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@edawson
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@edawson edawson commented Feb 17, 2016

I've updated a few of the tests in the test suite to match the latest GFA spec. The previous md5sum values used a malformed header that looked like H HVN:Z:1.0; it should (and now does) look like H VN:Z:1.0.

The new parser also:

  • forces lexicographic sort
  • sorts output by sequence elements
  • allows comments, alignments and unaligned regions
  • can parse both paths with ranks and paths without ranks
  • makes adding a line type very easy.
  • parses header lines properly
  • parses extra fields in sequence elements.

@ekg
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ekg commented Feb 19, 2016

I need to merge this ASAP, before it gets stale. However, I can't do it today.

EDIT: I'm just going for it. Cheers.

At the hackathon in Sendai we need to get a binary distributed, so I'm going to make a release (v1.4) and then a point release including this.

ekg added a commit that referenced this pull request Feb 19, 2016
Incorporate new GFA parser + updated GFA spec
@ekg ekg merged commit 0acdf4a into vgteam:master Feb 19, 2016
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2 participants