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walk by reference 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1323 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kcibul 2009-07-27 20:21:04 +00:00
parent 089ae85be7
commit 1d6d99ed9c
1 changed files with 3 additions and 0 deletions
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3
java/src/org/broadinstitute/sting/playground/gatk/walkers/HybSelPerformanceWalker.java
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@ -2,6 +2,8 @@ package org.broadinstitute.sting.playground.gatk.walkers;
import org.broadinstitute.sting.gatk.LocusContext;
import org.broadinstitute.sting.gatk.walkers.LocusWalker;
import org.broadinstitute.sting.gatk.walkers.By;
import org.broadinstitute.sting.gatk.walkers.DataSource;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.utils.cmdLine.Argument;
import org.broadinstitute.sting.utils.Pair;
@ -18,6 +20,7 @@ import net.sf.picard.reference.ReferenceSequence;
import edu.mit.broad.picard.util.Interval;
import edu.mit.broad.picard.util.OverlapDetector;
@By(DataSource.REFERENCE)
public class HybSelPerformanceWalker extends LocusWalker<Integer, HybSelPerformanceWalker.TargetInfo> {
@Argument(fullName="min_mapq", shortName="mmq", required=false, doc="Minimum mapping quality of reads to consider")
public Integer MIN_MAPQ = 1;