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 6d7631a13..90e8a2c3a 100755
--- a/java/src/org/broadinstitute/sting/gatk/datasources/providers/AllLocusView.java
+++ b/java/src/org/broadinstitute/sting/gatk/datasources/providers/AllLocusView.java
@@ -1,5 +1,6 @@
 package org.broadinstitute.sting.gatk.datasources.providers;
 
+import java.util.List;
 import java.util.NoSuchElementException;
 import java.util.ArrayList;
 import java.util.Collections;
@@ -97,7 +98,9 @@ public class AllLocusView extends LocusView {
      * @param site Site at which to create the blank locus context.
      * @return empty context.
      */
-    private AlignmentContext createEmptyLocus( GenomeLoc site ) {        
-        return new AlignmentContext(site,new ReadBackedPileupImpl(site,new ArrayList<SAMRecord>(), new ArrayList<Integer>()));
+    private final static List<SAMRecord> EMPTY_PILEUP_READS = Collections.emptyList();
+    private final static List<Integer> EMPTY_PILEUP_OFFSETS = Collections.emptyList();
+    private AlignmentContext createEmptyLocus( GenomeLoc site ) {
+        return new AlignmentContext(site,new ReadBackedPileupImpl(site, EMPTY_PILEUP_READS, EMPTY_PILEUP_OFFSETS));
     }
 }
diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/providers/ManagingReferenceOrderedView.java b/java/src/org/broadinstitute/sting/gatk/datasources/providers/ManagingReferenceOrderedView.java
index b4b1d7f8a..a91e169c1 100755
--- a/java/src/org/broadinstitute/sting/gatk/datasources/providers/ManagingReferenceOrderedView.java
+++ b/java/src/org/broadinstitute/sting/gatk/datasources/providers/ManagingReferenceOrderedView.java
@@ -50,8 +50,8 @@ public class ManagingReferenceOrderedView implements ReferenceOrderedView {
      * @return A tracker containing information about this locus.
      */
     public RefMetaDataTracker getReferenceOrderedDataAtLocus( GenomeLoc loc ) {
-        RefMetaDataTracker tracks = new RefMetaDataTracker();
-        for (ReferenceOrderedDataState state: states )
+        RefMetaDataTracker tracks = new RefMetaDataTracker(states.size());
+        for ( ReferenceOrderedDataState state: states )
             tracks.bind( state.dataSource.getName(), state.iterator.seekForward(loc) );
         return tracks;
     }
diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/providers/RodLocusView.java b/java/src/org/broadinstitute/sting/gatk/datasources/providers/RodLocusView.java
index e2ce6b331..feed2ab85 100644
--- a/java/src/org/broadinstitute/sting/gatk/datasources/providers/RodLocusView.java
+++ b/java/src/org/broadinstitute/sting/gatk/datasources/providers/RodLocusView.java
@@ -138,7 +138,7 @@ public class RodLocusView extends LocusView implements ReferenceOrderedView {
     }
 
     private RefMetaDataTracker createTracker( Collection<RODRecordList> allTracksHere ) {
-        RefMetaDataTracker t = new RefMetaDataTracker();
+        RefMetaDataTracker t = new RefMetaDataTracker(allTracksHere.size());
         for ( RODRecordList track : allTracksHere ) {
             if ( ! t.hasROD(track.getName()) )
                 t.bind(track.getName(), track);
diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/RefMetaDataTracker.java b/java/src/org/broadinstitute/sting/gatk/refdata/RefMetaDataTracker.java
index 48f3354d2..d5063d643 100644
--- a/java/src/org/broadinstitute/sting/gatk/refdata/RefMetaDataTracker.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/RefMetaDataTracker.java
@@ -28,9 +28,15 @@ Genotype * Traversal calls tracker.bind(name, RMD) for each RMDs in RMDs
  * Time: 3:05:23 PM
  */
 public class RefMetaDataTracker {
-    final HashMap<String, RODRecordList> map = new HashMap<String, RODRecordList>();
+    final Map<String, RODRecordList> map;
     protected static Logger logger = Logger.getLogger(RefMetaDataTracker.class);
 
+    public RefMetaDataTracker(int nBindings) {
+        if ( nBindings == 0 )
+            map = Collections.emptyMap();
+        else
+            map = new HashMap<String, RODRecordList>(nBindings);
+    }
 
     /**
      * get all the reference meta data associated with a track name.
diff --git a/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java b/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java
index 439cd41f7..717ced97f 100644
--- a/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java
+++ b/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java
@@ -106,10 +106,10 @@ public class GenomeLocParser {
      * @return the contig index, -1 if not found
      */
     public int getContigIndex(final String contig, boolean exceptionOut) {
-        if (contigInfo.getSequenceIndex(contig) == -1 && exceptionOut)
+        int idx = contigInfo.getSequenceIndex(contig);
+        if (idx == -1 && exceptionOut)
             throw new UserException.CommandLineException(String.format("Contig %s given as location, but this contig isn't present in the Fasta sequence dictionary", contig));
-
-        return contigInfo.getSequenceIndex(contig);
+        return idx;
     }
 
     /**