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Make the missing targets output never use stdout 

Problem
--------
Diagnose Targets is outputting missing intervals to stdout if the argument -missing is not provided

Solution
--------
Make it NOT default to stdout

[Delivers #50386741]
This commit is contained in:
Mauricio Carneiro 2013-05-22 14:22:54 -04:00
parent 32c33901d7
commit da21924b44
1 changed files with 1 additions and 1 deletions
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2
protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/ThresHolder.java
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@ -116,7 +116,7 @@ final class ThresHolder {
@Argument(fullName = "quality_status_threshold", shortName = "stQ", doc = "The proportion of the loci needed for calling POOR_QUALITY", required = false)
public double qualityStatusThreshold = 0.50;
@Output(fullName = "missing_intervals", shortName = "missing", doc ="Produces a file with the intervals that don't pass filters", required = false)
@Output(fullName = "missing_intervals", shortName = "missing", defaultToStdout = false, doc ="Produces a file with the intervals that don't pass filters", required = false)
public PrintStream missingTargets = null;
public final List<Metric> locusMetricList = new LinkedList<Metric>();