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Editing will fail if strand not set. #92

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yeban opened this issue Jan 7, 2015 · 0 comments
Open
2 tasks

Editing will fail if strand not set. #92

yeban opened this issue Jan 7, 2015 · 0 comments

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@yeban
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yeban commented Jan 7, 2015

I can't imagine unstranded features or why will strandedness be unknown, but since GFF3 spec allows it, we need the ability to deal with annotations for whose strand is not unknown or are unstranded.

  • markNonCanonicalSites and markNonCanonicalTranslationStart/Stop will need to be tolerant to non-stranded features. That is do not error out, nor mark any sites as non-canonical because we can't tell splice donor from acceptor and translation start from translation stop.
  • flipStrand should set positive strand if gene mode is un-stranded. User clicks 'Flip strand', and she has a forward stranded gene model to work with. Flip strand again, the gene model will be reverse stranded. (I think this is the approach taken by Apollo).
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