Fixed Funcotator VCF output renderer to keep B37 contig names in the VCF output file #8539
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jonn-smith
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Oct 4, 2023
src/main/java/org/broadinstitute/hellbender/tools/funcotator/FuncotatorEngine.java
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droazen
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Oct 4, 2023
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@jamesemery Looks reasonable, but I'm not sure we have adequate test coverage on the new code
src/main/java/org/broadinstitute/hellbender/tools/funcotator/Funcotator.java
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src/main/java/org/broadinstitute/hellbender/tools/funcotator/FuncotatorEngine.java
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@droazen back to you |
droazen
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Oct 5, 2023
| @@ -924,7 +923,10 @@ protected void enqueueAndHandleVariant(final VariantContext variant, final Refer | |||
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| final FuncotationMap funcotationMap = funcotatorEngine.createFuncotationMapForVariant(variant, referenceContext, featureContext); | |||
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| // 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. | |||
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This comment is still misleading -- can you make it clear that we don't always want to revert the variant contig name change, only in the very specific case where the input is b37 and the reference is hg19?
droazen
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Oct 5, 2023
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… names on output for B37 aligned files (#8539)
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Fixes a longstanding issue that resulted in mismatching sequence dictionary/vcf lines for B37 data provided to funcotator.