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Pysam
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Pysam is a python module for reading and manipulating files in the
SAM/BAM format. The SAM/BAM format is a way to store efficiently large
numbers of alignments (`Li 2009`_), such as those routinely created by
next-generation sequencing methods.

Pysam is a lightweight wrapper of the samtools_ C-API. Pysam also
includes an interface for tabix_.

If you are using the conda packaging manager (e.g. miniconda or anaconda),
you can install pysam from the `bioconda channel <https://bioconda.github.io/>`_::

   conda config --add channels defaults
   conda config --add channels conda-forge
   conda config --add channels bioconda
   conda install pysam

Installation through bioconda is the recommended way to install pysam
as it resolves non-python dependencies and uses pre-configured
compilation options. Especially for OS X this will potentially save a
lot of trouble.

The current version of pysam wraps 3rd-party code from htslib-1.9, samtools-1.9, and bcftools-1.9.

Pysam is available through `pypi
<https://pypi.python.org/pypi/pysam>`_. To install, type::

   pip install pysam

Pysam documentation is available
`here <http://pysam.readthedocs.org/en/latest/>`_

Questions and comments are very welcome and should be sent to the
`pysam user group <http://groups.google.com/group/pysam-user-group>`_

.. _samtools: http://samtools.sourceforge.net/
.. _tabix: http://samtools.sourceforge.net/tabix.shtml
.. _Li 2009: http://www.ncbi.nlm.nih.gov/pubmed/19505943

.. |build-status| image:: https://travis-ci.org/pysam-developers/pysam.svg
    :alt: build status
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    :target: https://travis-ci.org/pysam-developers/pysam

.. |docs| image:: https://readthedocs.org/projects/pysam/badge/?version=latest
    :alt: Documentation Status
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    :target: https://pysam.readthedocs.org/en/latest/?badge=latest
