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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
:file:`htslib`
Source code from htslib_ shipped with pysam. See
:file:`setup.py` about importing.
:file:`samtools`
Source code from :term:`csamtools` shipped with pysam. See
:file:`setup.py` about importing.
Importing new versions of htslib and samtools
=============================================
See instructions in :file:`setup.py` to import the latest
version of htslib_ and samtools_.
Unit testing
============
Unit tests are in the :file:`tests` directory. To run all unit tests,
run::
nosetests -s -v tests
Note to use the ``-s/--nocapture`` option to prevent nosetests from
captpuring standard output.
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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