Parse combined AS_QUALapprox values from older reblocked GVCFs properly #6442
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NON_REF but sometimes they get zeros
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@droazen this fix is the same as a bug you caught in another review -- #6079 (comment) Should be an easy review? |
droazen
suggested changes
Feb 7, 2020
| attribute(GATKVCFConstants.AS_RAW_QUAL_APPROX_KEY, goodQualList).make(); | ||
| final VariantContext withNoNonRefValue = new VariantContextBuilder(GATKVariantContextUtils.makeFromAlleles("good", "chr1", 10001, Arrays.asList("A","T", Allele.NON_REF_STRING))). | ||
| attribute(GATKVCFConstants.AS_RAW_QUAL_APPROX_KEY, trickyQualList).make(); | ||
| Assert.assertTrue(AS_QualByDepth.parseQualList(withNonRefValue).size() == withNonRefValue.getAlternateAlleles().size()); |
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assertEquals() would be more appropriate here
| attribute(GATKVCFConstants.AS_RAW_QUAL_APPROX_KEY, trickyQualList).make(); | ||
| Assert.assertTrue(AS_QualByDepth.parseQualList(withNonRefValue).size() == withNonRefValue.getAlternateAlleles().size()); | ||
| Assert.assertTrue(AS_QualByDepth.parseQualList(withNoNonRefValue).size() == withNonRefValue.getAlternateAlleles().size()); | ||
| } |
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Can you also add an assertion that the actual QD value assigned to NON_REF was 0 in the withNoNonRefValue case?
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@droazen back to you |
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@ldgauthier Looks like you have a test failure in |
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@droazen I immediately pushed another commit -- see "Derp" above. Looks green now. |
droazen
approved these changes
Feb 10, 2020
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Sometimes NON_REF gets a zero and sometimes it's empty. This seems isolated to a much older version of ReblockGVCF, but that was what we were running for production pipeline tests.
@droazen I'd like this to go into this week's release