Fix case where hom-ref "variant" with no data had wrong sized PLs and #7644
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didn't merge with adjacent block
vruano
suggested changes
Jan 27, 2022
| final Genotype longPls = VariantContextTestUtils.makeG("sample1", Allele.NO_CALL, Allele.NO_CALL, 0,0,0,0,0,0); | ||
| final VariantContext lotsOfZeroPls = makeNoDepthVC("lowQualVar", Arrays.asList(LONG_REF, DELETION, Allele.NON_REF_ALLELE), LONG_REF.length(), longPls); | ||
| final VariantContext properlySubset = reblocker.lowQualVariantToGQ0HomRef(lotsOfZeroPls).make(); | ||
| Assert.assertEquals(properlySubset.getGenotype(0).getPL().length, 3); |
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Can you check the content of PL also is correnct? is it all 0s or '.'?
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Assert.assertEquals(...getPL(), new int [] { 0, 0, 0}) may just work.
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It does work, thanks. This is done.
| null, GenotypeAssignmentMethod.BEST_MATCH_TO_ORIGINAL, lowQualVariant.getAttributeAsInt(VCFConstants.DEPTH_KEY, 0), false); //BEST_MATCH to avoid no-calling low qual genotypes | ||
| null, GenotypeAssignmentMethod.BEST_MATCH_TO_ORIGINAL, //BEST_MATCH to avoid no-calling low qual genotypes | ||
| lowQualVariant.getAttributeAsInt(VCFConstants.DEPTH_KEY, 0), | ||
| true); //emitEmptyPLs = true to make sure we always subset |
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Not sure what a true here results into looking at the subsetAllele code. If it is what you need and that behavior from subsetAlleles is stable then I don't a problem with that.
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The alternative is to drop the PLs, which I do not want. I've changed the parameter name to be a little more clear.
vruano
approved these changes
Jan 28, 2022
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didn't merge with adjacent block