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Tools (written in C using htslib) for manipulating next-generation sequencing data
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daviesrob Fix invalid SAM headers
For the new HTSlib header parser, which insists on @sq lines having
an LN: tag.
Latest commit cb6b3b5 Jul 15, 2019
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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
doc Add a little more documentation Jul 16, 2019
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 Fix plot-bamstats quality heatmap on newer gnuplot Jun 27, 2019
test Fix invalid SAM headers Jul 16, 2019
win32 * samtools-0.1.5-22 (r432) Aug 1, 2009
.appveyor.yml Show commit information after cloning. Feb 21, 2019
.gitattributes Prevent export of .appveyor.yml [minor] Mar 29, 2018
.gitignore Added Windows Mingw/MSYS support. Sep 25, 2017
.travis.yml Fixed travis build so address sanitizer build is optimised, as advert… Jul 3, 2019
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 Happy New Year Jan 1, 2019
Makefile Split fasta/fastq from view into its own source file. May 8, 2019
Makefile.mingw for WIN32 compatibility Jul 7, 2011
NEWS NEWS update Jul 9, 2019
README Release 1.9 Jul 18, 2018
README.md Download and status buttons Oct 17, 2018
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 Free memory when failing to set CRAM options Jun 10, 2019
bam_addrprg.c Minor fixes and rebase. Jul 3, 2019
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_fastq.c Remove need to specify index files with fastq -i (Casava) option Jul 9, 2019
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 Minor fixes and rebase. Jul 3, 2019
bam_mate.c Check return values in samtools fixmate. Mar 27, 2018
bam_md.c Change reference letters to upper case when creating the MD tag. Nov 29, 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 option `--output-sep` to set the separator character for tag lists. Jul 12, 2019
bam_quickcheck.c Add option to quickcheck to allow unmapped data Aug 14, 2018
bam_reheader.c Allow the header to be modified by an external program, then read back. Mar 7, 2019
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 Minor fixes and rebase. Jul 3, 2019
bam_split.c Add global --write-index option. Jul 3, 2019
bam_stat.c Improved multi-threading support for many more samtools commands. Feb 9, 2017
bam_tview.c Minor whitespace / formatting fixes. Jan 21, 2019
bam_tview.h Add support for customize index file locations with -X flag. Jan 21, 2019
bam_tview_curses.c Use a consistent formatting style. May 8, 2019
bam_tview_html.c Add support for customize index file locations with -X flag. Jan 21, 2019
bamshuf.c Add a fast paired collate option. May 3, 2018
bamtk.c Happy New Year Jan 1, 2019
bedcov.c Check for gzopen() failure and print error messages Feb 20, 2019
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 Fix incorrect macro definition on Windows Oct 1, 2018
cut_target.c Avoid a gcc 7.1 warning. Jan 12, 2018
dict.c Fixed very minor memory leaks. Aug 30, 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 Add global --write-index option. Jul 3, 2019
phase.c Check for gzopen() failure and print error messages Feb 20, 2019
sam.c Various tidying up and segfault fixes Apr 14, 2016
sam.h Minor whitespace / formatting fixes. Jan 21, 2019
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 Minor fixes and rebase. Jul 3, 2019
sam_opts.h Add global --write-index option. Jul 3, 2019
sam_utils.c Allow index name to be set in auto_index() using ##idx## delimiter Jul 3, 2019
sam_view.c Minor fixes and rebase. Jul 3, 2019
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.h Add global --write-index option. Jul 3, 2019
stats.c Fix proper float division. Apr 30, 2019
stats_isize.c More allocation checks for stats. Nov 23, 2018
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

Build Status Build status Github All Releases

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.

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