs for `reheader --in-place` docstring Aug 13, 2018
bam_rmdup.c Improved multi-threading support for many more samtools commands. Feb 9, 2017
bam_rmdupse.c Various tidying up and segfault fixes Apr 14, 2016
bam_sort.c Add missing Makefile dependencies Jul 5, 2018
bam_split.c Improved multi-threading support for many more samtools commands. Feb 9, 2017
bam_stat.c Improved multi-threading support for many more samtools commands. Feb 9, 2017
bam_tview.c Improved multi-threading support for many more samtools commands. Feb 9, 2017
bam_tview.h Inverse video mode for tview and also changed some colours. Aug 25, 2015
bam_tview_curses.c Make bam_tview_curses.c deal more gracefully with missing headers Jan 22, 2018
bam_tview_html.c Add #include <config.h> to all *.c source files [minor] Jan 28, 2016
bamshuf.c Add a fast paired collate option. May 3, 2018
bamtk.c Modifies faidx to work on FASTQ and adds fqidx sub-command. Jun 12, 2018
bedcov.c Remove trailing whitespace and fix test.pl perl warning Jun 28, 2018
bedidx.c Update / add bedidx.[ch] copyright boilerplate. Jul 5, 2018
bedidx.h Update / add bedidx.[ch] copyright boilerplate. Jul 5, 2018
config.mk.in Use htslib_static.mk to get static link flags Mar 2, 2017
configure.ac Added Windows Mingw/MSYS support. Sep 25, 2017
cut_target.c Avoid a gcc 7.1 warning. Jan 12, 2018
dict.c Change MD5 calculation to exactly match htslib's CRAM implementation Jan 12, 2018
faidx.c Make /rc the default faidx/fqidx --mark-strand option Jun 28, 2018
install-sh Add configure.ac script Dec 15, 2015
padding.c Remove trailing whitespace and tabs Sep 27, 2017
phase.c Remove the unnecessary argument request. May 18, 2018
sam.c Various tidying up and segfault fixes Apr 14, 2016
sam.h Improvements for C99/XOPEN compliance. Apr 7, 2017
sam_header.c Fix stray spaces [minor] Jan 26, 2018
sam_header.h Canonicalise whitespace -- USE -b/-w TO DIFF/BLAME ACROSS THIS COMMIT Aug 1, 2014
sam_opts.c Improved multi-threading support for many more samtools commands. Feb 9, 2017
sam_opts.h Improved multi-threading support for many more samtools commands. Feb 9, 2017
sam_utils.c Fix --version when built from a Git repository (PR #844) May 22, 2018
sam_view.c Document fastq/fasta default compression level. Aug 14, 2018
sample.c Add #include <config.h> to all *.c source files [minor] Jan 28, 2016
sample.h Canonicalise whitespace -- USE -b/-w TO DIFF/BLAME ACROSS THIS COMMIT Aug 1, 2014
samtools.1 Add option to quickcheck to allow unmapped data Aug 14, 2018
samtools.h Fix --version when built from a Git repository (PR #844) May 22, 2018
stats.c Fix the short options list, by removing the non-existent `-1`, Aug 15, 2018
stats_isize.c Add #include <config.h> to all *.c source files [minor] Jan 28, 2016
stats_isize.h Canonicalise whitespace -- USE -b/-w TO DIFF/BLAME ACROSS THIS COMMIT Aug 1, 2014
tmp_file.c Changed a memory check to catch buffer overflow. Aug 15, 2018
tmp_file.h Changed a memory check to catch buffer overflow. Aug 15, 2018
version.sh Release 1.9 Jul 18, 2018

README.md

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 http://github.com/samtools/

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 extra steps:

autoheader            # Build config.h.in (this may generate a warning about
                      # AC_CONFIG_SUBDIRS - please ignore it).
autoconf -Wno-syntax  # Generate the configure script
./configure           # 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.