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Catch HGVSInvalidIntervalError within guess-plausible-variant #605

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merged 1 commit into from Jul 21, 2020

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jtratner
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e.g., this dummy deletion was failing ATM:c.8816_8817del with an HGVSInvalidIntervalError. Otherwise it did work :) I think fair to skip it because you do recover other valid variants:

In [99]:  pv = list(generate_plausible_variants(hdp, hv, hp.parse_hgvs_variant('ATM:c.8816_8817del')))
DEBUG:__main__:generate_plausible_variants(ATM:c.8816_8817del)
DEBUG:__main__:  NM_001351835.1:c.8816_8817del: failed: HGVSInvalidIntervalError: c.8816 coordinate is out of bounds
DEBUG:hgvs.variantmapper:Replaced reference sequence in NM_001351834.1:c.8816_8817del with GA
DEBUG:__main__:  NM_001351834.1:c.8816_8817del: validated
DEBUG:__main__:  NM_001351836.1:c.8816_8817del: failed: HGVSInvalidIntervalError: c.8816 coordinate is out of bounds
DEBUG:__main__:  NM_000051.3:c.8816_8817del: validated

e.g., this dummy deletion was failing `ATM:c.8816_8817del` with an HGVSInvalidIntervalError
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coveralls commented Jul 21, 2020

Pull Request Test Coverage Report for Build 346

  • 0 of 0 changed or added relevant lines in 0 files are covered.
  • No unchanged relevant lines lost coverage.
  • Overall coverage remained the same at 92.4%

Totals Coverage Status
Change from base Build 345: 0.0%
Covered Lines: 2164
Relevant Lines: 2342

💛 - Coveralls

@reece
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reece commented Jul 21, 2020

Agreed. Thanks for the PR!

@reece reece merged commit 15c3937 into biocommons:master Jul 21, 2020
@jtratner jtratner deleted the patch-1 branch July 22, 2020 22:18
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Thanks @reece :)

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3 participants