File: developer.rst

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=================
Developer's guide
=================

Code organization
=================

The top level directory is organized in the following 
directories:

:file:`pysam`
   Code specific to pysam

:file:`doc`
   The documentation. To build the latest documention type::

       make -C doc html

:file:`tests`
   Code and data for testing and benchmarking

:file:`htslib`
   Source code from htslib_ shipped with pysam. See
   :file:`import.py` about importing.

:file:`samtools`
   Source code from :term:`csamtools` shipped with pysam. See
   :file:`import.py` about importing.

:file:`bcftools`
   Source code from :term:`cbcftools` shipped with pysam. See
   :file:`import.py` about importing.


Importing new versions of htslib and samtools
=============================================

See instructions in :file:`import.py` to import the latest
version of htslib_, samtools_ and bcftools_.

Unit testing
============

Unit tests are in the :file:`tests` directory. To run all unit tests,
run::

   pytest tests

Benchmarking
============

To run the benchmarking suite, make sure that `pytest-benchmark
<https://github.com/ionelmc/pytest-benchmark>`_ is installed. To run
all benchmarks, type::

   pytest tests/*_bench.py

See :ref:`Benchmarking` for more on this topic.

Contributors
============

Please see github for a list of all contributors:

https://github.com/pysam-developers/pysam/graphs/contributors

Many thanks to all contributors for helping in making pysam
useful.