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Track unmatched variants in match_variants #8

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smlmbrt opened this issue Aug 22, 2022 · 2 comments · Fixed by #13 or #20
Closed

Track unmatched variants in match_variants #8

smlmbrt opened this issue Aug 22, 2022 · 2 comments · Fixed by #13 or #20
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bug Something isn't working enhancement New feature or request

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@smlmbrt
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smlmbrt commented Aug 22, 2022

Currently we don't have indications of why certain scoring file variants didn't match. We should track/output whether they did match but were excluded because they were:

  • Strand ambiguous (A/T, C/G)
  • Matched to a multi-allelic variant that was excluded
  • Strand flip (that we didn't correct because of the flag)
  • etc.
@smlmbrt smlmbrt added the enhancement New feature or request label Aug 22, 2022
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smlmbrt commented Sep 12, 2022

Only partially addressed by #13, still outstanding:

  • Allow multi-allelic matches to occur instead of removing them from the target. Use a label function to select whether these matches are excluded from the final scoring file. [The labelling of duplicate best_match function we already implemented should handle this case]
  • Allow flipped matches for scoring file lines without better matches. Use a label function to select whether these matches are excluded from the final scoring file.
    • Add information about whether the match has been flipped to the [dataset]_summary.csv file

@smlmbrt smlmbrt added the bug Something isn't working label Sep 20, 2022
@smlmbrt smlmbrt linked a pull request Oct 10, 2022 that will close this issue
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smlmbrt commented Oct 11, 2022

Closed in #26

@smlmbrt smlmbrt closed this as completed Oct 11, 2022
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