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.

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

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

pytest tests

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.

Please see github for a list of all contributors:

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