From c869d1c9cf6a74db699309d65d3fae2106890640 Mon Sep 17 00:00:00 2001
From: hanna <hanna@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Mon, 28 Feb 2011 21:14:18 +0000
Subject: [PATCH] Fix misc issues in new protosharder regarding proper iterator
 termination when an unexpectedly small amount of data is present.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5338 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/datasources/reads/BinTree.java         | 11 +++++++++--
 .../datasources/reads/LowMemoryIntervalSharder.java   |  7 +++++++
 2 files changed, 16 insertions(+), 2 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/reads/BinTree.java b/java/src/org/broadinstitute/sting/gatk/datasources/reads/BinTree.java
index 95c33d552..94cebe9e7 100644
--- a/java/src/org/broadinstitute/sting/gatk/datasources/reads/BinTree.java
+++ b/java/src/org/broadinstitute/sting/gatk/datasources/reads/BinTree.java
@@ -160,14 +160,16 @@ class BinTreeIterator implements Iterator<BinTree> {
         final int firstBinInLowestLevel = GATKBAMIndex.getFirstBinInLevel(lowestLevel);
         final int binsInLowestLevel = index.getLevelSize(lowestLevel);
 
-        currentBinInLowestLevel++;
-
         GATKBin[] bins = new GATKBin[GATKBAMIndex.getNumIndexLevels()];
         nextBinTree = null;
         while(nextBinTree == null) {
+            currentBinInLowestLevel++;
+            boolean levelIteratorsExhausted = true;
+
             for(int level = lowestLevel; level >= 0; level--) {
                 if(!levelIterators[level].hasNext())
                     continue;
+                levelIteratorsExhausted = false;
 
                 final int firstBinInThisLevel = GATKBAMIndex.getFirstBinInLevel(level);
                 final int binsInThisLevel = index.getLevelSize(level);
@@ -180,6 +182,11 @@ class BinTreeIterator implements Iterator<BinTree> {
                     bins[level] = levelIterators[level].peek();
             }
 
+            // No more bins available for this reference sequence?  Break out of the loop.
+            if(levelIteratorsExhausted)
+                break;
+
+            // Found a compelling bin tree?  Break out of the loop.
             for(int level = 0; level <= lowestLevel; level++) {
                 if(bins[level] != null) {
                     nextBinTree = new BinTree(index,bins);
diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/reads/LowMemoryIntervalSharder.java b/java/src/org/broadinstitute/sting/gatk/datasources/reads/LowMemoryIntervalSharder.java
index 45ad7e081..e44261d63 100644
--- a/java/src/org/broadinstitute/sting/gatk/datasources/reads/LowMemoryIntervalSharder.java
+++ b/java/src/org/broadinstitute/sting/gatk/datasources/reads/LowMemoryIntervalSharder.java
@@ -104,6 +104,13 @@ public class LowMemoryIntervalSharder implements Iterator<FilePointer> {
                 }
             }
 
+            // Early exit if no bins were found.
+            if(coveredRegion == null) {
+                nextFilePointer.addLocation(currentLocus);
+                currentLocus = locusIterator.next();
+                continue;
+            }
+
             // Define the initial range of the file pointer, aka the region where the locus currently being processed intersects the BAM list.
             GenomeLoc initialLocation = currentLocus.intersect(coveredRegion);
             nextFilePointer.addLocation(initialLocation);