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Added experimental support for reading bcf files.

Open danielecook opened this issue 10 years ago • 1 comments

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.

danielecook avatar Oct 19 '14 19:10 danielecook

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 of and condition == False)
  • maybe use os.path.splitext on the filename further up, to replace multiple endswith comparisons?

sambrightman avatar Jan 28 '17 17:01 sambrightman