From c638c29eeaa3b85a7bcacbd17677f6548c69723a Mon Sep 17 00:00:00 2001
From: asivache <asivache@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 9 Mar 2010 22:18:44 +0000
Subject: [PATCH] In reference traversals, this view did not expect a
 possibility of TWO alignment contexts (base pileup followed by extended event
 pileup) associated with the same location. As the result, extended event
 pileups were silently skipped even when enabled in the traversal engine.
 Fixed.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2970 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../datasources/providers/AllLocusView.java   | 32 +++++++++++++------
 1 file changed, 23 insertions(+), 9 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/providers/AllLocusView.java b/java/src/org/broadinstitute/sting/gatk/datasources/providers/AllLocusView.java
index d978e77f2..ba1d7ad72 100755
--- a/java/src/org/broadinstitute/sting/gatk/datasources/providers/AllLocusView.java
+++ b/java/src/org/broadinstitute/sting/gatk/datasources/providers/AllLocusView.java
@@ -30,13 +30,13 @@ public class AllLocusView extends LocusView {
     private GenomeLocusIterator locusIterator;
 
     /**
-     * Gets the current position in the view.
+     * Gets the next position in the view: next call to next() will jump there.
+     * Note that both nextPosition and nextLocus are PRE-read and cached.
      */
     private GenomeLoc nextPosition = null;
 
     /**
-     * What's the context for the last locus accessed?
-     * @param provider
+     * What's the next available context?
      */
     private AlignmentContext nextLocus = null;
 
@@ -49,6 +49,7 @@ public class AllLocusView extends LocusView {
         // Seed the state tracking members with the first possible seek position and the first possible locus context.
         locusIterator = new GenomeLocusIterator(provider.getLocus());
         if( locusIterator.hasNext() ) {
+            // cache next position and next alignment context
             nextPosition = locusIterator.next();
             nextLocus = hasNextLocus() ? nextLocus() : createEmptyLocus(nextPosition);
         }
@@ -59,22 +60,35 @@ public class AllLocusView extends LocusView {
     }
 
     public AlignmentContext next() {
+
         GenomeLoc currentPosition = nextPosition;
         if( currentPosition == null )
             throw new NoSuchElementException("No next is available in the all locus view");
 
-        // Determine the next locus.
-        nextPosition = locusIterator.hasNext() ? locusIterator.next() : null;
-
         // Crank the iterator to (if possible) or past the next context.
         while( nextLocus != null && nextLocus.getLocation().isBefore(currentPosition) && hasNextLocus() )
             nextLocus = nextLocus();
 
+        AlignmentContext currentLocus = null; // context we are gonna return
+
         // If actual data is present, return it.  Otherwise, return empty data.
-        if( nextLocus != null && nextLocus.getLocation().equals(currentPosition) )
-            return nextLocus;
+        if( nextLocus != null && nextLocus.getLocation().equals(currentPosition) ) {
+            currentLocus = nextLocus; // found alignment context at the current position
+            nextLocus = hasNextLocus() ? nextLocus() : null; 
+        }
         else
-            return createEmptyLocus( currentPosition );
+            currentLocus = createEmptyLocus( currentPosition );
+
+        // Determine the next locus. The trick is that we may have more than one alignment context at the same
+        // reference position (regular base pileup, then extended pileup). If next alignment context (that we just pre-read)
+        // is still at the current position, we do not increment current position and wait for next call to next() to return
+        // that context. If we know that next context is past the current position, we are done with current
+        // position
+        if ( nextLocus == null || ! nextLocus.getLocation().equals(currentPosition) )
+            nextPosition = locusIterator.hasNext() ? locusIterator.next() : null;
+
+
+        return currentLocus;
     }
 
     @Override