Update VariantContextConverter to replace VCF empty character with an…

… empty string and remove this from VariantFactoryImpl
exomiser · Jan 18, 2024 · 977133f · 977133f
1 parent 7ffa16d
commit 977133f
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Showing 2 changed files with 1 addition and 2 deletions.
diff --git a/...ore/src/main/java/org/monarchinitiative/exomiser/core/genome/VariantContextConverter.java b/...ore/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/...ser-core/src/main/java/org/monarchinitiative/exomiser/core/genome/VariantFactoryImpl.java b/...ser-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());