Add some missing methods to the pileup architecture.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3588 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/utils/pileup/ReadBackedExtendedEventPileup.java

@@ -29,6 +29,7 @@ import org.broadinstitute.sting.utils.collections.Pair;
 
 import java.util.Iterator;
 import java.util.List;
+import java.util.Collection;
 
 import net.sf.samtools.SAMRecord;
 
@@ -58,6 +59,19 @@ public interface ReadBackedExtendedEventPileup extends Iterable<ExtendedEventPil
      */
     public ReadBackedExtendedEventPileup getDownsampledPileup(int desiredCoverage);
 
+    /**
+     * Gets a list of all the samples stored in this pileup.
+     * @return List of samples in this pileup.
+     */
+    public Collection<String> getSamples();
+
+    /**
+     * Gets the particular subset of this pileup with the given sample name.
+     * @param sampleName Name of the sample to use.
+     * @return A subset of this pileup containing only reads with the given sample.
+     */
+    public ReadBackedExtendedEventPileup getPileupForSample(String sampleName);    
+
     /**
      * Returns the number of deletion events in this pileup
      *

java/src/org/broadinstitute/sting/utils/pileup/ReadBackedPileup.java

@@ -29,6 +29,7 @@ import org.broadinstitute.sting.gatk.iterators.IterableIterator;
 import net.sf.samtools.SAMRecord;
 
 import java.util.List;
+import java.util.Collection;
 
 /**
  * A data retrieval interface for accessing parts of the pileup.
@@ -95,6 +96,12 @@ public interface ReadBackedPileup extends Iterable<PileupElement> {
      */
     public ReadBackedPileup getDownsampledPileup(int desiredCoverage);
 
+    /**
+     * Gets a collection of all the samples stored in this pileup.
+     * @return Collection of samples in this pileup.
+     */
+    public Collection<String> getSamples();
+
     /**
      * Gets the particular subset of this pileup with the given sample name.
      * @param sampleName Name of the sample to use.

java/src/org/broadinstitute/sting/utils/pileup/SampleSplitReadBackedExtendedEventPileup.java

@@ -151,6 +151,24 @@ public class SampleSplitReadBackedExtendedEventPileup implements ReadBackedExten
         return downsampledPileup;
     }
 
+    /**
+     * Gets a list of all the samples stored in this pileup.
+     * @return List of samples in this pileup.
+     */
+    public Collection<String> getSamples() {
+        return pileupBySample.keySet();
+    }
+
+    /**
+     * Gets the particular subset of this pileup with the given sample name.
+     * @param sampleName Name of the sample to use.
+     * @return A subset of this pileup containing only reads with the given sample.
+     */
+    public ReadBackedExtendedEventPileup getPileupForSample(String sampleName) {
+        return pileupBySample.get(sampleName);
+    }
+
+
     @Override
     public Iterator<ExtendedEventPileupElement> iterator() {
         return new ExtendedEventCastingIterator(new MergingPileupElementIterator(pileupBySample));

java/src/org/broadinstitute/sting/utils/pileup/SampleSplitReadBackedPileup.java

@@ -226,6 +226,10 @@ public class SampleSplitReadBackedPileup implements ReadBackedPileup {
         return downsampledPileup;
     }
 
+    public Collection<String> getSamples() {
+        return pileupBySample.keySet();
+    }
+
     @Override
     public ReadBackedPileup getPileupForSample(String sampleName) {
         return pileupBySample.containsKey(sampleName) ? pileupBySample.get(sampleName) : null;

java/src/org/broadinstitute/sting/utils/pileup/UnifiedReadBackedExtendedEventPileup.java

@@ -194,6 +194,34 @@ public class UnifiedReadBackedExtendedEventPileup implements ReadBackedExtendedE
         return new UnifiedReadBackedExtendedEventPileup(getLocation(), downsampledPileup);
     }
 
+    @Override
+    public Collection<String> getSamples() {
+        Collection<String> sampleNames = new HashSet<String>();
+        for(PileupElement p: this) {
+            SAMRecord read = p.getRead();
+            String sampleName = read.getReadGroup() != null ? read.getReadGroup().getSample() : null;
+            sampleNames.add(sampleName);
+        }
+        return sampleNames;
+    }
+
+    @Override
+    public ReadBackedExtendedEventPileup getPileupForSample(String sampleName) {
+        List<ExtendedEventPileupElement> filteredPileup = new ArrayList<ExtendedEventPileupElement>();
+        for(ExtendedEventPileupElement p: this) {
+            SAMRecord read = p.getRead();
+            if(sampleName != null) {
+                if(read.getReadGroup() != null && sampleName.equals(read.getReadGroup().getSample()))
+                    filteredPileup.add(p);
+            }
+            else {
+                if(read.getReadGroup() == null || read.getReadGroup().getSample() == null)
+                    filteredPileup.add(p);
+            }
+        }
+        return filteredPileup.size()>0 ? new UnifiedReadBackedExtendedEventPileup(loc,filteredPileup) : null;
+    }
+
     // --------------------------------------------------------
     //
     // iterators

java/src/org/broadinstitute/sting/utils/pileup/UnifiedReadBackedPileup.java

@@ -299,6 +299,17 @@ public class UnifiedReadBackedPileup implements ReadBackedPileup {
         return new UnifiedReadBackedPileup(getLocation(), downsampledPileup);
     }
 
+    @Override
+    public Collection<String> getSamples() {
+        Collection<String> sampleNames = new HashSet<String>();
+        for(PileupElement p: this) {
+            SAMRecord read = p.getRead();
+            String sampleName = read.getReadGroup() != null ? read.getReadGroup().getSample() : null;
+            sampleNames.add(sampleName);
+        }
+        return sampleNames;
+    }
+
     @Override
     public ReadBackedPileup getPileupForSample(String sampleName) {
         List<PileupElement> filteredPileup = new ArrayList<PileupElement>();