Better error handling for merge LoFreq VCFs

bbimber · bbimber · commit 12a349e9aa6f · 2020-08-21T06:46:15.000-07:00
diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/MergeLoFreqVcfHandler.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/MergeLoFreqVcfHandler.java
@@ -566,7 +566,7 @@ private int getReadDepth(File vcf, Map<String, Integer> contigToOffset, String c
 
                 return Integer.parseInt(line[1]);
             }
-            catch (IOException e)
+            catch (Exception e)
             {
                 ctx.getLogger().error("Error parsing GATK depth: " + vcf.getName() + " / " + gatkDepth.getPath() + " / " + lineNo);
                 throw new PipelineJobException(e);

Original file line number	Diff line number	Diff line change
`@@ -566,7 +566,7 @@ private int getReadDepth(File vcf, Map<String, Integer> contigToOffset, String c`
`566`	`566`
`567`	`567`	`return Integer.parseInt(line[1]);`
`568`	`568`	`}`
`569`		`- catch (IOException e)`
	`569`	`+ catch (Exception e)`
`570`	`570`	`{`
`571`	`571`	`ctx.getLogger().error("Error parsing GATK depth: " + vcf.getName() + " / " + gatkDepth.getPath() + " / " + lineNo);`
`572`	`572`	`throw new PipelineJobException(e);`