samtools/samtools

Name: samtools

Owner: samtools

Description: Tools (written in C using htslib) for manipulating next-generation sequencing data

Created: 2012-03-09 02:49:58.0

Updated: 2018-01-15 02:15:37.0

Pushed: 2018-01-17 18:13:07.0

Homepage: http://htslib.org/

Size: 10970

Language: C

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README

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:

header            # Build config.h.in (this may generate a warning about
                  # AC_CONFIG_SUBDIRS - please ignore it).
conf -Wno-syntax  # Generate the configure script
nfigure           # Needed for choosing optional functionality

 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.