Fixed REF for DEL SV.

PolinaBevad · PolinaBevad · commit d9d3e56e7fc5 · 2019-05-27T14:30:03.000+03:00
diff --git a/src/main/java/com/astrazeneca/vardict/modules/ToVarsBuilder.java b/src/main/java/com/astrazeneca/vardict/modules/ToVarsBuilder.java
@@ -746,7 +746,7 @@ else if (deletionLength < instance().conf.SVMINLEN) {
                         startPosition++;
                     }
 
-                    if (varallele.equals("<DEL>") && refallele.length() > 1) {
+                    if (varallele.equals("<DEL>") && refallele.length() >= 1) {
                         refallele = ref.containsKey(startPosition) ? ref.get(startPosition).toString() : "";
                         if (refCoverage.containsKey(startPosition - 1)) {
                             totalPosCoverage = refCoverage.get(startPosition - 1);

Original file line number	Diff line number	Diff line change
`@@ -746,7 +746,7 @@ else if (deletionLength < instance().conf.SVMINLEN) {`
`746`	`746`	`startPosition++;`
`747`	`747`	`}`
`748`	`748`
`749`		`- if (varallele.equals("<DEL>") && refallele.length() > 1) {`
	`749`	`+ if (varallele.equals("<DEL>") && refallele.length() >= 1) {`
`750`	`750`	`refallele = ref.containsKey(startPosition) ? ref.get(startPosition).toString() : "";`
`751`	`751`	`if (refCoverage.containsKey(startPosition - 1)) {`
`752`	`752`	`totalPosCoverage = refCoverage.get(startPosition - 1);`