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Design codec interface #30

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magicDGS opened this issue Oct 27, 2018 · 0 comments
Open

Design codec interface #30

magicDGS opened this issue Oct 27, 2018 · 0 comments
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Module:Core Priority:Normal Type:API

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@magicDGS
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Should support:

  • Read/Write (e.g., tribble codecs should also write, see Tribble writing support htsjdk#822)
  • Both binary/text formats with the same public API
  • Versioning, to allow easier development of new versions of the hts-specs (e.g., VCF/BCF)

Would be nice:

  • Separate indexing from the codec. Currently in htsjdk2 there are methods to retrieve the tabix-indexing information
  • Shared between every locatable record (SAM/BAM/CRAM, VCF/BCF, tribble)
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@magicDGS