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.
See instructions in :file:`import.py` to import the latest version of htslib_, samtools_ and bcftools_.
Unit tests are in the :file:`tests` directory. To run all unit tests, run:
pytest tests
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.
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.