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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.
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