diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/BAMFileStat.java b/java/src/org/broadinstitute/sting/gatk/datasources/BAMFileStat.java
index 90d9a5fad..59f4208fa 100644
--- a/java/src/org/broadinstitute/sting/gatk/datasources/BAMFileStat.java
+++ b/java/src/org/broadinstitute/sting/gatk/datasources/BAMFileStat.java
@@ -74,7 +74,7 @@ public class BAMFileStat extends CommandLineProgram {
         inspector.inspect(System.out,null,null);
     }
 
-    private class BAMFileIndexContentInspector extends PreloadedBAMFileIndex {
+    private class BAMFileIndexContentInspector extends CachingBAMFileIndex {
         public BAMFileIndexContentInspector(File bamFileIndex) {
             super(bamFileIndex);    
         }
diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/shards/BAMFormatAwareShard.java b/java/src/org/broadinstitute/sting/gatk/datasources/shards/BAMFormatAwareShard.java
index 23ee0fade..a6fa87fd3 100644
--- a/java/src/org/broadinstitute/sting/gatk/datasources/shards/BAMFormatAwareShard.java
+++ b/java/src/org/broadinstitute/sting/gatk/datasources/shards/BAMFormatAwareShard.java
@@ -20,7 +20,7 @@ public interface BAMFormatAwareShard extends Shard {
      * Get the list of chunks delimiting this shard.
      * @return a list of chunks that contain data for this shard.
      */
-    public Map<SAMReaderID, BAMFileSpan> getFileSpans();
+    public Map<SAMReaderID,SAMFileSpan> getFileSpans();
 
     /**
      * Returns true if this shard is meant to buffer reads, rather
diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/shards/BlockDelimitedReadShard.java b/java/src/org/broadinstitute/sting/gatk/datasources/shards/BlockDelimitedReadShard.java
index 36db37d68..a52c466bf 100644
--- a/java/src/org/broadinstitute/sting/gatk/datasources/shards/BlockDelimitedReadShard.java
+++ b/java/src/org/broadinstitute/sting/gatk/datasources/shards/BlockDelimitedReadShard.java
@@ -26,7 +26,7 @@ public class BlockDelimitedReadShard extends ReadShard implements BAMFormatAware
     /**
      * The data backing the next chunks to deliver to the traversal engine.
      */
-    private final Map<SAMReaderID,BAMFileSpan> fileSpans;
+    private final Map<SAMReaderID,SAMFileSpan> fileSpans;
 
     /**
      * The reads making up this shard.
@@ -44,7 +44,7 @@ public class BlockDelimitedReadShard extends ReadShard implements BAMFormatAware
      */
     private final Shard.ShardType shardType;        
 
-    public BlockDelimitedReadShard(Reads sourceInfo, Map<SAMReaderID,BAMFileSpan> fileSpans, SamRecordFilter filter, Shard.ShardType shardType) {
+    public BlockDelimitedReadShard(Reads sourceInfo, Map<SAMReaderID,SAMFileSpan> fileSpans, SamRecordFilter filter, Shard.ShardType shardType) {
         this.sourceInfo = sourceInfo;
         this.fileSpans = fileSpans;
         this.filter = filter;
@@ -109,7 +109,7 @@ public class BlockDelimitedReadShard extends ReadShard implements BAMFormatAware
      * @return a list of chunks that contain data for this shard.
      */
     @Override
-    public Map<SAMReaderID,BAMFileSpan> getFileSpans() {
+    public Map<SAMReaderID,SAMFileSpan> getFileSpans() {
         return Collections.unmodifiableMap(fileSpans);
     }
 
@@ -128,7 +128,7 @@ public class BlockDelimitedReadShard extends ReadShard implements BAMFormatAware
     @Override
     public String toString() {
         StringBuilder sb = new StringBuilder();
-        for(Map.Entry<SAMReaderID,BAMFileSpan> entry: fileSpans.entrySet()) {
+        for(Map.Entry<SAMReaderID,SAMFileSpan> entry: fileSpans.entrySet()) {
             sb.append(entry.getKey());
             sb.append(": ");
             sb.append(entry.getValue());
diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/shards/BlockDelimitedReadShardStrategy.java b/java/src/org/broadinstitute/sting/gatk/datasources/shards/BlockDelimitedReadShardStrategy.java
index d50923055..66b18502e 100644
--- a/java/src/org/broadinstitute/sting/gatk/datasources/shards/BlockDelimitedReadShardStrategy.java
+++ b/java/src/org/broadinstitute/sting/gatk/datasources/shards/BlockDelimitedReadShardStrategy.java
@@ -55,7 +55,7 @@ public class BlockDelimitedReadShardStrategy extends ReadShardStrategy {
     /**
      * Ending position of the last shard in the file.
      */
-    private Map<SAMReaderID,BAMFileSpan> position;
+    private Map<SAMReaderID,SAMFileSpan> position;
 
     /**
      * Create a new read shard strategy, loading read shards from the given BAM file.
@@ -103,18 +103,18 @@ public class BlockDelimitedReadShardStrategy extends ReadShardStrategy {
     }
 
     public void advance() {
-        Map<SAMReaderID,BAMFileSpan> shardPosition = new HashMap<SAMReaderID,BAMFileSpan>();
+        Map<SAMReaderID,SAMFileSpan> shardPosition = new HashMap<SAMReaderID,SAMFileSpan>();
         nextShard = null;
         SamRecordFilter filter = null;
 
         if(locations != null) {
-            Map<SAMReaderID,BAMFileSpan> selectedReaders = new HashMap<SAMReaderID,BAMFileSpan>();
+            Map<SAMReaderID,SAMFileSpan> selectedReaders = new HashMap<SAMReaderID,SAMFileSpan>();
             while(selectedReaders.size() == 0 && currentFilePointer != null) {
                 shardPosition = currentFilePointer.fileSpans;
                 for(SAMReaderID id: shardPosition.keySet()) {
-                    BAMFileSpan fileSpans = shardPosition.get(id).removeBefore(position.get(id));
-                    if(!fileSpans.isEmpty())
-                        selectedReaders.put(id,fileSpans);
+                    SAMFileSpan fileSpan = shardPosition.get(id).removeContentsBefore(position.get(id));
+                    if(!fileSpan.isEmpty())
+                        selectedReaders.put(id,fileSpan);
                 }
 
                 if(selectedReaders.size() > 0) {
diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/shards/IndexDelimitedLocusShard.java b/java/src/org/broadinstitute/sting/gatk/datasources/shards/IndexDelimitedLocusShard.java
index 5d7ff317a..8719b8e6c 100755
--- a/java/src/org/broadinstitute/sting/gatk/datasources/shards/IndexDelimitedLocusShard.java
+++ b/java/src/org/broadinstitute/sting/gatk/datasources/shards/IndexDelimitedLocusShard.java
@@ -5,7 +5,7 @@ import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.gatk.iterators.StingSAMIterator;
 import org.broadinstitute.sting.gatk.datasources.simpleDataSources.SAMReaderID;
 import net.sf.samtools.SAMRecord;
-import net.sf.samtools.BAMFileSpan;
+import net.sf.samtools.SAMFileSpan;
 import net.sf.picard.filter.SamRecordFilter;
 
 import java.util.List;
@@ -44,7 +44,7 @@ public class IndexDelimitedLocusShard extends LocusShard implements BAMFormatAwa
     /**
      * A list of the chunks associated with this shard.
      */
-    private final Map<SAMReaderID, BAMFileSpan> fileSpans;
+    private final Map<SAMReaderID,SAMFileSpan> fileSpans;
 
     /**
      * An IndexDelimitedLocusShard can be used either for LOCUS or LOCUS_INTERVAL shard types.
@@ -58,7 +58,7 @@ public class IndexDelimitedLocusShard extends LocusShard implements BAMFormatAwa
      * @param fileSpans File spans associated with that interval.
      * @param shardType Type of the shard; must be either LOCUS or LOCUS_INTERVAL.
      */
-    IndexDelimitedLocusShard(List<GenomeLoc> intervals, Map<SAMReaderID,BAMFileSpan> fileSpans, ShardType shardType) {
+    IndexDelimitedLocusShard(List<GenomeLoc> intervals, Map<SAMReaderID,SAMFileSpan> fileSpans, ShardType shardType) {
         super(intervals);
         this.fileSpans = fileSpans;
         if(shardType != ShardType.LOCUS && shardType != ShardType.LOCUS_INTERVAL)
@@ -71,7 +71,7 @@ public class IndexDelimitedLocusShard extends LocusShard implements BAMFormatAwa
      * @return A list of the file spans to use when retrieving locus data.
      */
     @Override
-    public Map<SAMReaderID,BAMFileSpan> getFileSpans() {
+    public Map<SAMReaderID,SAMFileSpan> getFileSpans() {
         return fileSpans;
     }
 
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 64fdc8457..2504024d5 100755
--- a/java/src/org/broadinstitute/sting/gatk/datasources/shards/IndexDelimitedLocusShardStrategy.java
+++ b/java/src/org/broadinstitute/sting/gatk/datasources/shards/IndexDelimitedLocusShardStrategy.java
@@ -13,7 +13,7 @@ import java.util.*;
 
 import net.sf.samtools.SAMFileHeader;
 import net.sf.samtools.SAMSequenceRecord;
-import net.sf.samtools.BAMFileSpan;
+import net.sf.samtools.SAMFileSpan;
 
 /*
  * Copyright (c) 2009 The Broad Institute
@@ -126,7 +126,7 @@ public class IndexDelimitedLocusShardStrategy implements ShardStrategy {
      */
     public IndexDelimitedLocusShard next() {
         FilePointer nextFilePointer = filePointerIterator.next();
-        Map<SAMReaderID, BAMFileSpan> fileSpansBounding = nextFilePointer.fileSpans != null ? nextFilePointer.fileSpans : null;
+        Map<SAMReaderID,SAMFileSpan> fileSpansBounding = nextFilePointer.fileSpans != null ? nextFilePointer.fileSpans : null;
         return new IndexDelimitedLocusShard(nextFilePointer.locations,fileSpansBounding,Shard.ShardType.LOCUS_INTERVAL);
     }
 
diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/shards/IntervalSharder.java b/java/src/org/broadinstitute/sting/gatk/datasources/shards/IntervalSharder.java
index 4dba5cdf2..16b6934da 100644
--- a/java/src/org/broadinstitute/sting/gatk/datasources/shards/IntervalSharder.java
+++ b/java/src/org/broadinstitute/sting/gatk/datasources/shards/IntervalSharder.java
@@ -75,11 +75,11 @@ public class IntervalSharder {
         FilePointer lastFilePointer = null;
         BAMOverlap lastBAMOverlap = null;
 
-        Map<SAMReaderID,PreloadedBAMFileIndex> readerToIndexMap = new HashMap<SAMReaderID,PreloadedBAMFileIndex>();
+        Map<SAMReaderID,CachingBAMFileIndex> readerToIndexMap = new HashMap<SAMReaderID,CachingBAMFileIndex>();
         BinMergingIterator binMerger = new BinMergingIterator();
         for(SAMReaderID id: dataSource.getReaderIDs()) {
             final SAMSequenceRecord referenceSequence = dataSource.getHeader(id).getSequence(contig);
-            final PreloadedBAMFileIndex index = dataSource.getIndex(id);
+            final CachingBAMFileIndex index = dataSource.getIndex(id);
             binMerger.addReader(id,
                                 index,
                                 referenceSequence.getSequenceIndex(),
@@ -170,7 +170,7 @@ public class IntervalSharder {
 
         // Lookup the locations for every file pointer in the index.
         for(SAMReaderID id: dataSource.getReaderIDs()) {
-            PreloadedBAMFileIndex index = readerToIndexMap.get(id);
+            CachingBAMFileIndex index = readerToIndexMap.get(id);
             for(FilePointer filePointer: filePointers)
                 filePointer.addFileSpans(id,index.getChunksOverlapping(filePointer.overlap.getBin(id)));
             index.close();
@@ -183,7 +183,7 @@ public class IntervalSharder {
         private PriorityQueue<BinQueueState> binQueue = new PriorityQueue<BinQueueState>();
         private Queue<BAMOverlap> pendingOverlaps = new LinkedList<BAMOverlap>();
 
-        public void addReader(final SAMReaderID id, final PreloadedBAMFileIndex index, final int referenceSequence, Iterator<Bin> bins) {
+        public void addReader(final SAMReaderID id, final CachingBAMFileIndex index, final int referenceSequence, Iterator<Bin> bins) {
             binQueue.add(new BinQueueState(id,index,referenceSequence,new LowestLevelBinFilteringIterator(index,bins)));
         }
 
@@ -276,11 +276,11 @@ public class IntervalSharder {
 
         private class ReaderBin {
             public final SAMReaderID id;
-            public final PreloadedBAMFileIndex index;
+            public final CachingBAMFileIndex index;
             public final int referenceSequence;
             public final Bin bin;
 
-            public ReaderBin(final SAMReaderID id, final PreloadedBAMFileIndex index, final int referenceSequence, final Bin bin) {
+            public ReaderBin(final SAMReaderID id, final CachingBAMFileIndex index, final int referenceSequence, final Bin bin) {
                 this.id = id;
                 this.index = index;
                 this.referenceSequence = referenceSequence;
@@ -298,11 +298,11 @@ public class IntervalSharder {
 
         private class BinQueueState implements Comparable<BinQueueState> {
             public final SAMReaderID id;
-            public final PreloadedBAMFileIndex index;
+            public final CachingBAMFileIndex index;
             public final int referenceSequence;
             public final PeekableIterator<Bin> bins;
 
-            public BinQueueState(final SAMReaderID id, final PreloadedBAMFileIndex index, final int referenceSequence, final Iterator<Bin> bins) {
+            public BinQueueState(final SAMReaderID id, final CachingBAMFileIndex index, final int referenceSequence, final Iterator<Bin> bins) {
                 this.id = id;
                 this.index = index;
                 this.referenceSequence = referenceSequence;
@@ -334,12 +334,12 @@ public class IntervalSharder {
      * Filters out bins not at the lowest level in the tree.
      */
     private static class LowestLevelBinFilteringIterator implements Iterator<Bin> {
-        private PreloadedBAMFileIndex index;
+        private CachingBAMFileIndex index;
         private Iterator<Bin> wrappedIterator;
 
         private Bin nextBin;
 
-        public LowestLevelBinFilteringIterator(final PreloadedBAMFileIndex index, Iterator<Bin> iterator) {
+        public LowestLevelBinFilteringIterator(final CachingBAMFileIndex index, Iterator<Bin> iterator) {
             this.index = index;
             this.wrappedIterator = iterator;
             advance();
@@ -372,7 +372,7 @@ public class IntervalSharder {
  * Represents a small section of a BAM file, and every associated interval.
  */
 class FilePointer {
-    protected final Map<SAMReaderID,BAMFileSpan> fileSpans = new HashMap<SAMReaderID,BAMFileSpan>();
+    protected final Map<SAMReaderID,SAMFileSpan> fileSpans = new HashMap<SAMReaderID,SAMFileSpan>();
     protected final String referenceSequence;
     protected final BAMOverlap overlap;
     protected final List<GenomeLoc> locations;
@@ -393,7 +393,7 @@ class FilePointer {
         locations.add(location);
     }
 
-    public void addFileSpans(SAMReaderID id, BAMFileSpan fileSpan) {
+    public void addFileSpans(SAMReaderID id, SAMFileSpan fileSpan) {
         this.fileSpans.put(id,fileSpan);
     }
 }
diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/BlockDrivenSAMDataSource.java b/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/BlockDrivenSAMDataSource.java
index f25bcf357..cff278441 100644
--- a/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/BlockDrivenSAMDataSource.java
+++ b/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/BlockDrivenSAMDataSource.java
@@ -53,7 +53,7 @@ public class BlockDrivenSAMDataSource extends SAMDataSource {
     /**
      * How far along is each reader?
      */
-    private final Map<SAMReaderID,BAMFileSpan> readerPositions = new HashMap<SAMReaderID,BAMFileSpan>();
+    private final Map<SAMReaderID,SAMFileSpan> readerPositions = new HashMap<SAMReaderID,SAMFileSpan>();
 
     /**
      * Create a new block-aware SAM data source given the supplied read metadata.
@@ -129,16 +129,16 @@ public class BlockDrivenSAMDataSource extends SAMDataSource {
      * @param id Id of the reader.
      * @return The index.  Will preload the index if necessary.
      */
-    public PreloadedBAMFileIndex getIndex(final SAMReaderID id) {
+    public CachingBAMFileIndex getIndex(final SAMReaderID id) {
         SAMReaders readers = resourcePool.getReadersWithoutLocking();
-        return readers.getReader(id).getIndex(PreloadedBAMFileIndex.class);
+        return readers.getReader(id).getIndex(CachingBAMFileIndex.class);
     }
 
     /**
      * Retrieves the current position within the BAM file.
      * @return A mapping of reader to current position.
      */
-    public Map<SAMReaderID,BAMFileSpan> getCurrentPosition() {
+    public Map<SAMReaderID,SAMFileSpan> getCurrentPosition() {
         return readerPositions;
     }
 
@@ -182,7 +182,7 @@ public class BlockDrivenSAMDataSource extends SAMDataSource {
      * @param read The read to add to the shard.
      */
     private void addReadToBufferingShard(BAMFormatAwareShard shard,SAMReaderID id,SAMRecord read) {
-        BAMFileSpan endChunk = read.getFilePointer().getFilePointerFollowing();
+        SAMFileSpan endChunk = read.getFilePointer().getContentsFollowing();
         shard.addRead(read);
         readerPositions.put(id,endChunk);
     }
@@ -207,7 +207,7 @@ public class BlockDrivenSAMDataSource extends SAMDataSource {
      */
     private void initializeReaderPositions(SAMReaders readers) {
         for(SAMReaderID id: getReaderIDs())
-            readerPositions.put(id,readers.getReader(id).getStartOfDataSegment());
+            readerPositions.put(id,readers.getReader(id).getFilePointerSpanningReads());
     }
 
     public StingSAMIterator seek(Shard shard) {
@@ -386,7 +386,7 @@ public class BlockDrivenSAMDataSource extends SAMDataSource {
          */
         public SAMReaders(Reads sourceInfo) {
             for(File readsFile: sourceInfo.getReadsFiles()) {
-                SAMFileReader reader = new SAMFileReader(readsFile,true);
+                SAMFileReader reader = new SAMFileReader(readsFile,CachingBAMFileIndex.class,true);
                 reader.setValidationStringency(sourceInfo.getValidationStringency());
 
                 // If no read group is present, hallucinate one.
diff --git a/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java b/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java
index 0dd5a90f2..f4db442ae 100755
--- a/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java
+++ b/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java
@@ -341,5 +341,5 @@ public class GATKSAMRecord extends SAMRecord {
 
     public String toString() { return mRecord.toString(); }
 
-    public BAMFileSpan getFilePointer() { return mRecord.getFilePointer(); }
+    public SAMFileSpan getFilePointer() { return mRecord.getFilePointer(); }
 }
diff --git a/settings/repository/edu.mit.broad/picard-private-parts-1333-sharding-5.jar b/settings/repository/edu.mit.broad/picard-private-parts-1333-sharding-6.jar
similarity index 77%
rename from settings/repository/edu.mit.broad/picard-private-parts-1333-sharding-5.jar
rename to settings/repository/edu.mit.broad/picard-private-parts-1333-sharding-6.jar
index 840bb9824..f6aa3879f 100644
Binary files a/settings/repository/edu.mit.broad/picard-private-parts-1333-sharding-5.jar and b/settings/repository/edu.mit.broad/picard-private-parts-1333-sharding-6.jar differ
diff --git a/settings/repository/edu.mit.broad/picard-private-parts-1333-sharding-5.xml b/settings/repository/edu.mit.broad/picard-private-parts-1333-sharding-6.xml
similarity index 55%
rename from settings/repository/edu.mit.broad/picard-private-parts-1333-sharding-5.xml
rename to settings/repository/edu.mit.broad/picard-private-parts-1333-sharding-6.xml
index c358868fb..9142b18c2 100644
--- a/settings/repository/edu.mit.broad/picard-private-parts-1333-sharding-5.xml
+++ b/settings/repository/edu.mit.broad/picard-private-parts-1333-sharding-6.xml
@@ -1,3 +1,3 @@
 <ivy-module version="1.0">
-    <info organisation="edu.mit.broad" module="picard-private-parts" revision="1333-sharding-5" status="integration" publication="20100326102100" />
+    <info organisation="edu.mit.broad" module="picard-private-parts" revision="1333-sharding-6" status="integration" publication="20100330130700" />
 </ivy-module>
diff --git a/settings/repository/net.sf/picard-1.16.365-sharding.jar b/settings/repository/net.sf/picard-1.16.366-sharding.jar
similarity index 96%
rename from settings/repository/net.sf/picard-1.16.365-sharding.jar
rename to settings/repository/net.sf/picard-1.16.366-sharding.jar
index 654a6bd76..3c806124e 100644
Binary files a/settings/repository/net.sf/picard-1.16.365-sharding.jar and b/settings/repository/net.sf/picard-1.16.366-sharding.jar differ
diff --git a/settings/repository/net.sf/picard-1.16.365-sharding.xml b/settings/repository/net.sf/picard-1.16.366-sharding.xml
similarity index 76%
rename from settings/repository/net.sf/picard-1.16.365-sharding.xml
rename to settings/repository/net.sf/picard-1.16.366-sharding.xml
index f3f1d873c..6ad217e69 100644
--- a/settings/repository/net.sf/picard-1.16.365-sharding.xml
+++ b/settings/repository/net.sf/picard-1.16.366-sharding.xml
@@ -1,3 +1,3 @@
 <ivy-module version="1.0">
-    <info organisation="net.sf" module="picard" revision="1.16.365-sharding" status="release" />
+    <info organisation="net.sf" module="picard" revision="1.16.366-sharding" status="release" />
 </ivy-module>
diff --git a/settings/repository/net.sf/sam-1.16.365-sharding.jar b/settings/repository/net.sf/sam-1.16.366-sharding.jar
similarity index 86%
rename from settings/repository/net.sf/sam-1.16.365-sharding.jar
rename to settings/repository/net.sf/sam-1.16.366-sharding.jar
index 15571057f..acdf6f809 100644
Binary files a/settings/repository/net.sf/sam-1.16.365-sharding.jar and b/settings/repository/net.sf/sam-1.16.366-sharding.jar differ
diff --git a/settings/repository/net.sf/sam-1.16.365-sharding.xml b/settings/repository/net.sf/sam-1.16.366-sharding.xml
similarity index 52%
rename from settings/repository/net.sf/sam-1.16.365-sharding.xml
rename to settings/repository/net.sf/sam-1.16.366-sharding.xml
index f9aa3ca37..0a2878262 100644
--- a/settings/repository/net.sf/sam-1.16.365-sharding.xml
+++ b/settings/repository/net.sf/sam-1.16.366-sharding.xml
@@ -1,3 +1,3 @@
 <ivy-module version="1.0">
-    <info organisation="net.sf" module="sam" revision="1.16.365-sharding" status="release" />
+    <info organisation="net.sf" module="sam" revision="1.16.366-sharding" status="release" />
 </ivy-module>