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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 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.