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fix for RBP getPileupsForSamples() 

do not differentiate per sample pileups from generic pileups. Do the same for both -- it's O(n) either way.
This commit is contained in:
Mauricio Carneiro 2012-04-24 12:50:46 -04:00
parent 82b4798913
commit 902277856e
1 changed files with 19 additions and 25 deletions
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44
public/java/src/org/broadinstitute/sting/utils/pileup/AbstractReadBackedPileup.java
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@ -696,32 +696,26 @@ public abstract class AbstractReadBackedPileup<RBP extends AbstractReadBackedPil
@Override
public Map<String, ReadBackedPileup> getPileupsForSamples(Collection<String> sampleNames) {
Map<String, ReadBackedPileup> result = new HashMap<String, ReadBackedPileup>();
if (pileupElementTracker instanceof PerSamplePileupElementTracker) {
PerSamplePileupElementTracker<PE> tracker = (PerSamplePileupElementTracker<PE>) pileupElementTracker;
for (String sample : sampleNames) {
PileupElementTracker<PE> filteredElements = tracker.getElements(sampleNames);
if (filteredElements != null)
result.put(sample, createNewPileup(loc, filteredElements));
}
} else {
Map<String, UnifiedPileupElementTracker<PE>> trackerMap = new HashMap<String, UnifiedPileupElementTracker<PE>>();
for (String sample : sampleNames) { // initialize pileups for each sample
UnifiedPileupElementTracker<PE> filteredTracker = new UnifiedPileupElementTracker<PE>();
trackerMap.put(sample, filteredTracker);
}
for (PE p : pileupElementTracker) { // go through all pileup elements only once and add them to the respective sample's pileup
GATKSAMRecord read = p.getRead();
if (read.getReadGroup() != null) {
String sample = read.getReadGroup().getSample();
UnifiedPileupElementTracker<PE> tracker = trackerMap.get(sample);
if (tracker != null) // we only add the pileup the requested samples. Completely ignore the rest
tracker.add(p);
}
}
for (Map.Entry<String, UnifiedPileupElementTracker<PE>> entry : trackerMap.entrySet()) // create the RBP for each sample
result.put(entry.getKey(), createNewPileup(loc, entry.getValue()));
Map<String, UnifiedPileupElementTracker<PE>> trackerMap = new HashMap<String, UnifiedPileupElementTracker<PE>>();
for (String sample : sampleNames) { // initialize pileups for each sample
UnifiedPileupElementTracker<PE> filteredTracker = new UnifiedPileupElementTracker<PE>();
trackerMap.put(sample, filteredTracker);
}
for (PE p : pileupElementTracker) { // go through all pileup elements only once and add them to the respective sample's pileup
GATKSAMRecord read = p.getRead();
if (read.getReadGroup() != null) {
String sample = read.getReadGroup().getSample();
UnifiedPileupElementTracker<PE> tracker = trackerMap.get(sample);
if (tracker != null) // we only add the pileup the requested samples. Completely ignore the rest
tracker.add(p);
}
}
for (Map.Entry<String, UnifiedPileupElementTracker<PE>> entry : trackerMap.entrySet()) // create the RBP for each sample
result.put(entry.getKey(), createNewPileup(loc, entry.getValue()));
return result;
}