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Don't crash if cds file is not provided 

CDS file should be optional.
This commit is contained in:
Mauricio Carneiro 2013-06-10 13:42:00 -04:00
parent a95fbd48e5
commit c84f0deb1d
1 changed files with 3 additions and 2 deletions
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3
protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/missing/QualifyMissingIntervals.java
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@ -117,7 +117,7 @@ public final class QualifyMissingIntervals extends LocusWalker<Metrics, Metrics>
public File targetsFile; public File targetsFile;
@Argument(shortName = "cds", required = false) @Argument(shortName = "cds", required = false)
public File cdsFile; public File cdsFile = null;
GATKReport simpleReport; GATKReport simpleReport;
GenomeLocSortedSet target; GenomeLocSortedSet target;
@ -133,6 +133,7 @@ public final class QualifyMissingIntervals extends LocusWalker<Metrics, Metrics>
target = new GenomeLocSortedSet(parser); target = new GenomeLocSortedSet(parser);
cds = new GenomeLocSortedSet(parser); cds = new GenomeLocSortedSet(parser);
parseFile(targetsFile, target, parser); parseFile(targetsFile, target, parser);
if (cdsFile != null)
parseFile(cdsFile, cds, parser); parseFile(cdsFile, cds, parser);
} }