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Make coverage threshold in FindCoveredIntervals a command-line argument

This commit is contained in:
Eric Banks 2012-08-08 21:44:24 -04:00
parent 0a2a646a52
commit 35cec8530c
1 changed files with 5 additions and 2 deletions
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7
public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/FindCoveredIntervals.java
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@ -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<GenomeLoc, Long> {
@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<GenomeLoc, Long> {
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));
}