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 and benchmarking
htslib
Source code from htslib shipped with pysam. See import.py about importing.
samtools
Source code from csamtools shipped with pysam. See import.py about importing.
bcftools
Source code from cbcftools shipped with pysam. See import.py about importing.

Importing new versions of htslib and samtools

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

Unit testing

Unit tests are in the tests directory. To run all unit tests, run:

pytest tests

Benchmarking

To run the benchmarking suite, make sure that pytest-benchmark is installed. To run all benchmarks, type:

pytest tests/*_bench.py

See Benchmarking for more on this topic.

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.