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Review existing "read" interfaces as a first step in designing a new one #1

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tfenne opened this issue Jun 28, 2018 · 2 comments
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@tfenne
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tfenne commented Jun 28, 2018

Here are pointers to a few "Read" like interfaces that we might consider when discussing how we want to make a better interface for SAMRecord:

  1. HSJDK's SAMRecord
  2. GATK 4's GATKRead
  3. fgbio's SamRecord trait
  4. @magicDGS's existing PR in htsjdk
  5. pysam's API which largely mirrors htslib's I believe, but has easier to read docs
@magicDGS
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magicDGS commented Jul 3, 2018

Should we start better with a PR implementation and discuss there (similar to your low-level IO PR?)

@magicDGS
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magicDGS commented Jul 6, 2018

Also important to check @tfenne's PR in htsjdk about naming/docs for accessors/mutators.

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