Avoid NPE for PbsvJointCallingHandler

bbimber · bbimber · commit 9beb00548b71 · 2023-01-22T14:18:19.000-08:00
diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/PbsvJointCallingHandler.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/PbsvJointCallingHandler.java
@@ -139,7 +139,7 @@ public void processFilesRemote(List<SequenceOutputFile> inputFiles, JobContext c
                 outputBaseName = outputBaseName.replaceAll(".vcf$", "");
             }
 
-            if (getVariantPipelineJob(ctx.getJob()).isScatterJob())
+            if (getVariantPipelineJob(ctx.getJob()) != null && getVariantPipelineJob(ctx.getJob()).isScatterJob())
             {
                 outputBaseName = outputBaseName + "." + getVariantPipelineJob(ctx.getJob()).getIntervalSetName();
             }
@@ -149,7 +149,7 @@ public void processFilesRemote(List<SequenceOutputFile> inputFiles, JobContext c
             boolean jobCompleted = expectedFinalOutputIdx.exists();  // this would occur if the job died during the cleanup phase
 
             List<File> outputs = new ArrayList<>();
-            if (getVariantPipelineJob(ctx.getJob()).isScatterJob())
+            if (getVariantPipelineJob(ctx.getJob()) != null && getVariantPipelineJob(ctx.getJob()).isScatterJob())
             {
                 for (Interval i : getVariantPipelineJob(ctx.getJob()).getIntervalsForTask())
                 {

Original file line number	Diff line number	Diff line change
`@@ -139,7 +139,7 @@ public void processFilesRemote(List<SequenceOutputFile> inputFiles, JobContext c`
`139`	`139`	`outputBaseName = outputBaseName.replaceAll(".vcf$", "");`
`140`	`140`	`}`
`141`	`141`
`142`		`- if (getVariantPipelineJob(ctx.getJob()).isScatterJob())`
	`142`	`+ if (getVariantPipelineJob(ctx.getJob()) != null && getVariantPipelineJob(ctx.getJob()).isScatterJob())`
`143`	`143`	`{`
`144`	`144`	`outputBaseName = outputBaseName + "." + getVariantPipelineJob(ctx.getJob()).getIntervalSetName();`
`145`	`145`	`}`
`@@ -149,7 +149,7 @@ public void processFilesRemote(List<SequenceOutputFile> inputFiles, JobContext c`
`149`	`149`	`boolean jobCompleted = expectedFinalOutputIdx.exists(); // this would occur if the job died during the cleanup phase`
`150`	`150`
`151`	`151`	`List<File> outputs = new ArrayList<>();`
`152`		`- if (getVariantPipelineJob(ctx.getJob()).isScatterJob())`
	`152`	`+ if (getVariantPipelineJob(ctx.getJob()) != null && getVariantPipelineJob(ctx.getJob()).isScatterJob())`
`153`	`153`	`{`
`154`	`154`	`for (Interval i : getVariantPipelineJob(ctx.getJob()).getIntervalsForTask())`
`155`	`155`	`{`