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@danielecook
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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.

@sambrightman
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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?

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2 participants