From 78eddbca0492428841ee2eda56909f7802bca3c3 Mon Sep 17 00:00:00 2001 From: James Date: Thu, 5 Oct 2023 13:44:33 -0400 Subject: [PATCH] yet more comments --- .../broadinstitute/hellbender/tools/funcotator/Funcotator.java | 1 + 1 file changed, 1 insertion(+) diff --git a/src/main/java/org/broadinstitute/hellbender/tools/funcotator/Funcotator.java b/src/main/java/org/broadinstitute/hellbender/tools/funcotator/Funcotator.java index 630b0a77ee3..12843950a48 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/funcotator/Funcotator.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/funcotator/Funcotator.java @@ -924,6 +924,7 @@ protected void enqueueAndHandleVariant(final VariantContext variant, final Refer final FuncotationMap funcotationMap = funcotatorEngine.createFuncotationMapForVariant(variant, referenceContext, featureContext); // This is necessary because we want to revert the variant contig name change if it was applied in the FuncotatorEngine::getCorrectVariantContextForReference method before outputting the vcf. + // NOTE: this will only revert the variantContext if it was originally changed (only for B37 VCFs) final VariantContext variantContextForOutput = funcotatorEngine.getCorrectVariantContextForOutput(variant); // At this point there is only one transcript ID in the funcotation map if canonical or best effect are selected