Fixed a bug where force calling alleles were lost upon trimming by placing allele injection after trimming #7679
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…acing allele injection after trimming
davidbenjamin
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@ldgauthier The Travis failures were unrelated and went away after rebasing. |
ldgauthier
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Mar 8, 2022
| @@ -599,6 +599,11 @@ public ActivityProfileState isActive( final AlignmentContext context, final Refe | |||
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| final SortedSet<VariantContext> allVariationEvents = untrimmedAssemblyResult.getVariationEvents(hcArgs.maxMnpDistance); | |||
| for (final VariantContext given : givenAlleles) { | |||
| if (allVariationEvents.stream().noneMatch(vc -> vc.getStart() == given.getStart() && vc.getAlternateAllele(0).basesMatch(given.getAlternateAllele(0)))) { | |||
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These will always be trimmed right? (And always biallelic?) Because they're each for a single haplotype? If you agree, then let's add a comment for posterity.
| ReadThreadingAssembler.addAssembledVariantsToEventMapOutput(untrimmedAssemblyResult, assembledEventMapVariants, MTAC.maxMnpDistance, assembledEventMapVcfOutputWriter); | ||
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| final SortedSet<VariantContext> allVariationEvents = untrimmedAssemblyResult.getVariationEvents(MTAC.maxMnpDistance); | ||
| for (final VariantContext given : givenAlleles) { |
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I don't love the duplication here, but there's not enough to merit refactoring.
| * @param altAllele new allele, the bases of which replace those of refAllele | ||
| * @param insertLocation location in the genome at which the new allele starts | ||
| * | ||
| * Example: suppose this haplotype starts at position 100 on its contig and has bases ACCGTTATATCG and we wish to |
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Thanks for this -- very clear!
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Closes #7672.
@ldgauthier This is the bug fix for Sarah Calvo. The allele was lost when trimming caused its haplotype to start with a deletion. The solution is to inject force-calling alleles after trimming. Are you able to review?