Continuing refactoring of RefMetaDataTracker.

On the path towards converging getVariantContext() and getValues() in tracker so that we can have a single approach to get values from RODs with the new RodBinding() types

public/java/src/org/broadinstitute/sting/commandline/VariantContextRodBinding.java

@@ -1,82 +1,78 @@
-///*
+/*
-// * Copyright (c) 2011, The Broad Institute
+* Copyright (c) 2011, The Broad Institute
-// *
+*
-// * Permission is hereby granted, free of charge, to any person
+* Permission is hereby granted, free of charge, to any person
-// * obtaining a copy of this software and associated documentation
+* obtaining a copy of this software and associated documentation
-// * files (the "Software"), to deal in the Software without
+* files (the "Software"), to deal in the Software without
-// * restriction, including without limitation the rights to use,
+* restriction, including without limitation the rights to use,
-// * copy, modify, merge, publish, distribute, sublicense, and/or sell
+* copy, modify, merge, publish, distribute, sublicense, and/or sell
-// * copies of the Software, and to permit persons to whom the
+* copies of the Software, and to permit persons to whom the
-// * Software is furnished to do so, subject to the following
+* Software is furnished to do so, subject to the following
-// * conditions:
+* conditions:
-// *
+*
-// * The above copyright notice and this permission notice shall be
+* The above copyright notice and this permission notice shall be
-// * included in all copies or substantial portions of the Software.
+* included in all copies or substantial portions of the Software.
-// * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
-// * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
-// * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
-// * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
-// * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
-// * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
-// * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
-// * OTHER DEALINGS IN THE SOFTWARE.
+* OTHER DEALINGS IN THE SOFTWARE.
-// */
+*/
-//
+
-//package org.broadinstitute.sting.commandline;
+package org.broadinstitute.sting.commandline;
-//
+
-//import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-//import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-//import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.GenomeLoc;
-//import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-//
+
-//import java.util.Collection;
+import java.util.Collection;
-//
+
-///**
+/**
-// * A RodBinding representing a walker argument that gets bound to a ROD track containing VariantContexts
+* A RodBinding representing a walker argument that gets bound to a ROD track containing VariantContexts
-// */
+*/
-//public class VariantContextRodBinding extends RodBinding {
+public class VariantContextRodBinding extends RodBinding {
-//    /**
+    /**
-//     * Create a new RodBinding specialized to provide VariantContexts.
+     * Create a new RodBinding specialized to provide VariantContexts.
-//     * @param variableName the name of the field in the walker that we will bind the ROD track too
+     * @param variableName the name of the field in the walker that we will bind the ROD track too
-//     * @param sourceFile the data source from which we will read the VCs
+     * @param sourceFile the data source from which we will read the VCs
-//     * @param parser the Engine parser used to obtain information about this argument, such as its underlying file type
+     * @param parser the Engine parser used to obtain information about this argument, such as its underlying file type
-//     */
+     */
-//    protected VariantContextRodBinding(final String variableName, final String sourceFile, final ParsingEngine parser) {
+    protected VariantContextRodBinding(final String variableName, final String sourceFile, final ParsingEngine parser) {
-//        super(variableName, sourceFile, parser);
+        super(VariantContext.class, variableName, sourceFile, parser);
-//    }
+    }
-//
+
-//    /**
+    /**
-//     * Forwarding method to identical tracker method
+     * Forwarding method to identical tracker method
-//     */
+     */
-//    public Collection<VariantContext> getVariantContexts(final RefMetaDataTracker tracker,
+    public Collection<VariantContext> getVariantContexts(final RefMetaDataTracker tracker,
-//                                                         final ReferenceContext ref,
+                                                         final GenomeLoc curLocation,
-//                                                         final GenomeLoc curLocation,
+                                                         final boolean requireStartHere,
-//                                                         final boolean requireStartHere,
+                                                         final boolean takeFirstOnly ) {
-//                                                         final boolean takeFirstOnly ) {
+        return tracker.getVariantContexts(variableName, curLocation, requireStartHere, takeFirstOnly);
-//        return tracker.getVariantContexts(ref, variableName, curLocation, requireStartHere, takeFirstOnly);
+    }
-//    }
+
-//
+    /**
-//    /**
+     * Forwarding method to identical tracker method
-//     * Forwarding method to identical tracker method
+     * @param tracker
-//     * @param tracker
+     * @param curLocation
-//     * @param ref
+     * @param requireStartHere
-//     * @param curLocation
+     * @return
-//     * @param requireStartHere
+     */
-//     * @return
+    public VariantContext getVariantContext(final RefMetaDataTracker tracker,
-//     */
+                                            final GenomeLoc curLocation,
-//    public VariantContext getVariantContext(final RefMetaDataTracker tracker,
+                                            final boolean requireStartHere ) {
-//                                            final ReferenceContext ref,
+        return tracker.getVariantContext(variableName, curLocation, requireStartHere);
-//                                            final GenomeLoc curLocation,
+    }
-//                                            final boolean requireStartHere ) {
+
-//        return tracker.getVariantContext(ref, variableName, curLocation, requireStartHere);
+    /**
-//    }
+     * Forwarding method to identical tracker method
-//
+     */
-//    /**
+    public VariantContext getVariantContext(final RefMetaDataTracker tracker,
-//     * Forwarding method to identical tracker method
+                                            final GenomeLoc curLocation) {
-//     */
+        return tracker.getVariantContext(variableName, curLocation);
-//    public VariantContext getVariantContext(final RefMetaDataTracker tracker,
+    }
-//                                            final ReferenceContext ref,
+}
-//                                            final GenomeLoc curLocation) {
-//        return tracker.getVariantContext(ref, variableName, curLocation);
-//    }
-//}

public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ManagingReferenceOrderedView.java

@@ -1,5 +1,6 @@
 package org.broadinstitute.sting.gatk.datasources.providers;
 
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.refdata.utils.LocationAwareSeekableRODIterator;
@@ -49,8 +50,8 @@ public class ManagingReferenceOrderedView implements ReferenceOrderedView {
      * @param loc Locus at which to track.
      * @return A tracker containing information about this locus.
      */
-    public RefMetaDataTracker getReferenceOrderedDataAtLocus( GenomeLoc loc ) {
+    public RefMetaDataTracker getReferenceOrderedDataAtLocus( GenomeLoc loc, ReferenceContext referenceContext ) {
-        RefMetaDataTracker tracks = new RefMetaDataTracker(states.size());
+        RefMetaDataTracker tracks = new RefMetaDataTracker(states.size(), referenceContext);
         for ( ReferenceOrderedDataState state: states )
             tracks.bind( state.dataSource.getName(), state.iterator.seekForward(loc) );
         return tracks;

public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReferenceOrderedView.java

@@ -1,8 +1,9 @@
 package org.broadinstitute.sting.gatk.datasources.providers;
 
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.utils.GenomeLoc;
 
 public interface ReferenceOrderedView extends View {
-    RefMetaDataTracker getReferenceOrderedDataAtLocus( GenomeLoc loc );
+    RefMetaDataTracker getReferenceOrderedDataAtLocus( GenomeLoc loc, ReferenceContext refContext );
 }

public/java/src/org/broadinstitute/sting/gatk/datasources/providers/RodLocusView.java

@@ -26,6 +26,7 @@
 package org.broadinstitute.sting.gatk.datasources.providers;
 
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.refdata.utils.LocationAwareSeekableRODIterator;
@@ -45,7 +46,8 @@ public class RodLocusView extends LocusView implements ReferenceOrderedView {
      */
     private RODMergingIterator rodQueue = null;
 
-    RefMetaDataTracker tracker = null;
+    Collection<RODRecordList> allTracksHere;
+
     GenomeLoc lastLoc = null;
     RODRecordList interval = null;
 
@@ -98,8 +100,17 @@ public class RodLocusView extends LocusView implements ReferenceOrderedView {
         //throw new StingException("RodLocusView currently disabled");
     }
 
-    public RefMetaDataTracker getReferenceOrderedDataAtLocus( GenomeLoc loc ) {
+    public RefMetaDataTracker getReferenceOrderedDataAtLocus( GenomeLoc loc, ReferenceContext referenceContext ) {
-        return tracker;
+        RefMetaDataTracker t = new RefMetaDataTracker(allTracksHere.size(), referenceContext);
+        for ( RODRecordList track : allTracksHere ) {
+            if ( ! t.hasValues(track.getName()) )
+                t.bind(track.getName(), track);
+        }
+
+        // special case the interval again -- add it into the ROD
+        if ( interval != null ) { t.bind(interval.getName(), interval); }
+
+        return t;
     }
 
     public boolean hasNext() {
@@ -122,10 +133,7 @@ public class RodLocusView extends LocusView implements ReferenceOrderedView {
 
         if ( DEBUG ) System.out.printf("In RodLocusView.next(): creating tracker...%n");
 
-        // Update the tracker here for use
+        allTracksHere = getSpanningTracks(datum);
-        Collection<RODRecordList> allTracksHere = getSpanningTracks(datum);
-        tracker = createTracker(allTracksHere);
-
         GenomeLoc rodSite = datum.getLocation();
         GenomeLoc site = genomeLocParser.createGenomeLoc( rodSite.getContig(), rodSite.getStart(), rodSite.getStart());
 
@@ -137,19 +145,6 @@ public class RodLocusView extends LocusView implements ReferenceOrderedView {
         return new AlignmentContext(site, new ReadBackedPileupImpl(site), skippedBases);
     }
 
-    private RefMetaDataTracker createTracker( Collection<RODRecordList> allTracksHere ) {
-        RefMetaDataTracker t = new RefMetaDataTracker(allTracksHere.size());
-        for ( RODRecordList track : allTracksHere ) {
-            if ( ! t.hasValues(track.getName()) )
-                t.bind(track.getName(), track);
-        }
-
-        // special case the interval again -- add it into the ROD
-        if ( interval != null ) { t.bind(interval.getName(), interval); }
-
-        return t;
-    }
-
     private Collection<RODRecordList> getSpanningTracks(RODRecordList marker) {
         return rodQueue.allElementsLTE(marker);
     }
@@ -197,10 +192,6 @@ public class RodLocusView extends LocusView implements ReferenceOrderedView {
         return getSkippedBases(getLocOneBeyondShard());
     }
 
-    public RefMetaDataTracker getTracker() {
-        return tracker;
-    }
-
     /**
      * Closes the current view.
      */
@@ -209,6 +200,6 @@ public class RodLocusView extends LocusView implements ReferenceOrderedView {
             state.dataSource.close( state.iterator );
 
         rodQueue = null;
-        tracker = null;
+        allTracksHere = null;
     }
 }

public/java/src/org/broadinstitute/sting/gatk/refdata/RefMetaDataTracker.java

@@ -4,6 +4,7 @@ import org.apache.log4j.Logger;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
 import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList;
+import org.broadinstitute.sting.gatk.walkers.Reference;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
@@ -18,7 +19,7 @@ import java.util.*;
  * The standard interaction model is:
  *
  * Traversal system arrives at a site, which has a bunch of RMDs covering it
-Genotype * Traversal calls tracker.bind(name, RMD) for each RMDs in RMDs
+ Genotype * Traversal calls tracker.bind(name, RMD) for each RMDs in RMDs
  * Traversal passes tracker to the walker
  * walker calls lookup(name, default) to obtain the RMDs values at this site, or default if none was
  *   bound at this site.
@@ -29,15 +30,83 @@ Genotype * Traversal calls tracker.bind(name, RMD) for each RMDs in RMDs
  */
 public class RefMetaDataTracker {
     final Map<String, RODRecordList> map;
+    final ReferenceContext ref;
     protected static Logger logger = Logger.getLogger(RefMetaDataTracker.class);
 
-    public RefMetaDataTracker(int nBindings) {
+    public RefMetaDataTracker(int nBindings, ReferenceContext ref) {
+        this.ref = ref;
         if ( nBindings == 0 )
             map = Collections.emptyMap();
         else
             map = new HashMap<String, RODRecordList>(nBindings);
     }
 
+
+    // ------------------------------------------------------------------------------------------
+    //
+    //
+    // Special ENGINE interaction functions
+    //
+    //
+    // ------------------------------------------------------------------------------------------
+
+    /**
+     * Binds the list of reference ordered data records (RMDs) to track name at this site.  Should be used only by the traversal
+     * system to provide access to RMDs in a structured way to the walkers.
+     *
+     * DO NOT USE THIS FUNCTION UNLESS YOU ARE THE GATK ENGINE
+     *
+     * @param name the name of the track
+     * @param rod the collection of RMD data
+     */
+    public void bind(final String name, RODRecordList rod) {
+        //logger.debug(String.format("Binding %s to %s", name, rod));
+        map.put(canonicalName(name), maybeConvertToVariantContext(rod));
+    }
+
+    /**
+     * A private converter that transforms a RODRecordList of objects of type X into
+     * a list of VariantContexts, if possible.
+     *
+     * TODO: should be removed when Features like dbsnp and hapmap produce VCs directly
+     *
+     * @param bindings
+     * @return
+     */
+    private final RODRecordList maybeConvertToVariantContext(RODRecordList bindings) {
+        List<GATKFeature> values = new ArrayList<GATKFeature>(bindings.size());
+
+        for ( GATKFeature rec : bindings ) {
+            if ( VariantContextAdaptors.canBeConvertedToVariantContext(rec.getUnderlyingObject()) ) {
+                final VariantContext vc = VariantContextAdaptors.toVariantContext(bindings.getName(), rec.getUnderlyingObject(), ref);
+                if ( vc != null ) // it's possible that the conversion failed, but we continue along anyway
+                    values.add(new GATKFeature.TribbleGATKFeature(ref.getGenomeLocParser(), vc, rec.getName()));
+            }
+        }
+
+        return new RODRecordListImpl(bindings.getName(), values, bindings.getLocation());
+    }
+
+//    /**
+//     * Temporary setting for putting a reference context into the system.
+//     *
+//     * DO NOT USE THIS FUNCTION UNLESS YOU ARE THE GATK ENGINE
+//     *
+//     * @param ref
+//     */
+//    public void setRef(final ReferenceContext ref) {
+//        this.ref = ref;
+//    }
+
+
+    // ------------------------------------------------------------------------------------------
+    //
+    //
+    // Generic accessors
+    //
+    //
+    // ------------------------------------------------------------------------------------------
+
     /**
      * No-assumption version of getValues(name, class).  Returns Objects.
      */
@@ -60,18 +129,11 @@ public class RefMetaDataTracker {
         if (list == null)
             return Collections.emptyList();
         else {
-            List<T> objects = new ArrayList<T>();
+            return addValues(name, clazz, new ArrayList<T>(), list, list.getLocation(), false, false);
-            for (GATKFeature feature : list) {
-                final Object obj = feature.getUnderlyingObject();
-                if (!(clazz.isAssignableFrom(obj.getClass())))
-                    throw new UserException.CommandLineException("Unable to case track named " + name + " to type of " + clazz.toString()
-                            + " it's of type " + obj.getClass());
-                objects.add((T)obj);
-            }
-            return objects;
         }
     }
 
+
     /**
      * get a singleton record, given the name and a type.  This function will return the first record at the
      * current position seen.  The object is cast into a type clazz, or thoses an error if this isn't possible.
@@ -116,7 +178,7 @@ public class RefMetaDataTracker {
      *
      * @return collection of all rods
      */
-    public Collection<GATKFeature> getAllValuesAsGATKFeatures() {
+    public List<GATKFeature> getAllValuesAsGATKFeatures() {
         List<GATKFeature> l = new ArrayList<GATKFeature>();
         for ( RODRecordList rl : map.values() ) {
             if ( rl != null )
@@ -125,7 +187,7 @@ public class RefMetaDataTracker {
         return l;
     }
 
-        /**
+    /**
      * get all the GATK features associated with a specific track name
      * @param name the name of the track we're looking for
      * @return a list of GATKFeatures for the target rmd
@@ -141,9 +203,9 @@ public class RefMetaDataTracker {
      * Get all of the RMD tracks at the current site. Each track is returned as a single compound
      * object (RODRecordList) that may contain multiple RMD records associated with the current site.
      *
-     * @return collection of all tracks
+     * @return List of all tracks
      */
-    public Collection<RODRecordList> getBoundRodTracks() {
+    public List<RODRecordList> getBoundRodTracks() {
         LinkedList<RODRecordList> bound = new LinkedList<RODRecordList>();
 
         for ( RODRecordList value : map.values() ) {
@@ -167,21 +229,6 @@ public class RefMetaDataTracker {
         return n;
     }
 
-
-    /**
-     * Binds the list of reference ordered data records (RMDs) to track name at this site.  Should be used only by the traversal
-     * system to provide access to RMDs in a structured way to the walkers.
-     *
-     * DO NOT USE THIS FUNCTION UNLESS YOU ARE THE GATK ENGINE
-     *
-     * @param name the name of the track
-     * @param rod the collection of RMD data
-     */
-    public void bind(final String name, RODRecordList rod) {
-        //logger.debug(String.format("Binding %s to %s", name, rod));
-        map.put(canonicalName(name), rod);
-    }
-
     // ------------------------------------------------------------------------------------------
     //
     //
@@ -195,22 +242,20 @@ public class RefMetaDataTracker {
      * of entries per ROD.
      * The name of each VariantContext corresponds to the ROD name.
      *
-     * @param ref                reference context
      * @return variant context
      */
-    public Collection<VariantContext> getAllVariantContexts(final ReferenceContext ref) {
+    public List<VariantContext> getAllVariantContexts() {
-        return getAllVariantContexts(ref, null, false, false);
+        return getAllVariantContexts(null, false, false);
     }
 
     /**
      * Returns all of the variant contexts that start at the current location
-     * @param ref
+     *
      * @param curLocation
      * @return
      */
-    public Collection<VariantContext> getAllVariantContexts(final ReferenceContext ref,
+    public List<VariantContext> getAllVariantContexts(final GenomeLoc curLocation) {
-                                                            final GenomeLoc curLocation) {
+        return getAllVariantContexts(curLocation, true, false);
-        return getAllVariantContexts(ref, curLocation, true, false);
     }
 
     /**
@@ -224,20 +269,19 @@ public class RefMetaDataTracker {
      *
      * The name of each VariantContext corresponds to the ROD name.
      *
-     * @param ref                reference context
+     *
      * @param curLocation        location
      * @param requireStartHere   do we require the rod to start at this location?
      * @param takeFirstOnly      do we take the first rod only?
      * @return variant context
      */
-    public Collection<VariantContext> getAllVariantContexts(final ReferenceContext ref,
+    public List<VariantContext> getAllVariantContexts(final GenomeLoc curLocation,
-                                                            final GenomeLoc curLocation,
+                                                      final boolean requireStartHere,
-                                                            final boolean requireStartHere,
+                                                      final boolean takeFirstOnly) {
-                                                            final boolean takeFirstOnly ) {
         List<VariantContext> contexts = new ArrayList<VariantContext>();
 
         for ( RODRecordList rodList : getBoundRodTracks() ) {
-            addVariantContexts(contexts, rodList, ref, curLocation, requireStartHere, takeFirstOnly);
+            addVariantContexts(contexts, rodList, curLocation, requireStartHere, takeFirstOnly);
         }
 
         return contexts;
@@ -248,33 +292,31 @@ public class RefMetaDataTracker {
      *
      * see getVariantContexts for more information.
      *
-     * @param ref                ReferenceContext to enable conversion to variant context
+     *
      * @param name               name
      * @param curLocation        location
      * @param requireStartHere   do we require the rod to start at this location?
      * @param takeFirstOnly      do we take the first rod only?
      * @return variant context
      */
-    public Collection<VariantContext> getVariantContexts(final ReferenceContext ref,
+    public List<VariantContext> getVariantContexts(final String name,
-                                                         final String name,
+                                                   final GenomeLoc curLocation,
-                                                         final GenomeLoc curLocation,
+                                                   final boolean requireStartHere,
-                                                         final boolean requireStartHere,
+                                                   final boolean takeFirstOnly) {
-                                                         final boolean takeFirstOnly ) {
+        return getVariantContexts(Arrays.asList(name), curLocation, requireStartHere, takeFirstOnly);
-        return getVariantContexts(ref, Arrays.asList(name), curLocation, requireStartHere, takeFirstOnly);
     }
 
-    public Collection<VariantContext> getVariantContexts(final ReferenceContext ref,
+    public List<VariantContext> getVariantContexts(final Collection<String> names,
-                                                         final Collection<String> names,
+                                                   final GenomeLoc curLocation,
-                                                         final GenomeLoc curLocation,
+                                                   final boolean requireStartHere,
-                                                         final boolean requireStartHere,
+                                                   final boolean takeFirstOnly) {
-                                                         final boolean takeFirstOnly ) {
+        List<VariantContext> contexts = new ArrayList<VariantContext>();
-        Collection<VariantContext> contexts = new ArrayList<VariantContext>();
 
         for ( String name : names ) {
             RODRecordList rodList = getTrackDataByName(name); // require that the name is an exact match
 
             if ( rodList != null )
-                addVariantContexts(contexts, rodList, ref, curLocation, requireStartHere, takeFirstOnly );
+                addVariantContexts(contexts, rodList, curLocation, requireStartHere, takeFirstOnly );
         }
 
         return contexts;
@@ -284,16 +326,16 @@ public class RefMetaDataTracker {
      * Gets the variant context associated with name, and assumes the system only has a single bound track at this location.  Throws an exception if not.
      * see getVariantContexts for more information.
      *
+     *
      * @param name               name
      * @param curLocation        location
      * @param requireStartHere   do we require the rod to start at this location?
      * @return variant context
      */
-    public VariantContext getVariantContext(final ReferenceContext ref,
+    public VariantContext getVariantContext(final String name,
-                                            final String name,
                                             final GenomeLoc curLocation,
-                                            final boolean requireStartHere ) {
+                                            final boolean requireStartHere) {
-        Collection<VariantContext> contexts = getVariantContexts(ref, name, curLocation, requireStartHere, false );
+        List<VariantContext> contexts = getVariantContexts(name, curLocation, requireStartHere, false );
 
         if ( contexts.size() > 1 )
             throw new ReviewedStingException("Requested a single VariantContext object for track " + name + " but multiple variants were present at position " + curLocation);
@@ -307,45 +349,52 @@ public class RefMetaDataTracker {
      * Very simple accessor that gets the first (and only!) VC associated with name at the current location, or
      * null if there's no binding here.
      *
-     * @param ref
+     *
      * @param name
      * @param curLocation
      * @return
      */
-    public VariantContext getVariantContext(final ReferenceContext ref,
+    public VariantContext getVariantContext(final String name,
-                                            final String name,
                                             final GenomeLoc curLocation) {
-        return getVariantContext(ref, name, curLocation, true);
+        return getVariantContext(name, curLocation, true);
     }
 
-    private void addVariantContexts(final Collection<VariantContext> contexts,
+    private void addVariantContexts(final List<VariantContext> contexts,
                                     final RODRecordList rodList,
-                                    final ReferenceContext ref,
                                     final GenomeLoc curLocation,
                                     final boolean requireStartHere,
                                     final boolean takeFirstOnly ) {
+        addValues("xxx", VariantContext.class, contexts, rodList, curLocation, requireStartHere, takeFirstOnly);
+    }
+
+    private static <T> List<T> addValues(final String name,
+                                         final Class<T> type,
+                                         final List<T> values,
+                                         final RODRecordList rodList,
+                                         final GenomeLoc curLocation,
+                                         final boolean requireStartHere,
+                                         final boolean takeFirstOnly ) {
         for ( GATKFeature rec : rodList ) {
-            if ( VariantContextAdaptors.canBeConvertedToVariantContext(rec.getUnderlyingObject()) ) {
+            if ( ! requireStartHere || rec.getLocation().getStart() == curLocation.getStart() ) {  // ok, we are going to keep this thing
-                // ok, we might actually be able to turn this record in a variant context
+                Object obj = rec.getUnderlyingObject();
-                final VariantContext vc = VariantContextAdaptors.toVariantContext(rodList.getName(), rec.getUnderlyingObject(), ref);
+                if (!(type.isAssignableFrom(obj.getClass())))
+                    throw new UserException.CommandLineException("Unable to cast track named " + name + " to type of " + type.toString()
+                            + " it's of type " + obj.getClass());
 
-                if ( vc == null ) // sometimes the track has odd stuff in it that can't be converted
+                values.add((T)obj);
-                    continue;
 
-                if ( ! requireStartHere || rec.getLocation().getStart() == curLocation.getStart() ) {  // ok, we are going to keep this thing
+                if ( takeFirstOnly )
-                    contexts.add(vc);
+                    // we only want the first passing instance, so break the loop over records in rodList
-
+                    break;
-                    if ( takeFirstOnly )
-                        // we only want the first passing instance, so break the loop over records in rodList
-                        break;
-                }
             }
         }
+
+        return values;
     }
 
     /**
      * Finds the reference metadata track named 'name' and returns all ROD records from that track associated
-     * with the current site as a RODRecordList collection object. If no data track with specified name is available,
+     * with the current site as a RODRecordList List object. If no data track with specified name is available,
      * returns defaultValue wrapped as RODRecordList object. NOTE: if defaultValue is null, it will be wrapped up
      * with track name set to 'name' and location set to null; otherwise the wrapper object will have name and
      * location set to defaultValue.getName() and defaultValue.getLocation(), respectively (use caution,

public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseLoci.java

@@ -65,13 +65,13 @@ public class TraverseLoci<M,T> extends TraversalEngine<M,T,LocusWalker<M,T>,Locu
                     referenceView.expandBoundsToAccomodateLoc(location);
                 }
 
-                // Iterate forward to get all reference ordered data covering this location
-                final RefMetaDataTracker tracker = referenceOrderedDataView.getReferenceOrderedDataAtLocus(locus.getLocation());
-
                 // create reference context. Note that if we have a pileup of "extended events", the context will
                 // hold the (longest) stretch of deleted reference bases (if deletions are present in the pileup).
                 ReferenceContext refContext = referenceView.getReferenceContext(location);
 
+                // Iterate forward to get all reference ordered data covering this location
+                final RefMetaDataTracker tracker = referenceOrderedDataView.getReferenceOrderedDataAtLocus(locus.getLocation(), refContext);
+
                 final boolean keepMeP = walker.filter(tracker, refContext, locus);
                 if (keepMeP) {
                     M x = walker.map(tracker, refContext, locus);

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java

@@ -202,7 +202,7 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> {
         if ( tracker == null )
             return 0;
 
-        Collection<VariantContext> VCs = tracker.getVariantContexts(ref, "variant", context.getLocation(), true, false);
+        Collection<VariantContext> VCs = tracker.getVariantContexts("variant", context.getLocation(), true, false);
         if ( VCs.size() == 0 )
             return 0;
 

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java

@@ -203,7 +203,7 @@ public class VariantAnnotatorEngine {
                     infoAnnotations.put(VariantContext.ID_KEY, rsID);
             } else {
                 boolean overlapsComp = false;
-                for ( VariantContext comp : tracker.getVariantContexts(ref, dbSet.getKey(), ref.getLocus(), false, false) ) {
+                for ( VariantContext comp : tracker.getVariantContexts(dbSet.getKey(), ref.getLocus(), false, false) ) {
                     if ( !comp.isFiltered() ) {
                         overlapsComp = true;
                         break;
@@ -216,7 +216,7 @@ public class VariantAnnotatorEngine {
 
     private void annotateExpressions(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, Object> infoAnnotations) {
         for ( VAExpression expression : requestedExpressions ) {
-            Collection<VariantContext> VCs = tracker.getVariantContexts(ref, expression.bindingName, ref.getLocus(), false, true);
+            Collection<VariantContext> VCs = tracker.getVariantContexts(expression.bindingName, ref.getLocus(), false, true);
             if ( VCs.size() == 0 )
                 continue;
 

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/GenomicAnnotator.java

@@ -244,7 +244,7 @@ public class GenomicAnnotator extends RodWalker<Integer, Integer> implements Tre
             return 0;
 
         Set<VariantContext> results = new LinkedHashSet<VariantContext>();
-        for (VariantContext vc : tracker.getVariantContexts(ref, "variant", context.getLocation(), true, false)) {
+        for (VariantContext vc : tracker.getVariantContexts("variant", context.getLocation(), true, false)) {
             if ( (vc.isFiltered() && IGNORE_FILTERED_SITES) ||
                     (vc.isVariant() && !vc.isBiallelic()) ) {
                 results.add(vc);

public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCFWalker.java

@@ -119,9 +119,9 @@ public class BeagleOutputToVCFWalker  extends RodWalker<Integer, Integer> {
             return 0;
 
         GenomeLoc loc = context.getLocation();
-        VariantContext vc_input = tracker.getVariantContext(ref,INPUT_ROD_NAME, loc, true);
+        VariantContext vc_input = tracker.getVariantContext(INPUT_ROD_NAME, loc, true);
 
-        VariantContext vc_comp = tracker.getVariantContext(ref,COMP_ROD_NAME, loc, true);
+        VariantContext vc_comp = tracker.getVariantContext(COMP_ROD_NAME, loc, true);
 
         if ( vc_input == null  )
             return 0;

public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInputWalker.java

@@ -121,8 +121,8 @@ public class ProduceBeagleInputWalker extends RodWalker<Integer, Integer> {
     public Integer map( RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context ) {
         if( tracker != null ) {
             GenomeLoc loc = context.getLocation();
-            VariantContext variant_eval = tracker.getVariantContext(ref, ROD_NAME, loc, true);
+            VariantContext variant_eval = tracker.getVariantContext(ROD_NAME, loc, true);
-            VariantContext validation_eval = tracker.getVariantContext(ref,VALIDATION_ROD_NAME, loc, true);
+            VariantContext validation_eval = tracker.getVariantContext(VALIDATION_ROD_NAME, loc, true);
 
             if ( goodSite(variant_eval,validation_eval) ) {
                 if ( useValidation(validation_eval, ref) ) {

public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/VariantsToBeagleUnphasedWalker.java

@@ -102,7 +102,7 @@ public class VariantsToBeagleUnphasedWalker extends RodWalker<Integer, Integer>
     public Integer map( RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context ) {
         if( tracker != null ) {
             GenomeLoc loc = context.getLocation();
-            VariantContext vc = tracker.getVariantContext(ref, ROD_NAME, loc, true);
+            VariantContext vc = tracker.getVariantContext(ROD_NAME, loc, true);
 
             if ( ProduceBeagleInputWalker.canBeOutputToBeagle(vc) ) {
                 // do we want to hold back this site?

public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceWalker.java

@@ -57,7 +57,7 @@ public class FastaAlternateReferenceWalker extends FastaReferenceWalker {
 
         String refBase = String.valueOf((char)ref.getBase());
 
-        Collection<VariantContext> vcs = tracker.getAllVariantContexts(ref);
+        Collection<VariantContext> vcs = tracker.getAllVariantContexts();
 
         // Check to see if we have a called snp
         for ( VariantContext vc : vcs ) {

public/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java

@@ -149,7 +149,7 @@ public class VariantFiltrationWalker extends RodWalker<Integer, Integer> {
         if ( tracker == null )
             return 0;
 
-        Collection<VariantContext> VCs = tracker.getVariantContexts(ref, INPUT_VARIANT_ROD_BINDING_NAME, context.getLocation(), true, false);
+        Collection<VariantContext> VCs = tracker.getVariantContexts(INPUT_VARIANT_ROD_BINDING_NAME, context.getLocation(), true, false);
 
         // is there a SNP mask present?
         boolean hasMask = tracker.getValues("mask").size() > 0;

public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java

@@ -321,7 +321,7 @@ public class IndelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihood
             haplotypeMap.clear();
 
             if (getAlleleListFromVCF) {
-                 for( final VariantContext vc_input : tracker.getVariantContexts(ref, "alleles", ref.getLocus(), false, false) ) {
+                 for( final VariantContext vc_input : tracker.getVariantContexts("alleles", ref.getLocus(), false, false) ) {
                       if( vc_input != null &&
                               allowableTypes.contains(vc_input.getType()) &&
                               ref.getLocus().getStart() == vc_input.getStart()) {

public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java

@@ -63,7 +63,7 @@ public class SNPGenotypeLikelihoodsCalculationModel extends GenotypeLikelihoodsC
         VariantContext vc = null;
 
         // search for usable record
-        for( final VariantContext vc_input : tracker.getVariantContexts(ref, "alleles", ref.getLocus(), true, false) ) {
+        for( final VariantContext vc_input : tracker.getVariantContexts("alleles", ref.getLocus(), true, false) ) {
             if ( vc_input != null && ! vc_input.isFiltered() && (! requireSNP || vc_input.isSNP() )) {
                 if ( vc == null ) {
                     vc = vc_input;

public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UGCallVariants.java

@@ -96,7 +96,7 @@ public class UGCallVariants extends RodWalker<VariantCallContext, Integer> {
 
         List<VariantContext> VCs = new ArrayList<VariantContext>();
         for ( String name : trackNames ) {
-            Collection<VariantContext> vc = tracker.getVariantContexts(ref, name, context.getLocation(), true, true);
+            Collection<VariantContext> vc = tracker.getVariantContexts(name, context.getLocation(), true, true);
             VCs.addAll(vc);
         }
 

public/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java

@@ -110,7 +110,7 @@ public class RealignerTargetCreator extends RodWalker<RealignerTargetCreator.Eve
 
         // look at the rods for indels or SNPs
         if ( tracker != null ) {
-            for ( VariantContext vc : tracker.getAllVariantContexts(ref) ) {
+            for ( VariantContext vc : tracker.getAllVariantContexts() ) {
                 switch ( vc.getType() ) {
                     case INDEL:
                         hasIndel = true;

public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/AnnotateMNPsWalker.java

@@ -64,7 +64,7 @@ public class AnnotateMNPsWalker extends RodWalker<Integer, Integer> {
     @Argument(fullName = "emitOnlyMNPs", shortName = "emitOnlyMNPs", doc = "Only output MNP records; [default:false]", required = false)
     protected boolean emitOnlyMNPs = false;    
 
-    private LinkedList<String> rodNames = null;
+    private String rodName = "variant";
     private GenomeLocParser locParser = null;
     private TreeMap<GenomeLoc, Set<GenomeLoc>> MNPstartToStops = null; // Must be TreeMap sorted by START sites!
 
@@ -105,9 +105,6 @@ public class AnnotateMNPsWalker extends RodWalker<Integer, Integer> {
     protected final static String REFSEQ_HAS_MULT_AA_CHANGES = "alleleHasMultAAchanges";
 
     public void initialize() {
-        rodNames = new LinkedList<String>();
-        rodNames.add(VARIANT_ROD_NAME);
-
         locParser = getToolkit().getGenomeLocParser();
         MNPstartToStops = new TreeMap<GenomeLoc, Set<GenomeLoc>>(); // sorted by start sites
 
@@ -125,8 +122,8 @@ public class AnnotateMNPsWalker extends RodWalker<Integer, Integer> {
         hInfo.addAll(VCFUtils.getHeaderFields(getToolkit()));
         hInfo.add(new VCFHeaderLine("reference", getToolkit().getArguments().referenceFile.getName()));
 
-        Map<String, VCFHeader> rodNameToHeader = getVCFHeadersFromRods(getToolkit(), rodNames);
+        Map<String, VCFHeader> rodNameToHeader = getVCFHeadersFromRods(getToolkit(), Arrays.asList(rodName));
-        writer.writeHeader(new VCFHeader(hInfo, new TreeSet<String>(rodNameToHeader.get(rodNames.get(0)).getGenotypeSamples())));
+        writer.writeHeader(new VCFHeader(hInfo, new TreeSet<String>(rodNameToHeader.get(rodName).getGenotypeSamples())));
     }
 
     public boolean generateExtendedEvents() {
@@ -155,7 +152,7 @@ public class AnnotateMNPsWalker extends RodWalker<Integer, Integer> {
 
         boolean requireStartHere = false; // see EVERY site of the MNP
         boolean takeFirstOnly = false; // take as many entries as the VCF file has
-        for (VariantContext vc : tracker.getVariantContexts(ref, rodNames, context.getLocation(), requireStartHere, takeFirstOnly)) {
+        for (VariantContext vc : tracker.getVariantContexts(rodName, context.getLocation(), requireStartHere, takeFirstOnly)) {
             GenomeLoc vcLoc = VariantContextUtils.getLocation(locParser, vc);
             boolean atStartOfVc = curLocus.getStart() == vcLoc.getStart();
             boolean atEndOfVc = curLocus.getStart() == vcLoc.getStop();

public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeAndMatchHaplotypes.java

@@ -44,8 +44,8 @@ public class MergeAndMatchHaplotypes extends RodWalker<Integer, Integer> {
     @Override
     public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
         if (tracker != null) {
-            Collection<VariantContext> pbts = tracker.getVariantContexts(ref, "pbt", ref.getLocus(), true, true);
+            Collection<VariantContext> pbts = tracker.getVariantContexts("pbt", ref.getLocus(), true, true);
-            Collection<VariantContext> rbps = tracker.getVariantContexts(ref, "rbp", ref.getLocus(), true, true);
+            Collection<VariantContext> rbps = tracker.getVariantContexts("rbp", ref.getLocus(), true, true);
 
             VariantContext pbt = pbts.iterator().hasNext() ? pbts.iterator().next() : null;
             VariantContext rbp = rbps.iterator().hasNext() ? rbps.iterator().next() : null;

public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeMNPsWalker.java

@@ -58,12 +58,9 @@ public class MergeMNPsWalker extends RodWalker<Integer, Integer> {
     @Argument(fullName = "maxGenomicDistanceForMNP", shortName = "maxDistMNP", doc = "The maximum reference-genome distance between consecutive heterozygous sites to permit merging phased VCF records into a MNP record; [default:1]", required = false)
     protected int maxGenomicDistanceForMNP = 1;
 
-    private LinkedList<String> rodNames = null;
+    private String rodName = "variant";
 
     public void initialize() {
-        rodNames = new LinkedList<String>();
-        rodNames.add("variant");
-
         initializeVcfWriter();
     }
 
@@ -77,8 +74,8 @@ public class MergeMNPsWalker extends RodWalker<Integer, Integer> {
         hInfo.addAll(VCFUtils.getHeaderFields(getToolkit()));
         hInfo.add(new VCFHeaderLine("reference", getToolkit().getArguments().referenceFile.getName()));
 
-        Map<String, VCFHeader> rodNameToHeader = getVCFHeadersFromRods(getToolkit(), rodNames);
+        Map<String, VCFHeader> rodNameToHeader = getVCFHeadersFromRods(getToolkit(), Arrays.asList(rodName));
-        vcMergerWriter.writeHeader(new VCFHeader(hInfo, new TreeSet<String>(rodNameToHeader.get(rodNames.get(0)).getGenotypeSamples())));
+        vcMergerWriter.writeHeader(new VCFHeader(hInfo, new TreeSet<String>(rodNameToHeader.get(rodName).getGenotypeSamples())));
     }
 
     public boolean generateExtendedEvents() {
@@ -103,7 +100,7 @@ public class MergeMNPsWalker extends RodWalker<Integer, Integer> {
 
         boolean requireStartHere = true; // only see each VariantContext once
         boolean takeFirstOnly = false; // take as many entries as the VCF file has
-        for (VariantContext vc : tracker.getVariantContexts(ref, rodNames, context.getLocation(), requireStartHere, takeFirstOnly))
+        for (VariantContext vc : tracker.getVariantContexts(rodName, context.getLocation(), requireStartHere, takeFirstOnly))
             writeVCF(vc);
 
         return 0;

public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesWalker.java

@@ -81,12 +81,9 @@ public class MergeSegregatingAlternateAllelesWalker extends RodWalker<Integer, I
     @Argument(fullName = "dontRequireSomeSampleHasDoubleAltAllele", shortName = "dontRequireSomeSampleHasDoubleAltAllele", doc = "Should the requirement, that SUCCESSIVE records to be merged have at least one sample with a double alternate allele, be relaxed?; [default:false]", required = false)
     protected boolean dontRequireSomeSampleHasDoubleAltAllele = false;
 
-    private LinkedList<String> rodNames = null;
+    private String rodName = "variant";
 
     public void initialize() {
-        rodNames = new LinkedList<String>();
-        rodNames.add("variant");
-
         initializeVcfWriter();
     }
 
@@ -114,8 +111,8 @@ public class MergeSegregatingAlternateAllelesWalker extends RodWalker<Integer, I
         hInfo.addAll(VCFUtils.getHeaderFields(getToolkit()));
         hInfo.add(new VCFHeaderLine("reference", getToolkit().getArguments().referenceFile.getName()));
 
-        Map<String, VCFHeader> rodNameToHeader = getVCFHeadersFromRods(getToolkit(), rodNames);
+        Map<String, VCFHeader> rodNameToHeader = getVCFHeadersFromRods(getToolkit(), Arrays.asList(rodName));
-        vcMergerWriter.writeHeader(new VCFHeader(hInfo, new TreeSet<String>(rodNameToHeader.get(rodNames.get(0)).getGenotypeSamples())));
+        vcMergerWriter.writeHeader(new VCFHeader(hInfo, new TreeSet<String>(rodNameToHeader.get(rodName).getGenotypeSamples())));
     }
 
     public boolean generateExtendedEvents() {
@@ -140,7 +137,7 @@ public class MergeSegregatingAlternateAllelesWalker extends RodWalker<Integer, I
 
         boolean requireStartHere = true; // only see each VariantContext once
         boolean takeFirstOnly = false; // take as many entries as the VCF file has
-        for (VariantContext vc : tracker.getVariantContexts(ref, rodNames, context.getLocation(), requireStartHere, takeFirstOnly))
+        for (VariantContext vc : tracker.getVariantContexts(rodName, context.getLocation(), requireStartHere, takeFirstOnly))
             writeVCF(vc);
 
         return 0;

public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java

@@ -289,7 +289,7 @@ public class PhaseByTransmission extends RodWalker<Integer, Integer> {
     @Override
     public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
         if (tracker != null) {
-            Collection<VariantContext> vcs = tracker.getVariantContexts(ref, ROD_NAME, context.getLocation(), true, true);
+            Collection<VariantContext> vcs = tracker.getVariantContexts(ROD_NAME, context.getLocation(), true, true);
 
             for (VariantContext vc : vcs) {
                 Map<String, Genotype> genotypeMap = vc.getGenotypes();

public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java

@@ -98,7 +98,7 @@ public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, Ph
 
     private static PreciseNonNegativeDouble ZERO = new PreciseNonNegativeDouble(0.0);
 
-    private LinkedList<String> rodNames = null;
+    private String rodName = "variant";
 
     public static final String PQ_KEY = "PQ";
 
@@ -123,9 +123,6 @@ public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, Ph
         if (maxPhaseSites <= 2)
             maxPhaseSites = 2; // by definition, must phase a site relative to previous site [thus, 2 in total]
 
-        rodNames = new LinkedList<String>();
-        rodNames.add("variant");
-
         /*
          Since we cap each base quality (BQ) by its read's mapping quality (MQ) [in Read.updateBaseAndQuality()], then:
          if minBQ > minMQ, then we require that MQ be >= minBQ as well.
@@ -175,8 +172,8 @@ public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, Ph
         hInfo.add(new VCFInfoHeaderLine(PHASING_INCONSISTENT_KEY, 0, VCFHeaderLineType.Flag, "Are the reads significantly haplotype-inconsistent?"));
 
         // todo -- fix samplesToPhase
-        Map<String, VCFHeader> rodNameToHeader = getVCFHeadersFromRods(getToolkit(), rodNames);
+        Map<String, VCFHeader> rodNameToHeader = getVCFHeadersFromRods(getToolkit(), Arrays.asList(rodName));
-        Set<String> samples = new TreeSet<String>(samplesToPhase == null ? rodNameToHeader.get(rodNames.get(0)).getGenotypeSamples() : samplesToPhase);
+        Set<String> samples = new TreeSet<String>(samplesToPhase == null ? rodNameToHeader.get(rodName).getGenotypeSamples() : samplesToPhase);
         writer.writeHeader(new VCFHeader(hInfo, samples));
     }
 
@@ -209,7 +206,7 @@ public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, Ph
 
         boolean requireStartHere = true; // only see each VariantContext once
         boolean takeFirstOnly = false; // take as many entries as the VCF file has
-        for (VariantContext vc : tracker.getVariantContexts(ref, rodNames, context.getLocation(), requireStartHere, takeFirstOnly)) {
+        for (VariantContext vc : tracker.getVariantContexts(rodName, context.getLocation(), requireStartHere, takeFirstOnly)) {
             if (samplesToPhase != null) vc = reduceVCToSamples(vc, samplesToPhase);
 
             if (ReadBackedPhasingWalker.processVariantInPhasing(vc)) {

public/java/src/org/broadinstitute/sting/gatk/walkers/qc/RodSystemValidationWalker.java

@@ -84,7 +84,7 @@ public class RodSystemValidationWalker extends RodWalker<Integer,Integer> {
 
         // if the argument was set, check for equivalence
         if (allRecordsVariantContextEquivalent && tracker != null) {
-            Collection<VariantContext> col = tracker.getAllVariantContexts(ref);
+            Collection<VariantContext> col = tracker.getAllVariantContexts();
             VariantContext con = null;
             for (VariantContext contextInList : col)
                 if (con == null) con = contextInList;

public/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java

@@ -138,8 +138,8 @@ public class ValidationAmplicons extends RodWalker<Integer,Integer> {
         // step 3 (or 1 if not new):
         // build up the sequence
 
-        VariantContext mask = tracker.getVariantContext(ref,"MaskAlleles",ref.getLocus());
+        VariantContext mask = tracker.getVariantContext("MaskAlleles",ref.getLocus());
-        VariantContext validate = tracker.getVariantContext(ref,"ValidateAlleles",ref.getLocus());
+        VariantContext validate = tracker.getVariantContext("ValidateAlleles",ref.getLocus());
 
         if ( mask == null && validate == null ) {
             if ( indelCounter > 0 ) {

public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Novelty.java

@@ -25,7 +25,7 @@ public class Novelty extends VariantStratifier implements StandardStratification
     public ArrayList<String> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
         if (tracker != null && eval != null) {
             for (final String knownName : knownNames) {
-                final Collection<VariantContext> knownComps = tracker.getVariantContexts(ref, knownName, ref.getLocus(), true, false);
+                final Collection<VariantContext> knownComps = tracker.getVariantContexts(knownName, ref.getLocus(), true, false);
                 for ( final VariantContext c : knownComps ) {
                     // loop over sites, looking for something that matches the type eval
                     if ( eval.getType() == c.getType() ) {

public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java

@@ -336,7 +336,7 @@ public class VariantEvalUtils {
         for (String trackName : trackNames) {
             HashMap<String, VariantContext> vcs = new HashMap<String, VariantContext>();
 
-            Collection<VariantContext> contexts = tracker == null ? null : tracker.getVariantContexts(ref, trackName, ref.getLocus(), true, true);
+            Collection<VariantContext> contexts = tracker == null ? null : tracker.getVariantContexts(trackName, ref.getLocus(), true, true);
             VariantContext vc = contexts != null && contexts.size() == 1 ? contexts.iterator().next() : null;
 
             // First, filter the VariantContext to represent only the samples for evaluation

public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java

@@ -168,7 +168,7 @@ public class ApplyRecalibration extends RodWalker<Integer, Integer> {
             return 1;
         }
 
-        for( VariantContext vc : tracker.getVariantContexts(ref, inputNames, context.getLocation(), true, false) ) {
+        for( VariantContext vc : tracker.getVariantContexts(inputNames, context.getLocation(), true, false) ) {
             if( vc != null ) {
                 if( VariantRecalibrator.checkRecalibrationMode( vc, MODE ) && (vc.isNotFiltered() || ignoreInputFilterSet.containsAll(vc.getFilters())) ) {
                     String filterString = null;

public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java

@@ -258,7 +258,7 @@ public class VariantDataManager {
         datum.consensusCount = 0;
 
         for( final TrainingSet trainingSet : trainingSets ) {
-            for( final VariantContext trainVC : tracker.getVariantContexts( ref, trainingSet.name, context.getLocation(), false, false ) ) {
+            for( final VariantContext trainVC : tracker.getVariantContexts(trainingSet.name, context.getLocation(), false, false ) ) {
                 if( trainVC != null && trainVC.isNotFiltered() && trainVC.isVariant() &&
                         ((evalVC.isSNP() && trainVC.isSNP()) || ((evalVC.isIndel()||evalVC.isMixed()) && (trainVC.isIndel()||trainVC.isMixed()))) &&
                         (TRUST_ALL_POLYMORPHIC || !trainVC.hasGenotypes() || trainVC.isPolymorphic()) ) {

public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java

@@ -163,7 +163,7 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
             return mapList;
         }
 
-        for( final VariantContext vc : tracker.getVariantContexts(ref, inputNames, context.getLocation(), true, false) ) {
+        for( final VariantContext vc : tracker.getVariantContexts(inputNames, context.getLocation(), true, false) ) {
             if( vc != null && ( vc.isNotFiltered() || ignoreInputFilterSet.containsAll(vc.getFilters()) ) ) {
                 if( checkRecalibrationMode( vc, VRAC.MODE ) ) {
                     final VariantDatum datum = new VariantDatum();

public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java

@@ -25,7 +25,6 @@
 
 package org.broadinstitute.sting.gatk.walkers.variantutils;
 
-import org.apache.poi.hpsf.Variant;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Hidden;
 import org.broadinstitute.sting.commandline.Output;
@@ -150,7 +149,7 @@ public class CombineVariants extends RodWalker<Integer, Integer> {
 
         // get all of the vcf rods at this locus
         // Need to provide reference bases to simpleMerge starting at current locus
-        Collection<VariantContext> vcs = tracker.getAllVariantContexts(ref, context.getLocation(), true, false);
+        Collection<VariantContext> vcs = tracker.getAllVariantContexts(context.getLocation(), true, false);
 
         if ( sitesOnlyVCF ) {
             vcs = VariantContextUtils.sitesOnlyVariantContexts(vcs);

public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java

@@ -85,7 +85,7 @@ public class FilterLiftedVariants extends RodWalker<Integer, Integer> {
         if ( tracker == null )
             return 0;
 
-        Collection<VariantContext> VCs = tracker.getVariantContexts(ref, "variant", context.getLocation(), true, false);
+        Collection<VariantContext> VCs = tracker.getVariantContexts("variant", context.getLocation(), true, false);
         for ( VariantContext vc : VCs )
             filterAndWrite(ref.getBases(), vc);
 

public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java

@@ -68,7 +68,7 @@ public class LeftAlignVariants extends RodWalker<Integer, Integer> {
         if ( tracker == null )
             return 0;
 
-        Collection<VariantContext> VCs = tracker.getVariantContexts(ref, "variant", context.getLocation(), true, false);
+        Collection<VariantContext> VCs = tracker.getVariantContexts("variant", context.getLocation(), true, false);
 
         int changedSites = 0;
         for ( VariantContext vc : VCs )

public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java

@@ -143,7 +143,7 @@ public class LiftoverVariants extends RodWalker<Integer, Integer> {
         if ( tracker == null )
             return 0;
 
-        Collection<VariantContext> VCs = tracker.getVariantContexts(ref, "variant", context.getLocation(), true, false);
+        Collection<VariantContext> VCs = tracker.getVariantContexts("variant", context.getLocation(), true, false);
         for ( VariantContext vc : VCs )
             convertAndWrite(vc, ref);
 

public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/RandomlySplitVariants.java

@@ -97,7 +97,7 @@ public class RandomlySplitVariants extends RodWalker<Integer, Integer> {
         if ( tracker == null )
             return 0;
 
-        Collection<VariantContext> vcs = tracker.getVariantContexts(ref, INPUT_VARIANT_ROD_BINDING_NAME, context.getLocation(), true, false);
+        Collection<VariantContext> vcs = tracker.getVariantContexts(INPUT_VARIANT_ROD_BINDING_NAME, context.getLocation(), true, false);
         for ( VariantContext vc : vcs ) {
             int random = GenomeAnalysisEngine.getRandomGenerator().nextInt(1000);
             if ( random < iFraction )

public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java

@@ -25,38 +25,29 @@
 package org.broadinstitute.sting.gatk.walkers.variantutils;
 
 import org.broadinstitute.sting.commandline.Hidden;
-import org.broadinstitute.sting.commandline.Input;
 import org.broadinstitute.sting.utils.MathUtils;
 import org.broadinstitute.sting.utils.codecs.vcf.*;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.text.XReadLines;
-import org.broadinstitute.sting.utils.variantcontext.*;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.utils.MendelianViolation;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.commandline.Argument;
-import org.broadinstitute.sting.commandline.Hidden;
 import org.broadinstitute.sting.commandline.Output;
-import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.RMD;
 import org.broadinstitute.sting.gatk.walkers.Requires;
 import org.broadinstitute.sting.gatk.walkers.RodWalker;
-import org.broadinstitute.sting.utils.MathUtils;
-import org.broadinstitute.sting.utils.MendelianViolation;
 import org.broadinstitute.sting.utils.SampleUtils;
-import org.broadinstitute.sting.utils.codecs.vcf.*;
 import org.broadinstitute.sting.utils.variantcontext.Allele;
 import org.broadinstitute.sting.utils.variantcontext.Genotype;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 
 import java.io.File;
 import java.io.FileNotFoundException;
 import java.io.PrintStream;
-import java.lang.annotation.AnnotationFormatError;
 import java.util.*;
 
 /**
@@ -317,7 +308,7 @@ public class SelectVariants extends RodWalker<Integer, Integer> {
         if ( tracker == null )
             return 0;
 
-        Collection<VariantContext> vcs = tracker.getVariantContexts(ref, variantRodName, context.getLocation(), true, false);
+        Collection<VariantContext> vcs = tracker.getVariantContexts(variantRodName, context.getLocation(), true, false);
 
         if ( vcs == null || vcs.size() == 0) {
             return 0;
@@ -345,12 +336,12 @@ public class SelectVariants extends RodWalker<Integer, Integer> {
                     break;
             }
             if (DISCORDANCE_ONLY) {
-                Collection<VariantContext> compVCs = tracker.getVariantContexts(ref, discordanceRodName, context.getLocation(), true, false);
+                Collection<VariantContext> compVCs = tracker.getVariantContexts(discordanceRodName, context.getLocation(), true, false);
                 if (!isDiscordant(vc, compVCs))
                     return 0;
             }
             if (CONCORDANCE_ONLY) {
-                Collection<VariantContext> compVCs = tracker.getVariantContexts(ref, concordanceRodName, context.getLocation(), true, false);
+                Collection<VariantContext> compVCs = tracker.getVariantContexts(concordanceRodName, context.getLocation(), true, false);
                 if (!isConcordant(vc, compVCs))
                     return 0;
             }

public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java

@@ -86,7 +86,7 @@ public class ValidateVariants extends RodWalker<Integer, Integer> {
         if ( tracker == null )
             return 0;
 
-        Collection<VariantContext> VCs = tracker.getVariantContexts(ref, "variant", context.getLocation(), true, false);
+        Collection<VariantContext> VCs = tracker.getVariantContexts("variant", context.getLocation(), true, false);
         for ( VariantContext vc : VCs )
             validate(vc, tracker, ref);
 

public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantValidationAssessor.java

@@ -93,7 +93,7 @@ public class VariantValidationAssessor extends RodWalker<Pair<VariantContext, By
         if ( tracker == null )
             return null;
 
-        VariantContext vc = tracker.getVariantContext(ref, INPUT_VARIANT_ROD_BINDING_NAME, ref.getLocus());
+        VariantContext vc = tracker.getVariantContext(INPUT_VARIANT_ROD_BINDING_NAME, ref.getLocus());
         // ignore places where we don't have a variant
         if ( vc == null )
             return null;

public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java

@@ -132,7 +132,7 @@ public class VariantsToTable extends RodWalker<Integer, Integer> {
             return 0;
 
         if ( ++nRecords < MAX_RECORDS || MAX_RECORDS == -1 ) {
-            Collection<VariantContext> vcs = tracker.getAllVariantContexts(ref, context.getLocation());
+            Collection<VariantContext> vcs = tracker.getAllVariantContexts(context.getLocation());
             for ( VariantContext vc : vcs) {
                 if ( (keepMultiAllelic || vc.isBiallelic()) && ( showFiltered || vc.isNotFiltered() ) ) {
                     List<String> vals = extractFields(vc, fieldsToTake, ALLOW_MISSING_DATA);

public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTableNewRodStyle.java

@@ -138,7 +138,7 @@ public class VariantsToTableNewRodStyle extends RodWalker<Integer, Integer> {
             System.out.printf("VariantList binding %s tags=%s%n", binding, getToolkit().getTags(binding).getPositionalTags());
 
         if ( ++nRecords < MAX_RECORDS || MAX_RECORDS == -1 ) {
-            VariantContext vc = variants.getVariantContext(tracker, ref, context.getLocation());
+            VariantContext vc = variants.getVariantContext(tracker, context.getLocation());
             if ( (keepMultiAllelic || vc.isBiallelic()) && ( showFiltered || vc.isNotFiltered() ) ) {
                 List<String> vals = extractFields(vc, fieldsToTake, ALLOW_MISSING_DATA);
                 out.println(Utils.join("\t", vals));

public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java

@@ -162,7 +162,7 @@ public class VariantsToVCF extends RodWalker<Integer, Integer> {
         }
 
         // for everything else, we can just convert to VariantContext
-        return tracker.getVariantContexts(ref, INPUT_ROD_NAME, ref.getLocus(), true, false);
+        return tracker.getVariantContexts(INPUT_ROD_NAME, ref.getLocus(), true, false);
     }
 
     private DbSNPFeature getDbsnpFeature(String rsID) {

public/java/test/org/broadinstitute/sting/gatk/datasources/providers/ReferenceOrderedViewUnitTest.java

@@ -69,7 +69,7 @@ public class ReferenceOrderedViewUnitTest extends BaseTest {
         LocusShardDataProvider provider = new LocusShardDataProvider(shard, null, genomeLocParser, shard.getGenomeLocs().get(0), null, seq, Collections.<ReferenceOrderedDataSource>emptyList());
         ReferenceOrderedView view = new ManagingReferenceOrderedView( provider );
 
-        RefMetaDataTracker tracker = view.getReferenceOrderedDataAtLocus(genomeLocParser.createGenomeLoc("chrM",10));
+        RefMetaDataTracker tracker = view.getReferenceOrderedDataAtLocus(genomeLocParser.createGenomeLoc("chrM",10), null);
         Assert.assertEquals(tracker.getAllValuesAsGATKFeatures().size(), 0, "The tracker should not have produced any data");
     }
 
@@ -87,7 +87,7 @@ public class ReferenceOrderedViewUnitTest extends BaseTest {
         LocusShardDataProvider provider = new LocusShardDataProvider(shard, null, genomeLocParser, shard.getGenomeLocs().get(0), null, seq, Collections.singletonList(dataSource));
         ReferenceOrderedView view = new ManagingReferenceOrderedView( provider );
 
-        RefMetaDataTracker tracker = view.getReferenceOrderedDataAtLocus(genomeLocParser.createGenomeLoc("chrM",20));
+        RefMetaDataTracker tracker = view.getReferenceOrderedDataAtLocus(genomeLocParser.createGenomeLoc("chrM",20), null);
         TableFeature datum = tracker.getFirstValue("tableTest", TableFeature.class);
 
         Assert.assertEquals(datum.get("COL1"),"C","datum parameter for COL1 is incorrect");
@@ -113,7 +113,7 @@ public class ReferenceOrderedViewUnitTest extends BaseTest {
         LocusShardDataProvider provider = new LocusShardDataProvider(shard, null, genomeLocParser, shard.getGenomeLocs().get(0), null, seq, Arrays.asList(dataSource1,dataSource2));
         ReferenceOrderedView view = new ManagingReferenceOrderedView( provider );
 
-        RefMetaDataTracker tracker = view.getReferenceOrderedDataAtLocus(genomeLocParser.createGenomeLoc("chrM",20));
+        RefMetaDataTracker tracker = view.getReferenceOrderedDataAtLocus(genomeLocParser.createGenomeLoc("chrM",20), null);
         TableFeature datum1 = tracker.getFirstValue("tableTest1", TableFeature.class);
 
         Assert.assertEquals(datum1.get("COL1"),"C","datum1 parameter for COL1 is incorrect");