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 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.