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Moved DoC walker over to new pileup system so it no longer moves like it's stuck in molasses. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2208 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-12-02 02:46:39 +00:00
parent ba8a8febc6
commit 7c73496e72
1 changed files with 8 additions and 10 deletions
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18
java/src/org/broadinstitute/sting/gatk/walkers/DepthOfCoverageWalker.java
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@ -23,14 +23,13 @@
*/
package org.broadinstitute.sting.gatk.walkers;
import org.broadinstitute.sting.gatk.walkers.DataSource;
import org.broadinstitute.sting.gatk.walkers.By;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.utils.cmdLine.Argument;
import org.broadinstitute.sting.utils.Pair;
import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.utils.pileup.*;
import net.sf.samtools.SAMReadGroupRecord;
import java.util.HashMap;
@ -81,15 +80,14 @@ public class DepthOfCoverageWalker extends LocusWalker<Integer, Pair<Long, Long>
depthByReadGroup.put(rg.getReadGroupId(), 0);
}
for ( int i = 0; i < context.getReads().size(); i++ ) {
SAMRecord read = context.getReads().get(i);
int offset = context.getOffsets().get(i);
ReadBackedPileup pileup = context.getPileup();
for ( PileupElement p : pileup ) {
if ( read.getMappingQuality() < excludeMAPQBelowThis ) nBadMAPQReads++;
else if ( offset == -1 ) nDeletionReads++;
if ( p.getRead().getMappingQuality() < excludeMAPQBelowThis ) nBadMAPQReads++;
else if ( p.isDeletion() ) nDeletionReads++;
else nCleanReads++;
String readGroupName = read.getReadGroup().getReadGroupId();
String readGroupName = p.getRead().getReadGroup().getReadGroupId();
int oldDepth = depthByReadGroup.get(readGroupName);
depthByReadGroup.put(readGroupName, oldDepth + 1);
}
@ -131,6 +129,6 @@ public class DepthOfCoverageWalker extends LocusWalker<Integer, Pair<Long, Long>
public void onTraversalDone(Pair<Long, Long> result) {
out.printf("Average depth of coverage is: %.2f in %d total coverage over %d sites\n",
((double)result.getFirst() / (double)result.getSecond()), result.getFirst(), result.getSecond());
((double)result.getFirst() / result.getSecond()), result.getFirst(), result.getSecond());
}
}