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.
Importing new versions of htslib and samtools¶
See instructions in setup.py
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.
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.