Refactoring a confusing method in GATKVariantContextUtils #8690
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baking a null check into isInformative since it's always used with the check separating all cases out and reducing nesting of ifs
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@jamesemery @droazen I found that method pretty confusing so I did som rearrangments. The method I extracted probably needs a new name. |
lbergelson
commented
Feb 13, 2024
| final GenotypeAssignmentMethod assignmentMethod = GATKVariantContextUtils.isInformative(genotypeLikelihoods) | ||
| ? GenotypeAssignmentMethod.USE_PLS_TO_ASSIGN | ||
| : GenotypeAssignmentMethod.SET_TO_NO_CALL; | ||
| GATKVariantContextUtils.makeGenotypeCall(g.getPloidy(), gb, assignmentMethod, genotypeLikelihoods, allelesToUse, null); |
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Make it clear here that the only difference here is the assignment method.
lbergelson
commented
Feb 13, 2024
| @@ -308,66 +308,71 @@ public static void makeGenotypeCall(final int ploidy, | |||
| final List<Allele> allelesToUse, | |||
| final List<Allele> originalGT, | |||
| final GenotypePriorCalculator gpc) { | |||
| if(originalGT == null && assignmentMethod == GenotypeAssignmentMethod.BEST_MATCH_TO_ORIGINAL) { | |||
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I moved this special case down into the BEST_MATCH_TO_ORIGINAL
lbergelson
commented
Feb 13, 2024
| gb.alleles(Collections.nCopies(ploidy, ref)); | ||
| gb.PL(new int[genotypeLikelihoods.length]).log10PError(0); | ||
| } | ||
| case USE_PLS_TO_ASSIGN -> { |
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I separated these PREFER_PLS and USE_PLS_TO_ASSIGN so it's clear where they're different and pulled out the shared setUsingPls. That could probably use a better name.
lbergelson
commented
Feb 13, 2024
| } | ||
| case USE_POSTERIORS_ANNOTATION, DO_NOT_ASSIGN_GENOTYPES-> { } // do nothing in these cases |
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The case DO_NOT_ASSIGN_GENOTYPES previously just fell through, now it's at least listed.
lbergelson
commented
Feb 13, 2024
| } | ||
| } | ||
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| private static void setUsingPls(final int ploidy, final GenotypeBuilder gb, final double[] genotypeLikelihoods, final List<Allele> allelesToUse) { |
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baking a null check into isInformative since it's always used with the check
separating all cases out and reducing nesting of ifs