ReblockGVCFs cleanup #8411
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ReblockGVCFs cleanup #8411
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ldgauthier
approved these changes
Jul 14, 2023
| * @param vc variant context to remove format annotations from | ||
| * @return variant context with format annotations removed from genotype | ||
| */ | ||
| private VariantContext vcFormatAnnotationsRemoved(final VariantContext vc) { |
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The grammar of this method name feels weird. Like usually they're verb phrases. I would prefer "removeVCFormatAnnotations"
| @@ -317,7 +325,27 @@ protected void createAnnotationEngine() { | |||
| // get VariantContexts from input gVCFs and regenotype | |||
| @Override | |||
| public void apply(VariantContext variant, ReadsContext reads, ReferenceContext ref, FeatureContext features) { | |||
| regenotypeVC(variant); | |||
| if (!variant.hasAllele(Allele.NON_REF_ALLELE)) { | |||
| throw new GATKException("Variant Context at " + variant.getContig() + ":" + variant.getStart() + " does not contain a <NON-REF> allele. This tool is only intended for use with GVCFs."); | |||
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I would use a UserException instead -- I think it's a subclass
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Adds argument to remove FORMAT level annotations from every genotype in the GVCF (for example, for removing the G-length PRI annotation in dragen GVCFs).
Also adds check to make sure the input VCF is a GVCF rather than a single sample VCF.