[Samtools-devel] New on the block

[Marcus D. S. <md...@um...>]

I didn’t know where to really introduce this, so I figure devel was best. 

SAMtools and pysam are terrific. Hands down, they are what I cut my teeth on. However, we know that doing the things that SAMtools and pysam do in a Windows environment is complicated (if not impossible) for the uninitiated. In making a platform agnostic desktop app, I came right up against this problem. 

To overcome this issue, I stuck to the current specs and made a BAM (and only BAM) file parser written in pure Python from the ground up. The python package, called BAMnostic can perform both serial processing and random access on BAM files. It also preserves much of the pysam API namespaces for easy transition when working in an environment that requires the use of BAMnostic. 

Special care was taken to make sure that BAMnostic will work in any version of Python from version 2.7 onward. Additionally, it has no dependencies, outside of the Python standard library, which makes it fully compatible with all stable versions of PyPy. 

For those interested in playing around with it, or wholly using it in your pipelines, please do. I need all the feedback I can get right now. For those that know Python pretty well or have a spare moment, feel free to code review to your heart’s content. Nonetheless, I hope that BAMnostic can help someone out there.

BAMnostic is available through any of the links associated with this email or at the following locations:
GitHub: https://github.com/betteridiot/bamnostic 
Conda: conda install -c conda-forge bamnostic
PyPI: pip install bamnostic

Documentation can be found at https://bamnostic.readthedocs.io/en/latest/ 

Thank you for your time.

Marcus D. Sherman
DCMB PhD Candidate
Mills Lab
https://betteridiot.tech