Developer’s guide

Code organization

The top level directory is organized in the following directories:

Code specific to pysam

The documentation. To build the latest documention type:

make -C doc html
Code and data for testing
Source code from htslib shipped with pysam. See about importing.
Source code from csamtools shipped with pysam. See about importing.

Importing new versions of htslib and samtools

See instructions in to import the latest version of htslib and samtools.

Unit testing

Unit tests are in the 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.


Please see github for a list of all contributors:

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