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datum set incorrectly on n. variants #342

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reece opened this issue Jul 28, 2016 · 2 comments
Closed

datum set incorrectly on n. variants #342

reece opened this issue Jul 28, 2016 · 2 comments
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@reece
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reece commented Jul 28, 2016

Originally reported by: Reece Hart (Bitbucket: reece, GitHub: reece)


The datum is set to CDS_START for n. variants.

>>> v = hp.parse_hgvs_variant("NM_006158.3:n.10_12del")
>>> v.posedit.pos.start, v.posedit.pos.end
(BaseOffsetPosition(base=10, offset=0, datum=1, uncertain=False), BaseOffsetPosition(base=12, offset=0, datum=1, uncertain=False))

When projecting n. variants, the positions are correctly assumed to be relative to SEQ_START and datum is ignored. So, there's no functional bug as is.

Proposed changes:

  • Update the grammar. This is the ultimate source of incorrectly setting the datum (specifically, the def_cn_pos rule). As a consequence, all dependent "cn" rules will need to be decomposed to distinct c and n rules.
  • Add (more) assertions in mapping code to validate datum.

@reece
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reece commented Sep 15, 2016

Original comment by Reece Hart (Bitbucket: reece, GitHub: reece):


Related to #330. Patch submitted in pull request #42.

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reece commented Sep 15, 2016

Original comment by Reece Hart (Bitbucket: reece, GitHub: reece):


fixes #258, #330, #342: ensure that start and end datums are compatible

@reece reece added major bug Something isn't working labels Mar 9, 2017
@reece reece added this to the 0.5.0 milestone Mar 9, 2017
@reece reece closed this as completed Mar 9, 2017
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