Compute and cache the length of the longest deletion observed at the site; ReadBackedExtendedEventPileup now has a getter to access that value.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2487 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByState.java

@@ -320,15 +320,21 @@ public class LocusIteratorByState extends LocusIterator {
             if ( readInfo.generateExtendedEvents() && hasExtendedEvents ) {
                 ArrayList<ExtendedEventPileupElement> indelPile = new ArrayList<ExtendedEventPileupElement>(readStates.size());
 
+                int maxDeletionLength = 0;
+
                 for ( SAMRecordState state : readStates ) {
                     if ( state.hadIndel() ) {
                         size++;
-                        if ( state.getEventBases() == null ) nDeletions++;
+                        if ( state.getEventBases() == null ) {
+                            nDeletions++;
+                            maxDeletionLength = Math.max(maxDeletionLength,state.getEventLength());
+                        }
                         else nInsertions++;
                         indelPile.add ( new ExtendedEventPileupElement(state.getRead(),
                                                                        state.getReadEventStartOffset(),
                                                                        state.getEventLength(),
                                                                        state.getEventBases()) );
+
                     }   else {
                         if ( state.getCurrentCigarOperator() != CigarOperator.N ) {
                             // this read has no indel associated with the previous position on the ref;
@@ -358,7 +364,7 @@ public class LocusIteratorByState extends LocusIterator {
                 GenomeLoc loc = GenomeLocParser.incPos(our1stState.getLocation(),-1);
 //                System.out.println("Indel(s) at "+loc);
 //               for ( ExtendedEventPileupElement pe : indelPile ) { if ( pe.isIndel() ) System.out.println("  "+pe.toString()); }
-                return new AlignmentContext(loc, new ReadBackedExtendedEventPileup(loc, indelPile, size, nInsertions, nDeletions, nMQ0Reads));
+                return new AlignmentContext(loc, new ReadBackedExtendedEventPileup(loc, indelPile, size, maxDeletionLength, nInsertions, nDeletions, nMQ0Reads));
             }  else {
 
                 ArrayList<PileupElement> pile = new ArrayList<PileupElement>(readStates.size());

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

@@ -20,6 +20,7 @@ public class ReadBackedExtendedEventPileup implements Iterable<ExtendedEventPile
     private ArrayList<ExtendedEventPileupElement> pileup = null;
 
     private int size = 0;                   // cached value of the size of the pileup
+    private int maxDeletionLength = 0;      // cached value of the length of the longest deletion observed at the site
     private int nDeletions = 0;             // cached value of the number of deletions
     private int nInsertions = 0;
     private int nMQ0Reads = 0;              // cached value of the number of MQ0 reads
@@ -53,13 +54,15 @@ public class ReadBackedExtendedEventPileup implements Iterable<ExtendedEventPile
      * @param loc
      * @param pileup
      */
-    public ReadBackedExtendedEventPileup(GenomeLoc loc, ArrayList<ExtendedEventPileupElement> pileup, int size, int nInsertions, int nDeletions, int nMQ0Reads ) {
+    public ReadBackedExtendedEventPileup(GenomeLoc loc, ArrayList<ExtendedEventPileupElement> pileup, int size,
+                                         int maxDeletionLength, int nInsertions, int nDeletions, int nMQ0Reads ) {
         if ( loc == null ) throw new StingException("Illegal null genomeloc in ReadBackedExtendedEventPileup");
         if ( pileup == null ) throw new StingException("Illegal null pileup in ReadBackedExtendedEventPileup");
 
         this.loc = loc;
         this.pileup = pileup;
         this.size = size;
+        this.maxDeletionLength = maxDeletionLength;
         this.nDeletions = nDeletions;
         this.nInsertions = nInsertions;
         this.nMQ0Reads = nMQ0Reads;
@@ -78,9 +81,11 @@ public class ReadBackedExtendedEventPileup implements Iterable<ExtendedEventPile
         nMQ0Reads = 0;
 
         for ( ExtendedEventPileupElement p : this ) {
+
             size++;
             if ( p.isDeletion() ) {
                 nDeletions++;
+                maxDeletionLength = Math.max(maxDeletionLength, p.getEventLength());
             } else {
                 if ( p.isInsertion() ) nInsertions++;
             }
@@ -200,6 +205,16 @@ public class ReadBackedExtendedEventPileup implements Iterable<ExtendedEventPile
         return nInsertions;
     }
 
+
+    /** Returns the length of the longest deletion observed at the site this
+     * pileup is associated with (NOTE: by convention, both insertions and deletions
+     * are associated with genomic location immediately before the actual event). If
+     * there are no deletions at the site, returns 0.
+     * @return
+     */
+    public int getMaxDeletionLength() {
+        return maxDeletionLength;
+    }
     /**
      * Returns the number of mapping quality zero reads in this pileup.
      * @return