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.
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.