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BamTools: Command line toolkit for dealing with BAM files

Overview of package

Package: BamTools
Description: Command line toolkit for dealing with BAM files
For more information: https://github.com/pezmaster31/bamtools
Categories: Genomics
DataFormat
License: OpenSource (MIT)

General Usage

BamTools is a toolkit of command-line utilities for reading, writing, or otherwise manipulating BAM (genome alignment) files.

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

  • $BAMTOOLS_ROOT has been set to the root of the bamtools installation
  • $BAMTOOLS_LIBDIR points to the directory containing the libraries
  • $BAMTOOLS_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$BAMTOOLS_INCDIR

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

  • -L$BAMTOOLS_LIBDIR -Wl,-rpath,$BAMTOOLS_LIBDIR

Available versions by cluster

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

Versions available on the Zaratan cluster

Version Module tags CPU(s) optimized for GPU ready?
2.5.2 2.5.2 icelake, x86_64, zen2 Yes
2.5.1 2.5.1 zen, zen2 Yes