From 2e2a4b9565fc0713479a0f86a41ccf6a75b2201e Mon Sep 17 00:00:00 2001 From: James Date: Thu, 5 Oct 2023 10:18:49 -0400 Subject: [PATCH] responding to comments --- .../broadinstitute/hellbender/tools/funcotator/Funcotator.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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 577463ed562..630b0a77ee3 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/funcotator/Funcotator.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/funcotator/Funcotator.java @@ -923,7 +923,7 @@ 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 namechange if it was applied in the VariantWalkerBase::apply method before output. + // 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. 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