Samtools implements various utilities for post-processing alignments in the
SAM, BAM, and CRAM formats, including indexing, variant calling (in conjunction
with bcftools), and a simple alignment viewer.

See INSTALL for building and installation instructions.


Using an optimised zlib library
===============================

Samtools has been minimally tested against both the Intel-optimised and
CloudFlare-optimised zlibs and shown to work.

They can be downloaded from:

    https://github.com/jtkukunas/zlib     # Intel
    https://github.com/cloudflare/zlib    # CloudFlare

Neither Samtools nor HTSlib needs recompiling to use these optimised libraries,
but the LD_LIBRARY_PATH environment variable should be set to a directory
containing the libz.so.1 file.

Benchmarks comparing the various zlibs are available at:

    https://www.snellman.net/blog/archive/2014-08-04-comparison-of-intel-and-cloudflare-zlib-patches.html

It is recommended that you perform your own rigorous tests for an entire
pipeline if you wish to switch to one of the optimised zlib implementations.
