Bugfix LoFreq variant import

bbimber · bbimber · commit cec2e5a88520 · 2021-03-15T16:42:48.000-07:00
diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/LofreqAnalysis.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/LofreqAnalysis.java
@@ -926,7 +926,7 @@ private void importNtSnps(AnalysisModel model, File inputBam, File outDir) throw
 
                 if (vc.isFiltered())
                 {
-                    return;
+                    continue;
                 }
 
                 double pct = vc.getAttributeAsDouble("AF", 0.0);

Original file line number	Diff line number	Diff line change
`@@ -926,7 +926,7 @@ private void importNtSnps(AnalysisModel model, File inputBam, File outDir) throw`
`926`	`926`
`927`	`927`	`if (vc.isFiltered())`
`928`	`928`	`{`
`929`		`- return;`
	`929`	`+ continue;`
`930`	`930`	`}`
`931`	`931`
`932`	`932`	`double pct = vc.getAttributeAsDouble("AF", 0.0);`