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Optionally lists read depths by read group. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1990 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kiran 2009-11-08 16:39:19 +00:00
parent a679bdde18
commit 567f5758d2
1 changed files with 26 additions and 0 deletions
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26
java/src/org/broadinstitute/sting/gatk/walkers/DepthOfCoverageWalker.java
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@ -30,6 +30,11 @@ 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 net.sf.samtools.SAMReadGroupRecord;
import java.util.HashMap;
import java.util.Collections;
import java.util.ArrayList;
/**
* Display the depth of coverage at a given locus.
@ -50,6 +55,9 @@ public class DepthOfCoverageWalker extends LocusWalker<Integer, Pair<Long, Long>
@Argument(fullName="minMAPQ", shortName = "minMAPQ", doc="If provided, we will exclude reads with MAPQ < this value at a locus in coverage",required=false)
public int excludeMAPQBelowThis = -1;
@Argument(fullName="byReadGroup", shortName="byRG", doc="List read depths for each read group")
public boolean byReadGroup = false;
public boolean includeReadsWithDeletionAtLoci() { return ! excludeDeletionsInCoverage; }
public void initialize() {
@ -66,6 +74,11 @@ public class DepthOfCoverageWalker extends LocusWalker<Integer, Pair<Long, Long>
public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
int nCleanReads = 0, nBadMAPQReads = 0, nDeletionReads = 0;
HashMap<String, Integer> depthByReadGroup = new HashMap<String, Integer>();
for (SAMReadGroupRecord rg : this.getToolkit().getSAMFileHeader().getReadGroups()) {
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);
@ -73,6 +86,10 @@ public class DepthOfCoverageWalker extends LocusWalker<Integer, Pair<Long, Long>
if ( read.getMappingQuality() < excludeMAPQBelowThis ) nBadMAPQReads++;
else if ( offset == -1 ) nDeletionReads++;
else nCleanReads++;
String readGroupName = read.getReadGroup().getReadGroupId();
int oldDepth = depthByReadGroup.get(readGroupName);
depthByReadGroup.put(readGroupName, oldDepth + 1);
}
int nTotalReads = nCleanReads + (excludeDeletionsInCoverage ? 0 : nDeletionReads);
@ -86,6 +103,15 @@ public class DepthOfCoverageWalker extends LocusWalker<Integer, Pair<Long, Long>
break;
}
if (byReadGroup) {
ArrayList<String> rgs = new ArrayList<String>(depthByReadGroup.keySet());
Collections.sort(rgs);
for (String rg : rgs) {
out.printf(" %s %8d%n", rg, depthByReadGroup.get(rg));
}
}
return nTotalReads;
}