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Added getPileupForReadGroups to ReadBackPileup 

* returns a pileup for all the read groups provided.
   * saves us from multiple calls to getPileup (which is very inefficient)
This commit is contained in:
Mauricio Carneiro 2012-01-02 16:17:57 -05:00
parent caa5da2fd2
commit 3d4bf273de
2 changed files with 44 additions and 0 deletions
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36
public/java/src/org/broadinstitute/sting/utils/pileup/AbstractReadBackedPileup.java
View File

@ -526,6 +526,42 @@ public abstract class AbstractReadBackedPileup<RBP extends AbstractReadBackedPil
}
}
/**
* Gets the pileup for a set of read groups. Horrendously inefficient at this point.
* @param rgSet List of identifiers for the read groups.
* @return A read-backed pileup containing only the reads in the given read groups.
*/
@Override
public RBP getPileupForReadGroups(final HashSet<String> rgSet) {
if(pileupElementTracker instanceof PerSamplePileupElementTracker) {
PerSamplePileupElementTracker<PE> tracker = (PerSamplePileupElementTracker<PE>)pileupElementTracker;
PerSamplePileupElementTracker<PE> filteredTracker = new PerSamplePileupElementTracker<PE>();
for(final String sample: tracker.getSamples()) {
PileupElementTracker<PE> perSampleElements = tracker.getElements(sample);
AbstractReadBackedPileup<RBP,PE> pileup = createNewPileup(loc,perSampleElements).getPileupForReadGroups(rgSet);
if(pileup != null)
filteredTracker.addElements(sample,pileup.pileupElementTracker);
}
return filteredTracker.size()>0 ? (RBP)createNewPileup(loc,filteredTracker) : null;
}
else {
UnifiedPileupElementTracker<PE> filteredTracker = new UnifiedPileupElementTracker<PE>();
for(PE p: pileupElementTracker) {
GATKSAMRecord read = p.getRead();
if(rgSet != null && !rgSet.isEmpty()) {
if(read.getReadGroup() != null && rgSet.contains(read.getReadGroup().getReadGroupId()))
filteredTracker.add(p);
}
else {
if(read.getReadGroup() == null || read.getReadGroup().getReadGroupId() == null)
filteredTracker.add(p);
}
}
return filteredTracker.size()>0 ? (RBP)createNewPileup(loc,filteredTracker) : null;
}
}
@Override
public RBP getPileupForLane(String laneID) {
if(pileupElementTracker instanceof PerSamplePileupElementTracker) {

8
public/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedPileup.java
View File

@ -30,6 +30,7 @@ import org.broadinstitute.sting.utils.fragments.FragmentCollection;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import java.util.Collection;
import java.util.HashSet;
import java.util.List;
/**
@ -129,6 +130,13 @@ public interface ReadBackedPileup extends Iterable<PileupElement>, HasGenomeLoca
*/
public ReadBackedPileup getPileupForReadGroup(String readGroupId);
/**
* Gets all the reads associated with a given read groups.
* @param rgSet Set of identifiers for the read group.
* @return A pileup containing only the reads in the given read groups.
*/
public ReadBackedPileup getPileupForReadGroups(final HashSet<String> rgSet);
/**
* Gets all reads in a given lane id. (Lane ID is the read group
* id stripped of the last .XX sample identifier added by the GATK).