From da21924b44342321150d1f05ee9f6850969ffb44 Mon Sep 17 00:00:00 2001 From: Mauricio Carneiro Date: Wed, 22 May 2013 14:22:54 -0400 Subject: [PATCH] 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] --- .../gatk/walkers/diagnostics/diagnosetargets/ThresHolder.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/ThresHolder.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/ThresHolder.java index ebe2192b4..a6cbc1da3 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/ThresHolder.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/ThresHolder.java @@ -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 locusMetricList = new LinkedList();