PyVCF
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Added experimental support for reading bcf files.
I've added support for bcf files by using bcftools. Supports fetching specific regions and iteration. Includes checking that indices exist, and that bcftools is available.
This seems reasonable if it works. It would be good to:
- add tests to prove it works
- fix the merge conflicts with master
- probably remove
which
function - seems like a lot of code to add for something simple. there'll be an exception anyway if it's not executable. - PEP8-ify things a bit (e.g. spaces after commas, use
and not condition
instead ofand condition == False
) - maybe use
os.path.splitext
on the filename further up, to replace multipleendswith
comparisons?