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Make sure we output a full stack trace when we encounter Tribble error messages on VCF header merge.

This commit is contained in:
Matt Hanna 2011-10-27 11:30:04 -04:00
parent 86871bd1e3
commit 41ddc7bce7
1 changed files with 12 additions and 2 deletions
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14
public/java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java
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@ -1,6 +1,7 @@
package org.broadinstitute.sting.gatk.executive; package org.broadinstitute.sting.gatk.executive;
import net.sf.picard.reference.IndexedFastaSequenceFile; import net.sf.picard.reference.IndexedFastaSequenceFile;
import org.broad.tribble.TribbleException;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.gatk.datasources.reads.SAMDataSource; import org.broadinstitute.sting.gatk.datasources.reads.SAMDataSource;
import org.broadinstitute.sting.gatk.datasources.reads.Shard; import org.broadinstitute.sting.gatk.datasources.reads.Shard;
@ -263,8 +264,17 @@ public class HierarchicalMicroScheduler extends MicroScheduler implements Hierar
traverser.waitForComplete(); traverser.waitForComplete();
OutputMergeTask mergeTask = traverser.getOutputMergeTask(); OutputMergeTask mergeTask = traverser.getOutputMergeTask();
if( mergeTask != null ) if( mergeTask != null ) {
mergeTask.merge(); try {
mergeTask.merge();
}
catch(TribbleException ex) {
// Specifically catch Tribble I/O exceptions and rethrow them as Reviewed. We don't expect
// any issues here because we created the Tribble output file mere moments ago and expect it to
// be completely valid.
throw new ReviewedStingException("Unable to merge temporary Tribble output file.",ex);
}
}
} }
long endTime = System.currentTimeMillis(); long endTime = System.currentTimeMillis();