removing A,R, and G length attributes when ReblockGVCF subsets an allele #8209
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Github actions tests reported job failures from actions build 4195524107
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@ldgauthier can you please suggest a reviewer? Thanks! |
ldgauthier
approved these changes
Feb 28, 2023
| @@ -249,6 +251,15 @@ public void onTraversalStart() { | |||
| } | |||
| } | |||
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| //Allele length and Genotype length annotations need to be subset or removed if alleles are dropped so we need to parse the header for annotation count types | |||
| for(final VCFFormatHeaderLine formatHeaderLine : inputHeader.getFormatHeaderLines()) { | |||
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Occasionally the header is wrong, but it's usually A should be R or vice versa, not const should be A. I think this is fine since we're just using this as a list to remove, but it's something to keep in mind.
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Hmm, in that case I'll add a warning for the logs that at least lists which annotations have been removed for easier debugging in the future.
| final int[] newAnnot = IntStream.range(0, allelesToKeep.size()).map(n -> oldAnnot[allelePermutation.fromIndex(n)]).toArray(); | ||
| final int nonRefIndex = allelesToKeep.indexOf(Allele.NON_REF_ALLELE); | ||
| if (nonRefIndex != -1 && nonRefIndex < newAnnot.length) { | ||
| newAnnot[nonRefIndex] = 0; //we will "lose" coverage here, but otherwise merging NON_REF AD counts with other alleles "creates" reads |
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To be honest, I can't follow my own logic here, but you just copied so you're not to blame.
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Previously if an input gVCF had allele length, reference length, or genotype length annotations in the FORMAT field, reblockGVCF would not remove all of them at sites where an allele was dropped. This makes the output gVCF invalid since the annotation length no longer matches the length described in the header at those sites. This PR fixes up F1R2, F2R1, and AF annotations and removes any other annotations that are not already handled that are defined as A, R, or G length in the header.