diff --git a/java/src/net/sf/samtools/BAMFileIndex2.java b/java/src/net/sf/samtools/BAMFileIndex2.java
index 5b303da03..1def4e694 100644
--- a/java/src/net/sf/samtools/BAMFileIndex2.java
+++ b/java/src/net/sf/samtools/BAMFileIndex2.java
@@ -106,7 +106,7 @@ public class BAMFileIndex2 extends BAMFileIndex
         final int level = getLevelForBinNumber(bin.binNumber);
         final int levelStart = LEVEL_STARTS[level];
         final int levelSize = ((level==getNumIndexLevels()-1) ? MAX_BINS-1 : LEVEL_STARTS[level+1]) - levelStart;
-        return (bin.binNumber - levelStart)*(BIN_SPAN/levelSize); 
+        return (bin.binNumber - levelStart)*(BIN_SPAN/levelSize)+1;
     }
 
     /**
@@ -118,7 +118,7 @@ public class BAMFileIndex2 extends BAMFileIndex
         final int level = getLevelForBinNumber(bin.binNumber);
         final int levelStart = LEVEL_STARTS[level];
         final int levelSize = ((level==getNumIndexLevels()-1) ? MAX_BINS-1 : LEVEL_STARTS[level+1]) - levelStart;
-        return (bin.binNumber - levelStart + 1)*(BIN_SPAN/levelSize) - 1;         
+        return (bin.binNumber-levelStart+1)*(BIN_SPAN/levelSize);         
     }
 
     /**
@@ -213,25 +213,9 @@ public class BAMFileIndex2 extends BAMFileIndex
         }
         
         List<Chunk> chunkList = new ArrayList<Chunk>();
-        for(Bin coveringBin: binTree)
-            chunkList.addAll(binToChunks.get(coveringBin));
-
-        // Find the nearest adjacent bin.  This can act as a minimum offset
-        Bin closestAdjacentBin = null;
-        for(Bin adjacentBin: allBins) {
-            if(getLevelForBinNumber(adjacentBin.binNumber) != binLevel)
-                continue;
-            if(adjacentBin.binNumber<bin.binNumber && (closestAdjacentBin == null || closestAdjacentBin.binNumber < adjacentBin.binNumber))
-                closestAdjacentBin = adjacentBin;
-        }
-
-        // Find the offset of the closest bin.
-        long adjacentBinOffset = 0;
-        if(closestAdjacentBin != null) {
-            for(Chunk chunk: binToChunks.get(closestAdjacentBin)) {
-                if(adjacentBinOffset < chunk.getChunkEnd())
-                    adjacentBinOffset = chunk.getChunkEnd();
-            }
+        for(Bin coveringBin: binTree) {
+            for(Chunk chunk: binToChunks.get(coveringBin))
+                chunkList.add(chunk.clone());
         }
 
         final int start = getFirstLocusInBin(bin)-1;
@@ -242,40 +226,7 @@ public class BAMFileIndex2 extends BAMFileIndex
             minimumOffset = index.indexEntries[regionLinearBin];
 
         chunkList = optimizeChunkList(chunkList, minimumOffset);
-        long[] chunkArray = convertToArray(chunkList);
-
-        // Trim off anything before the first desired bin.
-        int location = Arrays.binarySearch(chunkArray,adjacentBinOffset);
-        // location not found, but insertion point was determined.
-        long trimmedChunkArray[] = chunkArray;
-
-        // If the location of the element is in an even bucket (a start position), trim everything before it.
-        if(location >= 0) {
-            if(location%2==0) {
-                trimmedChunkArray = new long[chunkArray.length-location];
-                System.arraycopy(chunkArray,location,trimmedChunkArray,0,trimmedChunkArray.length);                
-            }
-            else {
-                trimmedChunkArray = new long[chunkArray.length-location-1];
-                System.arraycopy(chunkArray,location+1,trimmedChunkArray,0,trimmedChunkArray.length);
-            }
-        }
-        else {
-            location = -(location+1);
-            if(location < chunkArray.length) {
-                if(location%2==0) {
-                    trimmedChunkArray = new long[chunkArray.length-location];
-                    System.arraycopy(chunkArray,location,trimmedChunkArray,0,trimmedChunkArray.length);
-                }
-                else {
-                    trimmedChunkArray = new long[chunkArray.length-location+1];
-                    trimmedChunkArray[0] = adjacentBinOffset;
-                    System.arraycopy(chunkArray,location,trimmedChunkArray,1,trimmedChunkArray.length-1);
-                }
-            }
-        }
-
-        return trimmedChunkArray;
+        return convertToArray(chunkList);
     }
 
     /**
@@ -296,8 +247,10 @@ public class BAMFileIndex2 extends BAMFileIndex
         }
 
         List<Chunk> chunkList = new ArrayList<Chunk>();
-        for(Bin bin: bins)
-            chunkList.addAll(binToChunks.get(bin));
+        for(Bin bin: bins) {
+            for(Chunk chunk: binToChunks.get(bin))
+                chunkList.add(chunk.clone());
+        }
 
         if (chunkList.isEmpty()) {
             return null;
diff --git a/java/src/net/sf/samtools/Chunk.java b/java/src/net/sf/samtools/Chunk.java
index f5109a3eb..ee9ae4a5d 100644
--- a/java/src/net/sf/samtools/Chunk.java
+++ b/java/src/net/sf/samtools/Chunk.java
@@ -12,7 +12,7 @@ import java.util.ArrayList;
  * @author mhanna
  * @version 0.1
  */
-public class Chunk implements Comparable<Chunk> {
+public class Chunk implements Cloneable,Comparable<Chunk> {
 
     private long mChunkStart;
     private long mChunkEnd;
@@ -22,6 +22,10 @@ public class Chunk implements Comparable<Chunk> {
         mChunkEnd = end;
     }
 
+    protected Chunk clone() {
+        return new Chunk(mChunkStart,mChunkEnd);
+    }
+
     public long getChunkStart() {
         return mChunkStart;
     }
diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/shards/IndexDelimitedLocusShardStrategy.java b/java/src/org/broadinstitute/sting/gatk/datasources/shards/IndexDelimitedLocusShardStrategy.java
index 8a17cbc64..b4dcab9a1 100755
--- a/java/src/org/broadinstitute/sting/gatk/datasources/shards/IndexDelimitedLocusShardStrategy.java
+++ b/java/src/org/broadinstitute/sting/gatk/datasources/shards/IndexDelimitedLocusShardStrategy.java
@@ -120,13 +120,6 @@ public class IndexDelimitedLocusShardStrategy implements ShardStrategy {
      */
     public IndexDelimitedLocusShard next() {
         FilePointer nextFilePointer = filePointerIterator.next();
-        String contig = null;
-        long start = Long.MAX_VALUE, stop = 0;
-        for(GenomeLoc loc: nextFilePointer.locations) {
-            contig = loc.getContig();
-            start = Math.min(loc.getStart(),start);
-            stop = Math.max(loc.getStop(),stop);
-        }
         Map<SAMFileReader2,List<Chunk>> chunksBounding = blockDrivenDataSource.getFilePointersBounding(nextFilePointer.bin);
         return new IndexDelimitedLocusShard(nextFilePointer.locations,chunksBounding,Shard.ShardType.LOCUS_INTERVAL);
     }