From 6580211c2a37f38a206d9801c80db8b6a251e2d1 Mon Sep 17 00:00:00 2001 From: mmelgar Date: Mon, 6 Jul 2009 18:22:46 +0000 Subject: [PATCH] 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 --- .../walkers/variants/VECDepthOfCoverage.java | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100755 java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VECDepthOfCoverage.java diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VECDepthOfCoverage.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VECDepthOfCoverage.java new file mode 100755 index 000000000..e26c72291 --- /dev/null +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VECDepthOfCoverage.java @@ -0,0 +1,25 @@ +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; + } +}