====== Pysam ======

**Pysam** is a software module available on **Comet**.

===== Pysam overview =====

To access **Pysam** on Comet, run ''module load Pysam''. This will load the //default// version of **Pysam**.

An overview of the module information is shown below (''module -r spider ^Pysam$''):

<code lang=text>
  Pysam:
    Description:
      Pysam is a python module for reading and manipulating Samfiles. It's a lightweight wrapper of the samtools C-API. Pysam also
      includes an interface for tabix.

     Versions:
        Pysam/0.22.0-GCC-12.3.0
        Pysam/0.22.1-GCC-13.3.0

  For detailed information about a specific "Pysam" package (including how to load the modules) use the module's full name.
  Note that names that have a trailing (E) are extensions provided by other modules.
  For example:

     $ module spider Pysam/0.22.1-GCC-13.3.0
</code>

If there are multiple versions of **Pysam** listed, then you can load a //specific// version as follows:
<code lang=bash>
$ module load Pysam/version_string
</code>

You can find the most //up to date information// whilst logged on to Comet by running ''module -r spider ^Pysam$''.

----

===== Pysam Help =====

The module **Pysam** has the following embedded help text (''module help Pysam''):

<code lang=text>Description
===========
Pysam is a python module for reading and manipulating Samfiles.
 It's a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix.

More information
================
 - Homepage: https://github.com/pysam-developers/pysam

</code>

----

===== Pysam Dependencies =====

The //default// version of the module **Pysam** has the following dependencies:

   * GCC/13.3.0
   * Python/3.12.3-GCCcore-13.3.0
   * Python-bundle-PyPI/2024.06-GCCcore-13.3.0
   * ncurses/6.5-GCCcore-13.3.0
   * cURL/8.7.1-GCCcore-13.3.0
   * XZ/5.4.5-GCCcore-13.3.0

----

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