From 977133fd9fb9eaf3a21d22b9a82c4c8e1cf48877 Mon Sep 17 00:00:00 2001 From: Jules Jacobsen Date: Thu, 18 Jan 2024 10:02:11 +0000 Subject: [PATCH] Update VariantContextConverter to replace VCF empty character with an empty string and remove this from VariantFactoryImpl --- .../exomiser/core/genome/VariantContextConverter.java | 2 +- .../exomiser/core/genome/VariantFactoryImpl.java | 1 - 2 files changed, 1 insertion(+), 2 deletions(-) diff --git a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/genome/VariantContextConverter.java b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/genome/VariantContextConverter.java index fdef0772e..1264d7f81 100644 --- a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/genome/VariantContextConverter.java +++ b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/genome/VariantContextConverter.java @@ -69,7 +69,7 @@ public GenomicVariant convertToVariant(@Nonnull VariantContext variantContext, @ logger.debug("Unknown contig for {} unable to convert to variant", variantContext); return null; } - String id = variantContext.getID(); + String id = variantContext.hasID() ? variantContext.getID() : ""; int start = variantContext.getStart(); String ref = getBaseString(variantContext.getReference().getBases()); // Symbolic variants are 'symbolic' in that they have no reported bases and/or contain non-base characters '<>[].' diff --git a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/genome/VariantFactoryImpl.java b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/genome/VariantFactoryImpl.java index a4c85b427..bef66da5c 100644 --- a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/genome/VariantFactoryImpl.java +++ b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/genome/VariantFactoryImpl.java @@ -182,7 +182,6 @@ private VariantEvaluation.Builder createVariantBuilder(VariantContext variantCon .genomeAssembly(genomeAssembly) .variantContext(variantContext) .altAlleleId(altAlleleId) - .id((".".equals(variantContext.getID())) ? "" : variantContext.getID()) .sampleGenotypes(sampleGenotypes) //quality is the only value from the VCF file directly required for analysis .quality(variantContext.getPhredScaledQual());