Improve pacbio error checking

bbimber · bbimber · commit 0e124f9ea131 · 2022-10-20T21:00:33.000-07:00
diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/PbsvJointCallingHandler.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/PbsvJointCallingHandler.java
@@ -237,10 +237,14 @@ private File runPbsvCall(JobContext ctx, List<File> inputs, ReferenceGenome geno
                     {
                         ctx.getLogger().info("Sample is missing contig: " + contig + ", skipping: " + s.getPath());
                     }
-                    else
+                    else if ("1".equals(ret))
                     {
                         samplesToUse.add(s);
                     }
+                    else
+                    {
+                        throw new PipelineJobException("Unknown output: " + ret);
+                    }
                 }
             }
             else

Original file line number	Diff line number	Diff line change
`@@ -237,10 +237,14 @@ private File runPbsvCall(JobContext ctx, List<File> inputs, ReferenceGenome geno`
`237`	`237`	`{`
`238`	`238`	`ctx.getLogger().info("Sample is missing contig: " + contig + ", skipping: " + s.getPath());`
`239`	`239`	`}`
`240`		`- else`
	`240`	`+ else if ("1".equals(ret))`
`241`	`241`	`{`
`242`	`242`	`samplesToUse.add(s);`
`243`	`243`	`}`
	`244`	`+ else`
	`245`	`+ {`
	`246`	`+ throw new PipelineJobException("Unknown output: " + ret);`
	`247`	`+ }`
`244`	`248`	`}`
`245`	`249`	`}`
`246`	`250`	`else`