Developer’s guide¶

Code organization¶

The top level directory is organized in the following directories:

pysam

Code specific to pysam

doc

The documentation. To build the latest documention type:

make -C doc html

tests

Code and data for testing

htslib

Source code from htslib shipped with pysam. See setup.py about importing.

samtools

Source code from csamtools shipped with pysam. See setup.py about importing.

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

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.