Bugfix to handling of indels in lofreq merge

bbimber · bbimber · commit 312eb471e244 · 2020-09-12T21:29:37.000-07:00
diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/MergeLoFreqVcfHandler.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/MergeLoFreqVcfHandler.java
@@ -209,7 +209,8 @@ protected String extractAlleleForPosition(VariantContext vc, Allele a, Logger lo
                 {
                     return Allele.SPAN_DEL.getBaseString();
                 }
-                else if (offset == 0 && a.length() == 1)
+                //simple SNP or insertion
+                else if (offset == 0 && a.length() >= vc.getReference().length())
                 {
                     return _ref.getBaseString().equals(a.getBaseString()) ? null : a.getBaseString();
                 }

Original file line number	Diff line number	Diff line change
`@@ -209,7 +209,8 @@ protected String extractAlleleForPosition(VariantContext vc, Allele a, Logger lo`
`209`	`209`	`{`
`210`	`210`	`return Allele.SPAN_DEL.getBaseString();`
`211`	`211`	`}`
`212`		`- else if (offset == 0 && a.length() == 1)`
	`212`	`+ //simple SNP or insertion`
	`213`	`+ else if (offset == 0 && a.length() >= vc.getReference().length())`
`213`	`214`	`{`
`214`	`215`	`return _ref.getBaseString().equals(a.getBaseString()) ? null : a.getBaseString();`
`215`	`216`	`}`