From 35cec8530c302d0ad1b8e13e569041c9df899b71 Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Wed, 8 Aug 2012 21:44:24 -0400 Subject: [PATCH] Make coverage threshold in FindCoveredIntervals a command-line argument --- .../walkers/diagnostics/targets/FindCoveredIntervals.java | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/FindCoveredIntervals.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/FindCoveredIntervals.java index 0c856c6df..23e4d5ae0 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/FindCoveredIntervals.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/FindCoveredIntervals.java @@ -24,6 +24,7 @@ package org.broadinstitute.sting.gatk.walkers.diagnostics.targets; +import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.gatk.CommandLineGATK; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; @@ -46,6 +47,9 @@ public class FindCoveredIntervals extends ActiveRegionWalker { @Output(required = true) private PrintStream out; + @Argument(fullName = "coverage_threshold", shortName = "cov", doc = "The minimum allowable coverage to be considered covered", required = false) + private int coverageThreshold = 20; + @Override // Look to see if the region has sufficient coverage public ActivityProfileResult isActive(final RefMetaDataTracker tracker, final ReferenceContext ref, final AlignmentContext context) { @@ -53,8 +57,7 @@ public class FindCoveredIntervals extends ActiveRegionWalker { int depth = ThresHolder.DEFAULTS.getFilteredCoverage(context.getBasePileup()); // note the linear probability scale - int coverageThreshold = 20; - return new ActivityProfileResult(Math.min((double) depth / coverageThreshold, 1)); + return new ActivityProfileResult(Math.min(depth / coverageThreshold, 1)); }