From b8b2b9b2de6270e1aead4f17ecf01b27d7f123f7 Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Sun, 13 Jan 2013 20:44:28 -0500
Subject: [PATCH] ManagingReferenceOrderedView optimization: don't allow a
 fresh RefMetaDataTracker in the frequent case where there's no reference meta
 data

---
 .../providers/ManagingReferenceOrderedView.java    | 14 +++++++++-----
 .../sting/gatk/refdata/RefMetaDataTracker.java     |  1 +
 2 files changed, 10 insertions(+), 5 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ManagingReferenceOrderedView.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ManagingReferenceOrderedView.java
index 7d3cac33d..09b72f5eb 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ManagingReferenceOrderedView.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ManagingReferenceOrderedView.java
@@ -77,13 +77,17 @@ public class ManagingReferenceOrderedView implements ReferenceOrderedView {
      * @return A tracker containing information about this locus.
      */
     public RefMetaDataTracker getReferenceOrderedDataAtLocus( GenomeLoc loc, ReferenceContext referenceContext ) {
-        List<RODRecordList> bindings = states.isEmpty() ? Collections.<RODRecordList>emptyList() : new ArrayList<RODRecordList>(states.size());
+        if ( states.isEmpty() )
+            return RefMetaDataTracker.EMPTY_TRACKER;
+        else {
+            List<RODRecordList> bindings = new ArrayList<RODRecordList>(states.size());
 
-        for ( ReferenceOrderedDataState state: states )
-            // todo -- warning, I removed the reference to the name from states
-            bindings.add( state.iterator.seekForward(loc) );
+            for ( ReferenceOrderedDataState state: states )
+                // todo -- warning, I removed the reference to the name from states
+                bindings.add( state.iterator.seekForward(loc) );
 
-        return new RefMetaDataTracker(bindings);
+            return new RefMetaDataTracker(bindings);
+        }
     }
 
     /**
diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/RefMetaDataTracker.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/RefMetaDataTracker.java
index 9cb38b840..5a1b015fe 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/refdata/RefMetaDataTracker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/RefMetaDataTracker.java
@@ -61,6 +61,7 @@ public class RefMetaDataTracker {
 
     final Map<String, RODRecordList> bindings;
     final protected static Logger logger = Logger.getLogger(RefMetaDataTracker.class);
+    public final static RefMetaDataTracker EMPTY_TRACKER = new RefMetaDataTracker();
 
     // ------------------------------------------------------------------------------------------
     //