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HTSlib: Library for accessing high-throughput sequencing data formats

Overview of package

Package: HTSlib
Description: Library for accessing high-throughput sequencing data formats
For more information: http://github.com/samtools/htslib
Categories: Genomics
License: OpenSource (MIT/Expat)

General Usage

HTSlib is a C library for accessing common high-throughput sequencing data formats, e.g. SAM, CRAM, and VCF.

In case you need to link against this library in your code, the following environmental variables have been defined:

  • $HTSLIB_ROOT has been set to the root of the htslib installation
  • $HTSLIB_LIBDIR points to the directory containing the libraries
  • $HTSLIB_INCDIR points to the directory containing the header files

You will probably wish to use these by adding the following flags to your compilation command (e.g. to CFLAGS in your Makefile):

  • -I$HTSLIB_INCDIR

and the following flags to your link command (e.g. LDFLAGS in your Makefile):

  • -L$HTSLIB_LIBDIR -Wl,-rpath,$HTSLIB_LIBDIR

This module will add the htsfile and related commands to your PATH.

Available versions by cluster

This section lists the available versions of the package HTSlibon the UMD HPC clusters.

Versions available on the Zaratan cluster

Version Module tags CPU(s) optimized for GPU ready?
1.17 1.17 icelake, x86_64, zen2 Yes
1.14 1.14 zen2 Yes
1.10.2 1.10.2 zen Yes