Fix NPE

bbimber · bbimber · commit 861ebaddc72a · 2021-05-22T07:58:15.000-07:00
diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/LofreqAnalysis.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/LofreqAnalysis.java
@@ -423,7 +423,7 @@ public Output performAnalysisPerSampleRemote(Readset rs, File inputBam, Referenc
 
         boolean runPindel = getProvider().getParameterByName("runPindel").extractValue(getPipelineCtx().getJob(), getProvider(), getStepIdx(), Boolean.class, false);
 
-        List<VariantContext> pindelConsensusVariants = null;
+        List<VariantContext> pindelConsensusVariants = new ArrayList<>();
         int totalPindelConsensusVariants = 0;
         if (runPindel)
         {

Original file line number	Diff line number	Diff line change
`@@ -423,7 +423,7 @@ public Output performAnalysisPerSampleRemote(Readset rs, File inputBam, Referenc`
`423`	`423`
`424`	`424`	`boolean runPindel = getProvider().getParameterByName("runPindel").extractValue(getPipelineCtx().getJob(), getProvider(), getStepIdx(), Boolean.class, false);`
`425`	`425`
`426`		`- List<VariantContext> pindelConsensusVariants = null;`
	`426`	`+ List<VariantContext> pindelConsensusVariants = new ArrayList<>();`
`427`	`427`	`int totalPindelConsensusVariants = 0;`
`428`	`428`	`if (runPindel)`
`429`	`429`	`{`