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Correct rendered range of symbolic VCF alleles #1580

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merged 3 commits into from
Sep 26, 2024
Merged

Correct rendered range of symbolic VCF alleles #1580

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bccc10a
Correct rendered range of symbolic VCF alleles
ctsa Sep 24, 2024
498f31f
Update src/main/java/org/broad/igv/variant/vcf/VCFVariant.java
ctsa Sep 25, 2024
2d5bf6d
Update VCFVariant.java
ctsa Sep 25, 2024
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9 changes: 9 additions & 0 deletions src/main/java/org/broad/igv/variant/vcf/VCFVariant.java
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Original file line number Diff line number Diff line change
Expand Up @@ -385,6 +385,15 @@ private void calcStart() {
if (variantContext.getType() == VariantContext.Type.INDEL || variantContext.getType() == VariantContext.Type.MIXED) {
prefixLength = findCommonPrefixLength();
}

/**
* The VCF spec defines POS as the base preceding the polymorphism for non-ref symbolic alleles.
*
*/
if (variantContext.getType(true) == VariantContext.Type.SYMBOLIC) {
prefixLength = 1;
}

this.start = (variantContext.getStart() - 1) + prefixLength;
}

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