diff --git a/build.xml b/build.xml
index 4861d577f..584e0808c 100644
--- a/build.xml
+++ b/build.xml
@@ -329,8 +329,8 @@
         <junit printsummary="yes" showoutput="yes" maxmemory="${test.maxmemory}" clonevm="yes" haltonfailure="${halt}" failureProperty="test.failure">
             <formatter type="${testOutput}" usefile="${usefile}" />
             <classpath>
-                <path refid="runtime.dependencies"/>
                 <pathelement location="${dist.dir}/GenomeAnalysisTK.jar"/>
+                <path refid="runtime.dependencies"/>
                 <pathelement location="${test.classes}"/>
                 <pathelement location="lib/junit-4.4.jar"/>
             </classpath>
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 0e38f7782..5d4c9537c 100755
--- a/java/src/org/broadinstitute/sting/gatk/datasources/shards/IndexDelimitedLocusShardStrategy.java
+++ b/java/src/org/broadinstitute/sting/gatk/datasources/shards/IndexDelimitedLocusShardStrategy.java
@@ -63,25 +63,35 @@ public class IndexDelimitedLocusShardStrategy implements ShardStrategy {
      * @param locations List of locations for which to load data.
      */
     IndexDelimitedLocusShardStrategy(SAMDataSource dataSource, GenomeLocSortedSet locations) {
-        if(!(dataSource instanceof BlockDrivenSAMDataSource))
-            throw new StingException("Cannot power an IndexDelimitedLocusShardStrategy with this data source.");
+        if(dataSource != null) {
+            // Shard based on reads.
+            // TODO: Push this sharding into the data source.
+            if(!(dataSource instanceof BlockDrivenSAMDataSource))
+                throw new StingException("Cannot power an IndexDelimitedLocusShardStrategy with this data source.");
 
-        List<GenomeLoc> intervals;
-        if(locations == null) {
-            // If no locations were passed in, shard the entire BAM file.
-            SAMFileHeader header = dataSource.getHeader();
-            intervals = new ArrayList<GenomeLoc>();
+            List<GenomeLoc> intervals;
+            if(locations == null) {
+                // If no locations were passed in, shard the entire BAM file.
+                SAMFileHeader header = dataSource.getHeader();
+                intervals = new ArrayList<GenomeLoc>();
 
-            for(SAMSequenceRecord sequenceRecord: header.getSequenceDictionary().getSequences())
-                intervals.add(GenomeLocParser.createGenomeLoc(sequenceRecord.getSequenceName(),1,sequenceRecord.getSequenceLength()));    
+                for(SAMSequenceRecord sequenceRecord: header.getSequenceDictionary().getSequences())
+                    intervals.add(GenomeLocParser.createGenomeLoc(sequenceRecord.getSequenceName(),1,sequenceRecord.getSequenceLength()));
+            }
+            else
+                intervals = locations.toList();
+
+
+            this.dataSource = (BlockDrivenSAMDataSource)dataSource;
+            filePointers.addAll(IntervalSharder.shardIntervals(this.dataSource,intervals,this.dataSource.getNumIndexLevels()-1));
+        }
+        else {
+            this.dataSource = null;
+            for(GenomeLoc interval: locations)
+                filePointers.add(new FilePointer(interval));
         }
-        else
-            intervals = locations.toList();
 
-
-        this.dataSource = (BlockDrivenSAMDataSource)dataSource;
-        filePointers.addAll(IntervalSharder.shardIntervals(this.dataSource,intervals,this.dataSource.getNumIndexLevels()-1));
-        filePointerIterator = filePointers.iterator();
+        filePointerIterator = filePointers.iterator();        
     }
 
     /**
@@ -100,7 +110,7 @@ public class IndexDelimitedLocusShardStrategy implements ShardStrategy {
      */
     public IndexDelimitedLocusShard next() {
         FilePointer nextFilePointer = filePointerIterator.next();
-        Map<SAMFileReader2,List<Chunk>> chunksBounding = dataSource.getFilePointersBounding(nextFilePointer.bin);
+        Map<SAMFileReader2,List<Chunk>> chunksBounding = dataSource!=null ? dataSource.getFilePointersBounding(nextFilePointer.bin) : null;
         return new IndexDelimitedLocusShard(nextFilePointer.locations,chunksBounding,Shard.ShardType.LOCUS_INTERVAL);
     }
 
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 0761e9480..13c4d91a9 100644
--- a/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/BlockDrivenSAMDataSource.java
+++ b/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/BlockDrivenSAMDataSource.java
@@ -64,8 +64,12 @@ public class BlockDrivenSAMDataSource extends SAMDataSource {
             ReadGroupMapping mapping = new ReadGroupMapping();
 
             List<SAMReadGroupRecord> readGroups = reader.getFileHeader().getReadGroups();
-            for(SAMReadGroupRecord readGroup: readGroups)
-                mapping.put(readGroup.getReadGroupId(),headerMerger.getReadGroupId(reader,readGroup.getReadGroupId()));    
+            for(SAMReadGroupRecord readGroup: readGroups) {
+                if(headerMerger.hasReadGroupCollisions())
+                    mapping.put(readGroup.getReadGroupId(),headerMerger.getReadGroupId(reader,readGroup.getReadGroupId()));
+                else
+                    mapping.put(readGroup.getReadGroupId(),readGroup.getReadGroupId());
+            }
 
             mergedReadGroupMappings.put(id,mapping);
         }
@@ -110,7 +114,10 @@ public class BlockDrivenSAMDataSource extends SAMDataSource {
         Map<SAMFileReader2,List<Chunk>> filePointers = new HashMap<SAMFileReader2,List<Chunk>>();
         for(SAMFileReader reader: readers) {
             SAMFileReader2 reader2 = (SAMFileReader2)reader;
-            filePointers.put(reader2,reader2.getFilePointersBounding(bin));
+            if(bin != null)
+                filePointers.put(reader2,reader2.getFilePointersBounding(bin));
+            else
+                filePointers.put(reader2,Collections.<Chunk>emptyList());
         }
         return filePointers;
     }