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added parameters for mapping quality and duplicate filters 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@563 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kcibul 2009-04-29 18:05:34 +00:00
parent 30218ee31a
commit 334f158e5a
1 changed files with 7 additions and 9 deletions
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16
java/src/org/broadinstitute/sting/playground/gatk/walkers/HybSelPerformanceWalker.java
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@ -2,7 +2,6 @@ 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.refdata.ReferenceOrderedDatum;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.utils.cmdLine.Argument;
import org.broadinstitute.sting.utils.Pair;
@ -13,6 +12,9 @@ import java.util.List;
import net.sf.samtools.SAMRecord;
public class HybSelPerformanceWalker extends LocusWalker<Integer, HybSelPerformanceWalker.TargetInfo> {
@Argument(fullName="min_mapq", shortName="mmq", required=false, defaultValue="1", doc="Minimum mapping quality of reads to consider") public Integer MIN_MAPQ;
@Argument(fullName="include_duplicates", shortName="idup", required=false, defaultValue="false", doc="consider duplicate reads") public Boolean INCLUDE_DUPLICATE_READS;
public static class TargetInfo {
public int counts = 0;
@ -35,14 +37,10 @@ public class HybSelPerformanceWalker extends LocusWalker<Integer, HybSelPerforma
{
SAMRecord read = reads.get(i);
// TODO: is there a better way to do this?
if (read.getNotPrimaryAlignmentFlag() ||
read.getDuplicateReadFlag() ||
read.getReadUnmappedFlag() ||
read.getMappingQuality() <= -1
) {
continue;
}
if (read.getNotPrimaryAlignmentFlag()) { continue; }
if (read.getReadUnmappedFlag()) { continue; }
if (!INCLUDE_DUPLICATE_READS && read.getDuplicateReadFlag()) { continue; }
if (read.getMappingQuality() < MIN_MAPQ) { continue; }
depth++;
}