Update src/main/java/org/broad/igv/variant/vcf/VCFVariant.java

ctsa · lbergelson · web-flow · commit 498f31f9b9f8 · 2024-09-25T10:11:48.000-07:00
Co-authored-by: Louis Bergelson &lt;louisb@broadinstitute.org&gt;
diff --git a/src/main/java/org/broad/igv/variant/vcf/VCFVariant.java b/src/main/java/org/broad/igv/variant/vcf/VCFVariant.java
@@ -392,7 +392,7 @@ private void calcStart() {
          * https://github.com/samtools/hts-specs/blob/4cde0e235b4e4cfbd67a0c3a38abea611d56d256/VCFv4.1.tex#L165
          *
          */
-        if (variantContext.getType() == VariantContext.Type.SYMBOLIC) {
+        if (variantContext.getType(true) == VariantContext.Type.SYMBOLIC) {
             prefixLength = 1;
         }
 

Original file line number	Diff line number	Diff line change
`@@ -392,7 +392,7 @@ private void calcStart() {`
`392`	`392`	`* https://github.com/samtools/hts-specs/blob/4cde0e235b4e4cfbd67a0c3a38abea611d56d256/VCFv4.1.tex#L165`
`393`	`393`	`*`
`394`	`394`	`*/`
`395`		`- if (variantContext.getType() == VariantContext.Type.SYMBOLIC) {`
	`395`	`+ if (variantContext.getType(true) == VariantContext.Type.SYMBOLIC) {`
`396`	`396`	`prefixLength = 1;`
`397`	`397`	`}`
`398`	`398`