From 5bbad75402424c80789aef5496ea5004c5d26c93 Mon Sep 17 00:00:00 2001 From: Mauricio Carneiro Date: Fri, 20 Sep 2013 18:54:01 -0400 Subject: [PATCH] Changing max coverage threshold Because Integer.maxValue is not unit testable --- .../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 c330b3f02..b088951e5 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 @@ -77,7 +77,7 @@ final class ThresHolder { * If at any locus, a sample has more coverage than this, it will be reported as EXCESSIVE_COVERAGE */ @Argument(fullName = "maximum_coverage", shortName = "max", doc = "The maximum allowable coverage, used for calling EXCESSIVE_COVERAGE", required = false) - public int maximumCoverage = Integer.MAX_VALUE; + public int maximumCoverage = Integer.MAX_VALUE / 2; /** * If any sample has a paired read whose distance between alignment starts (between the pairs) is greater than this, it will be reported as BAD_MATE