Added RefMetaDataTracker system as a replacement for the List<RefenenceOrderedData> going into walkers. This system allows you to more easily get a tracker for processing using the lookup(name, default) system. See Pileup for an example.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@292 348d0f76-0448-11de-a6fe-93d51630548a

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

@@ -0,0 +1,54 @@
+package org.broadinstitute.sting.gatk.refdata;
+
+import org.apache.log4j.Logger;
+
+import java.util.HashMap;
+import java.util.List;
+import java.util.Collection;
+
+/**
+ * Created by IntelliJ IDEA.
+ * User: mdepristo
+ * Date: Apr 3, 2009
+ * Time: 3:05:23 PM
+ * To change this template use File | Settings | File Templates.
+ */
+public class RefMetaDataTracker {
+    final HashMap<String, ReferenceOrderedDatum> map = new HashMap<String, ReferenceOrderedDatum>();
+    protected static Logger logger = Logger.getLogger(RefMetaDataTracker.class);
+
+    /**
+     * Finds the reference meta data named name, if it exists, otherwise returns the defaultValue
+     *
+     * @param name
+     * @param defaultValue
+     * @return
+     */
+    public ReferenceOrderedDatum lookup(final String name, ReferenceOrderedDatum defaultValue) {
+        //logger.debug(String.format("Lookup %s%n", name));
+        if ( map.containsKey(name) )
+            return map.get(name);
+        else
+            return defaultValue;
+    }
+
+    public Object lookup(final String name, Object defaultValue) {
+        if ( map.containsKey(name) )
+            return map.get(name);
+        else
+            return defaultValue;
+    }
+
+    public Object hasROD(final String name) {
+       return map.containsKey(name);
+    }
+
+    public Collection<ReferenceOrderedDatum> getAllRods() {
+        return map.values();
+    }
+
+    public void bind(final String name, ReferenceOrderedDatum rod) {
+        //logger.debug(String.format("Binding %s to %s%n", name, rod));
+        map.put(name, rod);
+    }
+}

java/src/org/broadinstitute/sting/gatk/refdata/ReferenceOrderedData.java

@@ -35,6 +35,8 @@ public class ReferenceOrderedData<ROD extends ReferenceOrderedDatum> implements
         this.name = name;
     }
 
+    public String getName() { return name; }
+
     public RODIterator iterator() {
         return new RODIterator(new SimpleRODIterator());
     }

java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java

@@ -19,6 +19,7 @@ import org.apache.log4j.Logger;
 import org.broadinstitute.sting.gatk.iterators.*;
 import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedData;
 import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.LocusWalker;
 import org.broadinstitute.sting.gatk.walkers.ReadWalker;
 import org.broadinstitute.sting.gatk.walkers.Walker;
@@ -33,7 +34,7 @@ public abstract class TraversalEngine {
     protected List<ReferenceOrderedData<? extends ReferenceOrderedDatum>> rods = null;
 
     // Iterator over rods
-    List<ReferenceOrderedData<? extends ReferenceOrderedDatum>.RODIterator> rodIters;
+    List<Pair<String, ReferenceOrderedData<? extends ReferenceOrderedDatum>.RODIterator>> rodIters;
 
     // How strict should we be with SAM/BAM parsing?
     protected ValidationStringency strictness = ValidationStringency.STRICT;
@@ -411,13 +412,12 @@ public abstract class TraversalEngine {
      *
      * @return A list of ROD iterators for getting data from each ROD
      */
-    protected List<ReferenceOrderedData<? extends ReferenceOrderedDatum>.RODIterator> initializeRODs() {
+    protected void initializeRODs() {
         // set up reference ordered data
-        rodIters = new ArrayList<ReferenceOrderedData<? extends ReferenceOrderedDatum>.RODIterator>();
+        rodIters = new ArrayList<Pair<String, ReferenceOrderedData<? extends ReferenceOrderedDatum>.RODIterator>>();
         for (ReferenceOrderedData<? extends ReferenceOrderedDatum> data : rods) {
-            rodIters.add(data.iterator());
+            rodIters.add(new Pair<String, ReferenceOrderedData<? extends ReferenceOrderedDatum>.RODIterator>(data.getName(), data.iterator()));
         }
-        return rodIters;
     }
 
     /**
@@ -459,13 +459,13 @@ public abstract class TraversalEngine {
      * @param loc      The location to get the rods at
      * @return A list of ReferenceOrderDatum at loc.  ROD without a datum at loc will be null in the list
      */
-    protected List<ReferenceOrderedDatum> getReferenceOrderedDataAtLocus(List<ReferenceOrderedData<? extends ReferenceOrderedDatum>.RODIterator> rodIters,
+    protected RefMetaDataTracker getReferenceOrderedDataAtLocus(final GenomeLoc loc) {
-                                                                         final GenomeLoc loc) {
+        RefMetaDataTracker tracks = new RefMetaDataTracker();
-        List<ReferenceOrderedDatum> data = new ArrayList<ReferenceOrderedDatum>();
+        for (Pair<String, ReferenceOrderedData<? extends ReferenceOrderedDatum>.RODIterator> pair : rodIters) {
-        for (ReferenceOrderedData<? extends ReferenceOrderedDatum>.RODIterator iter : rodIters) {
+            String name = pair.getFirst();
-            data.add(iter.seekForward(loc));
+            tracks.bind(name, pair.getSecond().seekForward(loc));
         }
-        return data;
+        return tracks;
     }
 
     // --------------------------------------------------------------------------------------------------------------

java/src/org/broadinstitute/sting/gatk/traversals/TraverseByLoci.java

@@ -6,6 +6,7 @@ import org.broadinstitute.sting.gatk.walkers.Walker;
 import org.broadinstitute.sting.gatk.LocusContext;
 import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedData;
 import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.iterators.ReferenceIterator;
 import org.broadinstitute.sting.gatk.iterators.LocusIterator;
 import org.broadinstitute.sting.gatk.iterators.LocusIteratorByHanger;
@@ -120,9 +121,9 @@ public class TraverseByLoci extends TraversalEngine {
                 locus.setReferenceContig(refSite.getCurrentContig());
 
                 // Iterate forward to get all reference ordered data covering this locus
-                final List<ReferenceOrderedDatum> rodData = getReferenceOrderedDataAtLocus(rodIters, locus.getLocation());
+                final RefMetaDataTracker tracker = getReferenceOrderedDataAtLocus(locus.getLocation());
 
-                sum = walkAtLocus( walker, sum, locus, refSite, rodData );
+                sum = walkAtLocus( walker, sum, locus, refSite, tracker );
 
                 //System.out.format("Working at %s\n", locus.getLocation().toString());
 
@@ -144,7 +145,7 @@ public class TraverseByLoci extends TraversalEngine {
                                     T sum, 
                                     final LocusContext locus,
                                     final ReferenceIterator refSite,
-                                    final List<ReferenceOrderedDatum> rodData ) {
+                                    final RefMetaDataTracker tracker ) {
         final char refBase = refSite.getBaseAsChar();
 
         //logger.debug(String.format("  Reference: %s:%d %c", refSite.getCurrentContig().getName(), refSite.getPosition(), refBase));
@@ -152,9 +153,9 @@ public class TraverseByLoci extends TraversalEngine {
         //
         // Execute our contract with the walker.  Call filter, map, and reduce
         //
-        final boolean keepMeP = walker.filter(rodData, refBase, locus);
+        final boolean keepMeP = walker.filter(tracker, refBase, locus);
         if (keepMeP) {
-            M x = walker.map(rodData, refBase, locus);
+            M x = walker.map(tracker, refBase, locus);
             sum = walker.reduce(x, sum);
         }
 

java/src/org/broadinstitute/sting/gatk/traversals/TraverseByLociByReference.java

@@ -6,6 +6,7 @@ import org.broadinstitute.sting.gatk.walkers.Walker;
 import org.broadinstitute.sting.gatk.LocusContext;
 import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedData;
 import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.iterators.ReferenceIterator;
 import org.broadinstitute.sting.gatk.iterators.LocusIterator;
 import org.broadinstitute.sting.gatk.iterators.LocusIteratorByHanger;
@@ -64,7 +65,7 @@ public class TraverseByLociByReference extends TraverseByLoci {
             GenomeLoc current = refSite.getLocation();
             
             // Iterate forward to get all reference ordered data covering this locus
-            final List<ReferenceOrderedDatum> rodData = getReferenceOrderedDataAtLocus(rodIters, current);
+            final RefMetaDataTracker tracker = getReferenceOrderedDataAtLocus(current);
 
             LocusContext locus = null;
 
@@ -79,7 +80,7 @@ public class TraverseByLociByReference extends TraverseByLoci {
             locus.setReferenceContig(refSite.getCurrentContig());            
             if ( DOWNSAMPLE_BY_COVERAGE )
                 locus.downsampleToCoverage(downsamplingCoverage);
-            sum = walkAtLocus( walker, sum, locus, refSite, rodData );
+            sum = walkAtLocus( walker, sum, locus, refSite, tracker );
 
             if (this.maxReads > 0 && this.nRecords > this.maxReads) {
                 logger.warn(String.format("Maximum number of reads encountered, terminating traversal " + this.nRecords));

java/src/org/broadinstitute/sting/gatk/traversals/TraverseByReference.java

@@ -4,6 +4,7 @@ import org.broadinstitute.sting.gatk.walkers.LocusWalker;
 import org.broadinstitute.sting.gatk.LocusContext;
 import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedData;
 import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.iterators.ReferenceIterator;
 import org.broadinstitute.sting.utils.GenomeLoc;
 
@@ -90,11 +91,11 @@ public class TraverseByReference extends TraverseByLoci {
             GenomeLoc current = refSite.getLocation();
 
             // Iterate forward to get all reference ordered data covering this locus
-            final List<ReferenceOrderedDatum> rodData = getReferenceOrderedDataAtLocus(rodIters, current);
+            final RefMetaDataTracker tracker = getReferenceOrderedDataAtLocus(current);
 
             LocusContext locus = new LocusContext(current, NO_READS, NO_OFFSETS);    // make the empty locus that has no reads
             locus.setReferenceContig(refSite.getCurrentContig());
-            sum = walkAtLocus( walker, sum, locus, refSite, rodData );
+            sum = walkAtLocus( walker, sum, locus, refSite, tracker );
 
             if (this.maxReads > 0 && this.nRecords > this.maxReads) {
                 logger.warn(String.format("Maximum number of reads encountered, terminating traversal " + this.nRecords));

java/src/org/broadinstitute/sting/gatk/walkers/CountLociWalker.java

@@ -2,6 +2,7 @@ package org.broadinstitute.sting.gatk.walkers;
 
 import org.broadinstitute.sting.gatk.LocusContext;
 import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 
 import java.util.List;
 
@@ -13,7 +14,7 @@ import java.util.List;
  * To change this template use File | Settings | File Templates.
  */
 public class CountLociWalker extends LocusWalker<Integer, Integer> {
-    public Integer map(List<ReferenceOrderedDatum> rodData, char ref, LocusContext context) {
+    public Integer map(RefMetaDataTracker tracker, char ref, LocusContext context) {
         return 1;
     }
 

java/src/org/broadinstitute/sting/gatk/walkers/DepthOfCoverageWalker.java

@@ -2,6 +2,7 @@ package org.broadinstitute.sting.gatk.walkers;
 
 import org.broadinstitute.sting.gatk.LocusContext;
 import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.utils.cmdLine.Argument;
 import org.broadinstitute.sting.utils.Pair;
 import java.util.List;
@@ -17,7 +18,7 @@ public class DepthOfCoverageWalker extends LocusWalker<Integer, Pair<Long, Long>
     @Argument(fullName="suppressLocusPrinting",required=false,defaultValue="false")
     public boolean suppressPrinting;
 
-    public Integer map(List<ReferenceOrderedDatum> rodData, char ref, LocusContext context) {
+    public Integer map(RefMetaDataTracker tracker, char ref, LocusContext context) {
         if ( !suppressPrinting )
             out.printf("%s: %d%n", context.getLocation(), context.getReads().size() );
         return context.getReads().size();

java/src/org/broadinstitute/sting/gatk/walkers/LocusWalker.java

@@ -1,6 +1,7 @@
 package org.broadinstitute.sting.gatk.walkers;
 
 import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.LocusContext;
 
 import java.util.List;
@@ -14,7 +15,7 @@ import java.util.List;
  */
 public abstract class LocusWalker<MapType, ReduceType> extends Walker<MapType, ReduceType> {
     // Do we actually want to operate on the context?
-    public boolean filter(List<ReferenceOrderedDatum> rodData, char ref, LocusContext context) {
+    public boolean filter(RefMetaDataTracker tracker, char ref, LocusContext context) {
         return true;    // We are keeping all the reads
     }
 
@@ -26,7 +27,7 @@ public abstract class LocusWalker<MapType, ReduceType> extends Walker<MapType, R
     public boolean cannotHandleReads() { return false; }
 
     // Map over the org.broadinstitute.sting.gatk.LocusContext
-    public abstract MapType map(List<ReferenceOrderedDatum> rodData, char ref, LocusContext context);
+    public abstract MapType map(RefMetaDataTracker tracker, char ref, LocusContext context);
 
     // Given result of map function
     public abstract ReduceType reduceInit();

java/src/org/broadinstitute/sting/gatk/walkers/NullWalker.java

@@ -3,6 +3,7 @@ package org.broadinstitute.sting.gatk.walkers;
 import org.broadinstitute.sting.gatk.walkers.LocusWalker;
 import org.broadinstitute.sting.gatk.LocusContext;
 import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 
 import java.util.List;
 
@@ -14,12 +15,12 @@ public class NullWalker extends LocusWalker<Integer, Integer> {
     }
 
     // Do we actually want to operate on the context?
-    public boolean filter(List<ReferenceOrderedDatum> rodData, char ref, LocusContext context) {
+    public boolean filter(RefMetaDataTracker tracker, char ref, LocusContext context) {
         return true;    // We are keeping all the reads
     }
 
     // Map over the org.broadinstitute.sting.gatk.LocusContext
-    public Integer map(List<ReferenceOrderedDatum> rodData, char ref, LocusContext context) 
+    public Integer map(RefMetaDataTracker tracker, char ref, LocusContext context) 
     {
         return 1;
     }

java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java

@@ -3,6 +3,7 @@ package org.broadinstitute.sting.gatk.walkers;
 import org.broadinstitute.sting.gatk.LocusContext;
 import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
 import org.broadinstitute.sting.gatk.refdata.rodDbSNP;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.utils.cmdLine.Argument;
 import org.broadinstitute.sting.utils.Utils;
 import net.sf.samtools.SAMRecord;
@@ -24,11 +25,11 @@ public class PileupWalker extends LocusWalker<Integer, Integer> {
     }
 
     // Do we actually want to operate on the context?
-    public boolean filter(List<ReferenceOrderedDatum> rodData, char ref, LocusContext context) {
+    public boolean filter(RefMetaDataTracker tracker, char ref, LocusContext context) {
         return true;    // We are keeping all the reads
     }
 
-    public Integer map(List<ReferenceOrderedDatum> rodData, char ref, LocusContext context) {
+    public Integer map(RefMetaDataTracker tracker, char ref, LocusContext context) {
         List<SAMRecord> reads = context.getReads();
         List<Integer> offsets = context.getOffsets();
         String bases = Utils.basePileupAsString(reads, offsets);
@@ -39,17 +40,15 @@ public class PileupWalker extends LocusWalker<Integer, Integer> {
         }
 
         String rodString = "";
-        for ( ReferenceOrderedDatum datum : rodData ) {
+        for ( ReferenceOrderedDatum datum : tracker.getAllRods() ) {
-            if ( datum != null ) {
+            if ( datum != null && ! (datum instanceof rodDbSNP)) {
-                if ( datum instanceof rodDbSNP) {
-                    rodDbSNP dbsnp = (rodDbSNP)datum;
-                    rodString += dbsnp.toMediumString();
-                }
-                else {
                 rodString += datum.toSimpleString();
             }
         }
-        }
+        rodDbSNP dbsnp = (rodDbSNP)tracker.lookup("dbSNP", null);
+        if ( dbsnp != null )
+            rodString += dbsnp.toMediumString();
+
         if ( rodString != "" )
             rodString = "[ROD: " + rodString + "]";
 

java/src/org/broadinstitute/sting/playground/gatk/walkers/AlleleFrequencyWalker.java

@@ -3,6 +3,7 @@ package org.broadinstitute.sting.playground.gatk.walkers;
 import org.broadinstitute.sting.gatk.LocusContext;
 import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
 import org.broadinstitute.sting.gatk.refdata.rodDbSNP;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.LocusWalker;
 import org.broadinstitute.sting.playground.utils.AlleleFrequencyEstimate;
 import org.broadinstitute.sting.playground.utils.AlleleMetrics;
@@ -32,7 +33,7 @@ public class AlleleFrequencyWalker extends LocusWalker<AlleleFrequencyEstimate,
 
     public boolean requiresReads()     { return true; }    
 
-    public AlleleFrequencyEstimate map(List<ReferenceOrderedDatum> rodData, char ref, LocusContext context) 
+    public AlleleFrequencyEstimate map(RefMetaDataTracker tracker, char ref, LocusContext context) 
     {
         // Convert context data into bases and 4-base quals
         String bases = getBases(context);
@@ -103,7 +104,7 @@ public class AlleleFrequencyWalker extends LocusWalker<AlleleFrequencyEstimate,
 
         // Print dbSNP data if its there
         if (true) {
-            for ( ReferenceOrderedDatum datum : rodData ) {
+            for ( ReferenceOrderedDatum datum : tracker.getAllRods() ) {
                 if ( datum != null && datum instanceof rodDbSNP) {
                     rodDbSNP dbsnp = (rodDbSNP)datum;
                     //System.out.printf("  DBSNP %s on %s => %s%n", dbsnp.toSimpleString(), dbsnp.strand, Utils.join("/", dbsnp.getAllelesFWD()));
@@ -114,7 +115,7 @@ public class AlleleFrequencyWalker extends LocusWalker<AlleleFrequencyEstimate,
 
         logger.debug(String.format(" => result is %s", alleleFreq));
 
-        if (LOG_METRICS) metrics.nextPosition(alleleFreq, rodData);
+        if (LOG_METRICS) metrics.nextPosition(alleleFreq, tracker);
 
         return alleleFreq;
     }

java/src/org/broadinstitute/sting/playground/gatk/walkers/CoverageBySample.java

@@ -3,10 +3,7 @@ package org.broadinstitute.sting.playground.gatk.walkers;
 
 import net.sf.samtools.*;
 import org.broadinstitute.sting.gatk.*;
-import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedData;
+import org.broadinstitute.sting.gatk.refdata.*;
-import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
-import org.broadinstitute.sting.gatk.refdata.rodDbSNP;
-import org.broadinstitute.sting.gatk.refdata.rodGFF;
 import org.broadinstitute.sting.gatk.walkers.LocusWalker;
 import org.broadinstitute.sting.gatk.LocusContext;
 import org.broadinstitute.sting.playground.gatk.walkers.AlleleFrequencyWalker;
@@ -36,7 +33,7 @@ public class CoverageBySample extends LocusWalker<String, String>
         } 
     }
 
-    public String map(List<ReferenceOrderedDatum> rodData, char ref, LocusContext context) 
+    public String map(RefMetaDataTracker tracker, char ref, LocusContext context) 
     {
         String line = context.getLocation().getContig() + " " + context.getLocation().getStart() + " " ;
         for (int i = 0; i < sample_names.size(); i++)

java/src/org/broadinstitute/sting/playground/gatk/walkers/PoolCallingExperiment.java

@@ -4,6 +4,7 @@ package org.broadinstitute.sting.playground.gatk.walkers;
 import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
 import org.broadinstitute.sting.gatk.refdata.rodDbSNP;
 import org.broadinstitute.sting.gatk.refdata.rodGFF;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.LocusWalker;
 import org.broadinstitute.sting.gatk.LocusContext;
 import org.broadinstitute.sting.playground.gatk.walkers.AlleleFrequencyWalker;
@@ -20,7 +21,7 @@ public class PoolCallingExperiment extends LocusWalker<AlleleFrequencyEstimate,
 
     @Argument public int DOWNSAMPLE;
 
-    public AlleleFrequencyEstimate map(List<ReferenceOrderedDatum> rodData, char ref, LocusContext context) 
+    public AlleleFrequencyEstimate map(RefMetaDataTracker tracker, char ref, LocusContext context) 
     {
         for (int i = 0; i < context.getReads().size(); i++)
         {

java/src/org/broadinstitute/sting/playground/gatk/walkers/PopPriorWalker.java

@@ -6,6 +6,7 @@ import org.broadinstitute.sting.gatk.walkers.LocusWalker;
 import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
 import org.broadinstitute.sting.gatk.refdata.rodDbSNP;
 import org.broadinstitute.sting.gatk.refdata.HapMapAlleleFrequenciesROD;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.cmdLine.Argument;
 import net.sf.samtools.SAMRecord;
@@ -30,7 +31,7 @@ public class PopPriorWalker extends LocusWalker<Integer, Integer> {
     public String walkerType() { return "ByLocus"; }
 
     // Do we actually want to operate on the context?
-    public boolean filter(List<ReferenceOrderedDatum> rodData, char ref, LocusContext context) {
+    public boolean filter(RefMetaDataTracker tracker, char ref, LocusContext context) {
         return true;    // We are keeping all the reads
     }
 
@@ -95,7 +96,7 @@ public class PopPriorWalker extends LocusWalker<Integer, Integer> {
     }
 
     // Map over the org.broadinstitute.sting.gatk.LocusContext
-    public Integer map(List<ReferenceOrderedDatum> rodData, char ref, LocusContext context) {
+    public Integer map(RefMetaDataTracker tracker, char ref, LocusContext context) {
         char upRef = Character.toUpperCase(ref);
         List<SAMRecord> reads = context.getReads();
         List<Integer> offsets = context.getOffsets();
@@ -106,7 +107,7 @@ public class PopPriorWalker extends LocusWalker<Integer, Integer> {
         rodDbSNP dbsnpInfo = null;
         HapMapAlleleFrequenciesROD hapmap = null;
 
-        for ( ReferenceOrderedDatum datum : rodData )
+        for ( ReferenceOrderedDatum datum : tracker.getAllRods() )
         {
             if ( datum != null )
             {

java/src/org/broadinstitute/sting/playground/gatk/walkers/SingleSampleGenotyper.java

@@ -3,6 +3,7 @@ package org.broadinstitute.sting.playground.gatk.walkers;
 import org.broadinstitute.sting.gatk.LocusContext;
 import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
 import org.broadinstitute.sting.gatk.refdata.rodDbSNP;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.LocusWalker;
 import org.broadinstitute.sting.utils.Utils;
 import net.sf.samtools.SAMRecord;
@@ -13,7 +14,7 @@ import java.util.List;
 // j.maguire 3-7-2009
 
 public class SingleSampleGenotyper extends LocusWalker<Integer, Integer> {
-    public boolean filter(List<ReferenceOrderedDatum> rodData, char ref, LocusContext context) {
+    public boolean filter(RefMetaDataTracker tracker, char ref, LocusContext context) {
         return true;    // We are keeping all the reads
     }
 
@@ -82,7 +83,7 @@ public class SingleSampleGenotyper extends LocusWalker<Integer, Integer> {
     }
 
     // Map over the org.broadinstitute.sting.gatk.LocusContext
-    public Integer map(List<ReferenceOrderedDatum> rodData, char ref, LocusContext context) {
+    public Integer map(RefMetaDataTracker tracker, char ref, LocusContext context) {
         //System.out.printf("Reads %s:%d %d%n", context.getContig(), context.getPosition(), context.getReads().size());
         //for ( SAMRecord read : context.getReads() ) {
         //    System.out.println("  -> " + read.getReadName());
@@ -96,7 +97,7 @@ public class SingleSampleGenotyper extends LocusWalker<Integer, Integer> {
 
         // Look up hapmap and dbsnp priors
         String rodString = "";
-        for ( ReferenceOrderedDatum datum : rodData ) 
+        for ( ReferenceOrderedDatum datum : tracker.getAllRods() ) 
         {
             if ( datum != null ) 
             {

java/src/org/broadinstitute/sting/playground/utils/AlleleMetrics.java

@@ -3,6 +3,7 @@ package org.broadinstitute.sting.playground.utils;
 import org.broadinstitute.sting.gatk.refdata.rodGFF;
 import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
 import org.broadinstitute.sting.gatk.refdata.rodDbSNP;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.playground.gatk.walkers.AlleleFrequencyWalker;
 
 import java.util.List;
@@ -44,14 +45,14 @@ public class AlleleMetrics {
         }
     }
 
-    public void nextPosition(AlleleFrequencyEstimate alleleFreq, List<ReferenceOrderedDatum> rodData) {
+    public void nextPosition(AlleleFrequencyEstimate alleleFreq, RefMetaDataTracker tracker) {
         num_loci_total += 1;
 
         boolean is_dbSNP_SNP = false;
         boolean has_hapmap_chip_genotype = false;
         rodGFF hapmap_chip_genotype = null;
 
-        for ( ReferenceOrderedDatum datum : rodData )
+        for ( ReferenceOrderedDatum datum : tracker.getAllRods() )
         {
             if ( datum != null )
             {