From 74639463b948c660f232fd53cf6728881ad717b1 Mon Sep 17 00:00:00 2001 From: Mauricio Carneiro Date: Thu, 19 Sep 2013 23:07:20 -0400 Subject: [PATCH] Updating excessive coverage default parameter most people don't care about excessive coverage (unless you're very particular about your analysis). Therefore the best possible default value for this is Integer.maxValue so it doesn't get in the way. Itemized Changes: * change maximumCoverage threshold to Integer.maxValue [delivers #57353620] --- .../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 a6cbc1da3..c330b3f02 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 = 700; + public int maximumCoverage = Integer.MAX_VALUE; /** * 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