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First version of depth of coverage filter. Right now it takes in a maximum coverage threshold given by the user. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1175 348d0f76-0448-11de-a6fe-93d51630548a
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mmelgar 2009-07-06 18:22:46 +00:00
parent fac7ac5142
commit 6580211c2a
1 changed files with 25 additions and 0 deletions
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25
java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VECDepthOfCoverage.java 100755
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package org.broadinstitute.sting.playground.gatk.walkers.variants;
import org.broadinstitute.sting.gatk.LocusContext;
import org.broadinstitute.sting.gatk.refdata.rodVariants;
/**
* Created by IntelliJ IDEA.
* User: michaelmelgar
* Date: Jun 22, 2009
* Time: 6:04:58 PM
* To change this template use File | Settings | File Templates.
*/
public class VECDepthOfCoverage implements VariantExclusionCriterion {
private int maximum = 200;
public void initialize(String arguments) {
if (arguments != null && !arguments.isEmpty()) {
maximum = Integer.valueOf(arguments);
}
}
public boolean exclude(char ref, LocusContext context, rodVariants variant) {
return context.getReads().size() > maximum;
}
}