The top level directory is organized in the following directories:
- Code specific to pysam.
The documentation. To build the latest documentation, first install Sphinx and then type:
make -C doc html
- Code and data for testing and benchmarking.
- Source code from htslib shipped with pysam. See
- Source code from samtools shipped with pysam. See
- Source code from bcftools shipped with pysam. See
Importing new versions of htslib and samtools¶
See instructions in
import.py to import the latest
versions of htslib, samtools and bcftools.
Unit tests are in the
tests directory. To run all unit tests,
Most tests use test data from the
Some of these test data files are generated from other files in these
directories, which is done by running
make in each directory:
make -C tests/pysam_data # etc
Alternatively if any
tests/*_data/all.stamp file is not already
present, running the unit tests should generate that directory’s data
To run the benchmarking suite, make sure that pytest-benchmark is installed. To run all benchmarks, type:
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.