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Ideas for the next major release #315

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daler opened this issue Dec 27, 2019 · 0 comments
Open

Ideas for the next major release #315

daler opened this issue Dec 27, 2019 · 0 comments

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@daler
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daler commented Dec 27, 2019

Integration with other packages

If pybedtools.pkg_integration = True, then:

  1. Iterating over SAM or BAM yields pysam.AlignedRead objects
  2. Iterating over VCF yields cyvcf2.Variant objects
  3. (?) Iterating over GTF/GTF yields gffutils.Feature objects

Simplified iteration

The IntervalIterator in Cython has historically been problematic. It would be cleaner to re-implement in Python, especially if we're aiming for integration with other packages.

  • Can we reimplement IntervalIterator in pure Python?
  • How much speed does the cbedtool.pyx Cython module gain us in everyday usage?
  • How do we weigh any speed gains against maintenance burden?
  • If we re-implement Interval objects in Python, what is the bottleneck:
    • when iterating over a BedTool object
    • when sending Intervals to stdin

Evaluate MIT license

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