Bugfix to lofreq VCF merge

bbimber · bbimber · commit 0dc5a73d0220 · 2020-07-21T10:57:27.000-07:00
diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/MergeLoFreqVcfHandler.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/MergeLoFreqVcfHandler.java
@@ -156,7 +156,7 @@ public boolean isMergedRef()
 
             protected Allele extractAlleleForPosition(VariantContext vc, Allele a, Logger log)
             {
-                int offset = vc.getStart() - _start;
+                int offset = _start - vc.getStart();
                 if (offset < 0)
                 {
                     log.error("Site located after vc start: " + _start);

Original file line number	Diff line number	Diff line change
`@@ -156,7 +156,7 @@ public boolean isMergedRef()`
`156`	`156`
`157`	`157`	`protected Allele extractAlleleForPosition(VariantContext vc, Allele a, Logger log)`
`158`	`158`	`{`
`159`		`- int offset = vc.getStart() - _start;`
	`159`	`+ int offset = _start - vc.getStart();`
`160`	`160`	`if (offset < 0)`
`161`	`161`	`{`
`162`	`162`	`log.error("Site located after vc start: " + _start);`