Restructuring of ReferenceContext and ReadWalkers to accept a ReferenceContext. Now ReferenceContext is byte[] backed not char[]. Please no more chars for the reference. All of the tests pass now. Coming check-ins are going to clean up the char / byte problems in the GATK

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3397 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/alignment/AlignmentValidationWalker.java

@@ -27,6 +27,7 @@ package org.broadinstitute.sting.alignment;
 
 import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.ReadWalker;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.commandline.Argument;
@@ -69,14 +70,6 @@ public class AlignmentValidationWalker extends ReadWalker<Integer,Integer> {
         aligner = new BWACAligner(bwtFiles,configuration);
     }
 
-    /** Must return true for reads that need to be processed. Reads, for which this method return false will
-     * be skipped by the engine and never passed to the walker.
-     */
-    @Override
-    public boolean filter(char[] ref, SAMRecord read) {
-        return true;
-    }
-
     /**
      * Aligns a read to the given reference.
      * @param ref Reference over the read.  Read will most likely be unmapped, so ref will be null.
@@ -84,7 +77,7 @@ public class AlignmentValidationWalker extends ReadWalker<Integer,Integer> {
      * @return Number of reads aligned by this map (aka 1).
      */
     @Override
-    public Integer map(char[] ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
+    public Integer map(ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
         //logger.info(String.format("examining read %s", read.getReadName()));
 
         byte[] bases = read.getReadBases();

java/src/org/broadinstitute/sting/alignment/AlignmentWalker.java

@@ -29,6 +29,7 @@ import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.gatk.walkers.ReadWalker;
 import org.broadinstitute.sting.gatk.walkers.WalkerName;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.alignment.bwa.c.BWACAligner;
 import org.broadinstitute.sting.alignment.bwa.BWAConfiguration;
 import org.broadinstitute.sting.alignment.bwa.BWTFiles;
@@ -70,14 +71,6 @@ public class AlignmentWalker extends ReadWalker<Integer,Integer> {
      */
     private SAMFileHeader header;
 
-    /** Must return true for reads that need to be processed. Reads, for which this method return false will
-     * be skipped by the engine and never passed to the walker.
-     */
-    @Override
-    public boolean filter(char[] ref, SAMRecord read) {
-        return true;
-    }
-
     /**
      * Create an aligner object.  The aligner object will load and hold the BWT until close() is called.
      */    
@@ -109,7 +102,7 @@ public class AlignmentWalker extends ReadWalker<Integer,Integer> {
      * @return Number of alignments found for this read.
      */
     @Override
-    public Integer map(char[] ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
+    public Integer map(ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
         SAMRecord alignedRead = aligner.align(read,header);
         if (outputBam != null) {
             outputBam.addAlignment(alignedRead);

java/src/org/broadinstitute/sting/alignment/CountBestAlignmentsWalker.java

@@ -27,6 +27,7 @@ package org.broadinstitute.sting.alignment;
 
 import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.ReadWalker;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.alignment.bwa.BWTFiles;
 import org.broadinstitute.sting.alignment.bwa.BWAConfiguration;
 import org.broadinstitute.sting.alignment.bwa.c.BWACAligner;
@@ -75,7 +76,7 @@ public class CountBestAlignmentsWalker extends ReadWalker<Integer,Integer> {
      * @return Number of alignments found for this read.
      */
     @Override
-    public Integer map(char[] ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
+    public Integer map(ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
         Iterator<Alignment[]> alignmentIterator = aligner.getAllAlignments(read.getReadBases()).iterator();
         if(alignmentIterator.hasNext()) {
             int numAlignments = alignmentIterator.next().length;

java/src/org/broadinstitute/sting/gatk/contexts/ReferenceContext.java

@@ -51,18 +51,20 @@ public class ReferenceContext {
     /**
      * The bases in the window around the current locus.
      */
-    private char[] bases;
+    private byte[] bases;
+
+    private char[] basesAsCharCached = null;
 
     /**
      * Contructor for a simple, windowless reference context.
      * @param locus locus of interest.
      * @param base reference base at that locus.
      */
-    public ReferenceContext( GenomeLoc locus, char base ) {
+    public ReferenceContext( GenomeLoc locus, byte base ) {
-        this( locus, locus, new char[] { base } );
+        this( locus, locus, new byte[] { base } );
     }
 
-    public ReferenceContext( GenomeLoc locus, GenomeLoc window, char[] bases ) {
+    public ReferenceContext( GenomeLoc locus, GenomeLoc window, byte[] bases ) {
   //      if( !window.containsP(locus) )
   //          throw new StingException("Invalid locus or window; window does not contain locus");
 
@@ -87,10 +89,15 @@ public class ReferenceContext {
      * Get the base at the given locus.
      * @return The base at the given locus from the reference.
      */
-    public char getBase() {
+    public byte getBase() {
         return bases[(int)(locus.getStart() - window.getStart())];
     }
 
+    @Deprecated
+    public char getBaseAsChar() {
+        return (char)getBase();
+    }
+
     /**
      * Get the base at the given locus.
      * @return The base at the given locus from the reference.
@@ -104,10 +111,18 @@ public class ReferenceContext {
      * @return All bases available.  If the window is of size [0,0], the array will
      *         contain only the base at the given locus.
      */
-    public char[] getBases() {
+    public byte[] getBases() {
         return bases;
     }
 
+    @Deprecated
+    public char[] getBasesAsChars() {
+        if ( basesAsCharCached == null )
+            basesAsCharCached = new String(bases).toCharArray();
+        return basesAsCharCached;
+    }
+
+
     /** Extracts from the current window and returns n bases starting at this context's locus (NOT
      * from the window start!). The returned array of chars is newly allocated. If n is too large (runs beyond
      * the right boundary of this context's window), an exception will be thrown. If n==(-1), all bases starting
@@ -115,12 +130,12 @@ public class ReferenceContext {
      * @param n number of requested bases including and starting from the current locus
      * @return
      */
-    public char[] getBasesAtLocus(int n) {
+    public byte[] getBasesAtLocusAsByte(int n) {
 
         int start = (int)(locus.getStart()-window.getStart());
         int stop = ( n==(-1) ? bases.length : start+n );
 
-        char[] b = new char[stop-start];
+        byte[] b = new byte[stop-start];
 
         if ( stop > bases.length )
             throw new StingException("Bases beyond the current window requested: window="+window+", requested="+n);
@@ -129,4 +144,9 @@ public class ReferenceContext {
         for ( int j = start ;  j < stop ; j++) b[i++]=bases[j];
         return b;
     }
+
+    @Deprecated
+    public char[] getBasesAtLocus(int n) {
+        return new String(getBasesAtLocusAsByte(n)).toCharArray();
+    }
 }

java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/Allele.java

@@ -120,6 +120,16 @@ public class Allele implements Comparable<Allele> {
             throw new IllegalArgumentException("Unexpected base in allele bases " + new String(bases));
     }
 
+
+    public Allele(byte base, boolean isRef) {
+        this( base1ToBases(base), isRef);
+    }
+    
+    private static byte[] base1ToBases(byte base) {
+        byte[] bases = { base };
+        return bases;
+    }
+
     /**
      * @param bases  bases representing an allele
      * @return true if the bases represent the null allele
@@ -171,6 +181,7 @@ public class Allele implements Comparable<Allele> {
         this(bases.getBytes(), isRef);
     }
 
+
     /**
      * Creates a non-Ref allele.  @see Allele(byte[], boolean) for full information
      *

java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusReferenceView.java

@@ -174,27 +174,51 @@ public class LocusReferenceView extends ReferenceView {
         //validateLocation( genomeLoc );
 
         GenomeLoc window = GenomeLocParser.createGenomeLoc( genomeLoc.getContig(), getWindowStart(genomeLoc), getWindowStop(genomeLoc) );
-        char[] bases = null;
 
-        if(bounds != null) {
+        int refStart = -1;
+        if (bounds != null) {
             window = trimToBounds(window);
-            bases = StringUtil.bytesToString( referenceSequence.getBases(), (int)(window.getStart() - getWindowStart(bounds)), (int)window.size() ).toCharArray();
+            refStart = (int)(window.getStart() - getWindowStart(bounds));
         }
         else {
             if(referenceSequence == null || referenceSequence.getContigIndex() != genomeLoc.getContigIndex())
                 referenceSequence = reference.getSequence(genomeLoc.getContig());
-            bases = StringUtil.bytesToString( referenceSequence.getBases(), (int)window.getStart()-1, (int)window.size()).toCharArray();
+            refStart = (int)window.getStart()-1;
         }
+
+        // todo -- how often is this copy unnecessary?
+        int len = (int)window.size();
+        byte[] bases = new byte[len];
+        System.arraycopy(referenceSequence.getBases(), refStart, bases, 0, len);
         return new ReferenceContext( genomeLoc, window, bases );
     }
 
+//    public ReferenceContext getReferenceContext( GenomeLoc genomeLoc ) {
+//        //validateLocation( genomeLoc );
+//
+//        GenomeLoc window = GenomeLocParser.createGenomeLoc( genomeLoc.getContig(), getWindowStart(genomeLoc), getWindowStop(genomeLoc) );
+//        char[] bases = null;
+//
+//        if(bounds != null) {
+//            window = trimToBounds(window);
+//            bases = StringUtil.bytesToString( referenceSequence.getBases(), (int)(window.getStart() - getWindowStart(bounds)), (int)window.size() ).toCharArray();
+//        }
+//        else {
+//            if(referenceSequence == null || referenceSequence.getContigIndex() != genomeLoc.getContigIndex())
+//                referenceSequence = reference.getSequence(genomeLoc.getContig());
+//            bases = StringUtil.bytesToString( referenceSequence.getBases(), (int)window.getStart()-1, (int)window.size()).toCharArray();
+//        }
+//        return new ReferenceContext( genomeLoc, window, bases );
+//    }
+
+
     /**
      * Allow the user to pull reference info from any arbitrary region of the reference.
      * @param genomeLoc The locus.
      * @return A list of the bases starting at the start of the locus (inclusive) and ending
      *         at the end of the locus (inclusive).
      */
-    public char[] getReferenceBases( GenomeLoc genomeLoc ) {
+    public byte[] getReferenceBases( GenomeLoc genomeLoc ) {
         return super.getReferenceBases(genomeLoc);
     }
 

java/src/org/broadinstitute/sting/gatk/datasources/providers/ReadReferenceView.java

@@ -7,6 +7,7 @@ import net.sf.picard.reference.ReferenceSequence;
 import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 /*
  * Copyright (c) 2009 The Broad Institute
  *
@@ -61,10 +62,16 @@ public class ReadReferenceView extends ReferenceView {
      *         mapped to the reference, followed by X's coresponding to the rest of the read.
      *         This indicates that the rest lies off the end of the contig.
      */
-    public char[] getReferenceBases( SAMRecord read ) {
+//    public char[] getReferenceBases( SAMRecord read ) {
-        if (read.getReadUnmappedFlag())
+//        if (read.getReadUnmappedFlag())
-            return null;
+//            return null;
-        return getReferenceBases( GenomeLocParser.createGenomeLoc(read) );
+//        return getReferenceBases( GenomeLocParser.createGenomeLoc(read) );
+//    }
+
+    public ReferenceContext getReferenceContext( SAMRecord read ) {
+        GenomeLoc loc = GenomeLocParser.createGenomeLoc(read);
+        byte[] bases = super.getReferenceBases(loc);
+        return new ReferenceContext( loc, loc, bases );
     }
 
 }

java/src/org/broadinstitute/sting/gatk/datasources/providers/ReferenceView.java

@@ -3,11 +3,15 @@ package org.broadinstitute.sting.gatk.datasources.providers;
 import org.broadinstitute.sting.utils.fasta.IndexedFastaSequenceFile;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.Utils;
+import org.broadinstitute.sting.utils.StingException;
+import org.broadinstitute.sting.utils.GenomeLocParser;
 
 import java.util.Collections;
 import java.util.Collection;
+import java.util.Arrays;
 
 import net.sf.samtools.SAMSequenceRecord;
+import net.sf.samtools.SAMRecord;
 import net.sf.samtools.util.StringUtil;
 import net.sf.picard.reference.ReferenceSequence;
 /**
@@ -60,10 +64,41 @@ public class ReferenceView implements View {
      * @return A list of the bases starting at the start of the locus (inclusive) and ending
      *         at the end of the locus (inclusive).
      */
-    protected char[] getReferenceBases( GenomeLoc genomeLoc ) {
+//    protected char[] getReferenceBasesAsChars( GenomeLoc genomeLoc ) {
+////        SAMSequenceRecord sequenceInfo = reference.getSequenceDictionary().getSequence(genomeLoc.getContig());
+////        long stop = Math.min( genomeLoc.getStop(), sequenceInfo.getSequenceLength() );
+////        ReferenceSequence subsequence = reference.getSubsequenceAt(genomeLoc.getContig(),genomeLoc.getStart(),stop);
+////        return (StringUtil.bytesToString(subsequence.getBases()) + Utils.dupString('X', (int)(genomeLoc.getStop() - stop)) ).toCharArray();
+//        return new String(getReferenceBases(genomeLoc)).toCharArray();
+//    }
+
+    final static int BUFFER = 10000;
+    final static byte[] Xs = new byte[BUFFER];
+    static {
+        Arrays.fill(Xs, (byte)'X');
+    }
+
+    protected byte[] getReferenceBases( SAMRecord read ) {
+        return getReferenceBases(GenomeLocParser.createGenomeLoc(read));
+
+    }
+
+    protected byte[] getReferenceBases( GenomeLoc genomeLoc ) {
         SAMSequenceRecord sequenceInfo = reference.getSequenceDictionary().getSequence(genomeLoc.getContig());
         long stop = Math.min( genomeLoc.getStop(), sequenceInfo.getSequenceLength() );
-        ReferenceSequence subsequence = reference.getSubsequenceAt(genomeLoc.getContig(),genomeLoc.getStart(),stop);
+        ReferenceSequence subsequence = reference.getSubsequenceAt(genomeLoc.getContig(), genomeLoc.getStart(), stop);
-        return (StringUtil.bytesToString(subsequence.getBases()) + Utils.dupString('X', (int)(genomeLoc.getStop() - stop)) ).toCharArray();        
+
+        int overhang = (int)(genomeLoc.getStop() - stop);
+        if ( overhang > 0 ) {
+            if ( overhang > BUFFER ) // todo -- this is a bit dangerous
+                throw new StingException("Insufficient buffer size for Xs overhanging genome -- expand BUFFER");
+            byte[] all = new byte[subsequence.getBases().length + overhang];
+            System.arraycopy(subsequence.getBases(), 0, all, 0, subsequence.getBases().length);
+            System.arraycopy(Xs, 0, all, subsequence.getBases().length, overhang);
+            return all;
+        } else {
+            // fast path
+            return subsequence.getBases();
+        }
     }
 }

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

@@ -232,6 +232,7 @@ public class RefMetaDataTracker {
      *
      * see getVariantContexts for more information.
      *
+     * @param ref                ReferenceContext to enable conversion to variant context
      * @param name               name
      * @param curLocation        location
      * @param allowedTypes       allowed types
@@ -239,17 +240,17 @@ public class RefMetaDataTracker {
      * @param takeFirstOnly      do we take the first rod only?
      * @return variant context
      */
-    public Collection<VariantContext> getVariantContexts(String name, EnumSet<VariantContext.Type> allowedTypes, GenomeLoc curLocation, boolean requireStartHere, boolean takeFirstOnly ) {
+//    public Collection<VariantContext> getVariantContexts(String name, EnumSet<VariantContext.Type> allowedTypes, GenomeLoc curLocation, boolean requireStartHere, boolean takeFirstOnly ) {
-        return getVariantContexts(null, Arrays.asList(name), allowedTypes, curLocation, requireStartHere, takeFirstOnly);
+//        return getVariantContexts(null, Arrays.asList(name), allowedTypes, curLocation, requireStartHere, takeFirstOnly);
-    }
+//    }
 
     public Collection<VariantContext> getVariantContexts(ReferenceContext ref, String name, EnumSet<VariantContext.Type> allowedTypes, GenomeLoc curLocation, boolean requireStartHere, boolean takeFirstOnly ) {
         return getVariantContexts(ref, Arrays.asList(name), allowedTypes, curLocation, requireStartHere, takeFirstOnly);
     }
 
-    public Collection<VariantContext> getVariantContexts(Collection<String> names, EnumSet<VariantContext.Type> allowedTypes, GenomeLoc curLocation, boolean requireStartHere, boolean takeFirstOnly ) {
+//    public Collection<VariantContext> getVariantContexts(Collection<String> names, EnumSet<VariantContext.Type> allowedTypes, GenomeLoc curLocation, boolean requireStartHere, boolean takeFirstOnly ) {
-        return getVariantContexts(null, names, allowedTypes, curLocation, requireStartHere, takeFirstOnly);
+//        return getVariantContexts(null, names, allowedTypes, curLocation, requireStartHere, takeFirstOnly);
-    }
+//    }
 
     public Collection<VariantContext> getVariantContexts(ReferenceContext ref, Collection<String> names, EnumSet<VariantContext.Type> allowedTypes, GenomeLoc curLocation, boolean requireStartHere, boolean takeFirstOnly ) {
         Collection<VariantContext> contexts = new ArrayList<VariantContext>();
@@ -274,8 +275,8 @@ public class RefMetaDataTracker {
      * @param requireStartHere   do we require the rod to start at this location?
      * @return variant context
      */
-    public VariantContext getVariantContext(String name, EnumSet<VariantContext.Type> allowedTypes, GenomeLoc curLocation, boolean requireStartHere ) {
+    public VariantContext getVariantContext(ReferenceContext ref, String name, EnumSet<VariantContext.Type> allowedTypes, GenomeLoc curLocation, boolean requireStartHere ) {
-        Collection<VariantContext> contexts = getVariantContexts(name, allowedTypes, curLocation, requireStartHere, false );
+        Collection<VariantContext> contexts = getVariantContexts(ref, name, allowedTypes, curLocation, requireStartHere, false );
 
         if ( contexts.size() > 1 )
             throw new StingException("Requested a single VariantContext object for track " + name + " but multiple variants were present at position " + curLocation);

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

@@ -61,17 +61,17 @@ public class VariantContextAdaptors {
 
     /** generic superclass */
     private static abstract class VCAdaptor {
-        abstract VariantContext convert(String name, Object input);
+//        abstract VariantContext convert(String name, Object input);
         abstract VariantContext convert(String name, Object input, ReferenceContext ref);
     }
 
-    public static VariantContext toVariantContext(String name, Object variantContainingObject) {
+//    public static VariantContext toVariantContext(String name, Object variantContainingObject) {
-        if ( ! adaptors.containsKey(variantContainingObject.getClass()) )
+//        if ( ! adaptors.containsKey(variantContainingObject.getClass()) )
-            return null;
+//            return null;
-        else {
+//        else {
-            return adaptors.get(variantContainingObject.getClass()).convert(name, variantContainingObject);
+//            return adaptors.get(variantContainingObject.getClass()).convert(name, variantContainingObject);
-        }
+//        }
-    }
+//    }
 
     public static VariantContext toVariantContext(String name, Object variantContainingObject, ReferenceContext ref) {
         if ( ! adaptors.containsKey(variantContainingObject.getClass()) )
@@ -96,9 +96,9 @@ public class VariantContextAdaptors {
     // --------------------------------------------------------------------------------------------------------------
 
     private static class DBSnpAdaptor extends VCAdaptor {
-        VariantContext convert(String name, Object input) {
+//        VariantContext convert(String name, Object input) {
-            return convert(name, input, null);
+//            return convert(name, input, null);
-        }
+//        }
 
         VariantContext convert(String name, Object input, ReferenceContext ref) {
             DbSNPFeature dbsnp = (DbSNPFeature)input;
@@ -132,10 +132,10 @@ public class VariantContextAdaptors {
     }
 
     private static class VCFRecordAdaptor extends VCAdaptor {
-        // WARNING: do not use this method if you have anything other than point mutations in your VCF
+//        // WARNING: do not use this method if you have anything other than point mutations in your VCF
-        VariantContext convert(String name, Object input) {
+//        VariantContext convert(String name, Object input) {
-            return vcfToVariantContext(name, (VCFRecord)input, null);
+//            return vcfToVariantContext(name, (VCFRecord)input, null);
-        }
+//        }
 
         VariantContext convert(String name, Object input, ReferenceContext ref) {
             return vcfToVariantContext(name, (VCFRecord)input, ref);
@@ -168,7 +168,7 @@ public class VariantContextAdaptors {
                 Allele allele;
                 // special case: semi-deletion
                 if ( vcf.isDeletion() && refAllele.length() > alt.getLength() ) {
-                    char[] semiDeletion = new char[refAllele.length() - alt.getLength()];
+                    byte[] semiDeletion = new byte[refAllele.length() - alt.getLength()];
                     System.arraycopy(ref.getBases(), alt.getLength(), semiDeletion, 0, refAllele.length() - alt.getLength());
                     allele = new Allele(String.valueOf(semiDeletion), false);
                 } else {
@@ -223,13 +223,16 @@ public class VariantContextAdaptors {
     }
 
     private static Allele determineRefAllele(VCFRecord vcf, ReferenceContext ref) {
+        if ( ref == null )
+            throw new StingException("Illegal determineRefAllele call!");
+
         Allele refAllele;
         if ( vcf.isInsertion() ) {
             refAllele = new Allele(Allele.NULL_ALLELE_STRING, true);
-        } else if ( ref == null ) {
+//        } else if ( ref == null ) {
-            refAllele = new Allele(vcf.getReference(), true);
+//            refAllele = new Allele(vcf.getReference(), true);
         } else if ( !vcf.isIndel() ) {
-            refAllele = new Allele(Character.toString(ref.getBase()), true);
+            refAllele = new Allele(ref.getBase(), true);
         } else if ( vcf.isDeletion() ) {
             int start = (int)(ref.getLocus().getStart() - ref.getWindow().getStart() + 1);
             int delLength = 0;
@@ -240,9 +243,7 @@ public class VariantContextAdaptors {
             if ( delLength > ref.getWindow().getStop() - ref.getLocus().getStop() )
                 throw new IllegalArgumentException("Length of deletion is larger than reference context provided at " + ref.getLocus());
 
-            char[] deletion = new char[delLength];
+            refAllele = deletionAllele(ref, start, delLength);
-            System.arraycopy(ref.getBases(), start, deletion, 0, delLength);
-            refAllele = new Allele(String.valueOf(deletion), true);
         } else {
             throw new UnsupportedOperationException("Conversion of VCF type " + vcf.getType() + " is not supported.");
         }
@@ -250,6 +251,13 @@ public class VariantContextAdaptors {
         return refAllele;
     }
 
+    private static Allele deletionAllele(ReferenceContext ref, int start, int len) {
+        byte[] deletion = new byte[len];
+        System.arraycopy(ref.getBases(), start, deletion, 0, len);
+        return new Allele(deletion, true);
+    }
+
+
     public static VCFHeader createVCFHeader(Set<VCFHeaderLine> hInfo, VariantContext vc) {
         HashSet<String> names = new LinkedHashSet<String>();
         for ( Genotype g : vc.getGenotypesSortedByName() ) {
@@ -259,11 +267,11 @@ public class VariantContextAdaptors {
         return new VCFHeader(hInfo == null ? new HashSet<VCFHeaderLine>() : hInfo, names);
     }
 
-    public static VCFRecord toVCF(VariantContext vc, char vcfRefBase) {
+    public static VCFRecord toVCF(VariantContext vc, byte vcfRefBase) {
         return toVCF(vc, vcfRefBase, null, true, false);
     }
 
-    public static VCFRecord toVCF(VariantContext vc, char vcfRefBase, List<String> allowedGenotypeAttributeKeys, boolean filtersWereAppliedToContext, boolean filtersWereAppliedToGenotypes) {
+    public static VCFRecord toVCF(VariantContext vc, byte vcfRefBase, List<String> allowedGenotypeAttributeKeys, boolean filtersWereAppliedToContext, boolean filtersWereAppliedToGenotypes) {
         // deal with the reference
         String referenceBases = new String(vc.getReference().getBases());
 
@@ -293,21 +301,21 @@ public class VariantContextAdaptors {
                 if ( a.isNull() ) {
                     if ( a.isReference() ) {
                         // ref, where alt is insertion
-                        encoding = new VCFGenotypeEncoding(Character.toString(vcfRefBase));
+                        encoding = new VCFGenotypeEncoding(Character.toString((char)vcfRefBase));
                     } else {
                         // non-ref deletion
                         encoding = new VCFGenotypeEncoding("D" + Integer.toString(referenceBases.length()));
                     }
                 } else if ( a.isReference() ) {
                     // ref, where alt is deletion
-                    encoding = new VCFGenotypeEncoding(Character.toString(vcfRefBase));
+                    encoding = new VCFGenotypeEncoding(Character.toString((char)vcfRefBase));
                 } else {
                     // non-ref insertion
                     encoding = new VCFGenotypeEncoding("I" + alleleString);
                 }
             } else if ( vc.getType() == VariantContext.Type.NO_VARIATION ) {
                 // ref
-                encoding = new VCFGenotypeEncoding(Character.toString(vcfRefBase));
+                encoding = new VCFGenotypeEncoding(Character.toString((char)vcfRefBase));
             } else {
                 // ref or alt for snp
                 encoding = new VCFGenotypeEncoding(alleleString);
@@ -381,7 +389,7 @@ public class VariantContextAdaptors {
                 infoFields.put(key, outputValue);
         }
 
-        return new VCFRecord(Character.toString(vcfRefBase), contig, position, ID, vcfAltAlleles, qual, filters, infoFields, genotypeFormatString, genotypeObjects);
+        return new VCFRecord(Character.toString((char)vcfRefBase), contig, position, ID, vcfAltAlleles, qual, filters, infoFields, genotypeFormatString, genotypeObjects);
     }
 
     private static String formatVCFField(String key, Object val) {
@@ -389,7 +397,7 @@ public class VariantContextAdaptors {
         if ( val == null )
             result = VCFGenotypeRecord.getMissingFieldValue(key);
         else if ( val instanceof Double )
-            result = String.format("%.2f", val);
+            result = String.format("%.2f", (Double)val);
         else
             result = val.toString();
 
@@ -418,9 +426,9 @@ public class VariantContextAdaptors {
     // --------------------------------------------------------------------------------------------------------------
 
     private static class PlinkRodAdaptor extends VCAdaptor {
-        VariantContext convert(String name, Object input) {
+//        VariantContext convert(String name, Object input) {
-            return convert(name, input, null);
+//            return convert(name, input, null);
-        }
+//        }
 
         VariantContext convert(String name, Object input, ReferenceContext ref) {
             if ( ref == null )
@@ -487,16 +495,15 @@ public class VariantContextAdaptors {
         private Allele determineRefAllele(PlinkRod plink, ReferenceContext ref) {
             Allele refAllele;
             if ( !plink.isIndel() ) {
-                refAllele = new Allele(Character.toString(ref.getBase()), true);
+                refAllele = new Allele(ref.getBase(), true);
             } else if ( plink.isInsertion() ) {
                 refAllele = new Allele(Allele.NULL_ALLELE_STRING, true);
             } else {
                 long maxLength = ref.getWindow().getStop() - ref.getLocus().getStop();                
                 if ( plink.getLength() > maxLength )
                     throw new UnsupportedOperationException("Plink conversion currently can only handle indels up to length " + maxLength);
-                char[] deletion = new char[plink.getLength()];
+                refAllele = deletionAllele(ref, 1, plink.getLength());
-                System.arraycopy(ref.getBases(), 1, deletion, 0, plink.getLength());
+
-                refAllele = new Allele(String.valueOf(deletion), true);
             }
             return refAllele;
         }
@@ -588,9 +595,9 @@ public class VariantContextAdaptors {
          * @param input the Rod object, in this case a RodGeliText
          * @return a VariantContext object
          */
-        VariantContext convert(String name, Object input) {
+//        VariantContext convert(String name, Object input) {
-            return convert(name, input, null);
+//            return convert(name, input, null);
-        }
+//        }
 
         /**
          * convert to a Variant Context, given:
@@ -656,9 +663,9 @@ public class VariantContextAdaptors {
          * @param input the Rod object, in this case a RodGeliText
          * @return a VariantContext object
          */
-        VariantContext convert(String name, Object input) {
+//        VariantContext convert(String name, Object input) {
-            return convert(name, input, null);
+//            return convert(name, input, null);
-        }
+//        }
 
         /**
          * convert to a Variant Context, given:
@@ -729,9 +736,9 @@ public class VariantContextAdaptors {
          * @param input the Rod object, in this case a RodGeliText
          * @return a VariantContext object
          */
-        VariantContext convert(String name, Object input) {
+//        VariantContext convert(String name, Object input) {
-            return convert(name, input, null);
+//            return convert(name, input, null);
-        }
+//        }
 
         /**
          * convert to a Variant Context, given:
@@ -748,7 +755,7 @@ public class VariantContextAdaptors {
 
             // add the reference allele
             HashSet<Allele> alleles = new HashSet<Allele>();
-            Allele refAllele = new Allele(Character.toString(ref.getBase()), true);
+            Allele refAllele = new Allele(ref.getBase(), true);
             alleles.add(refAllele);
 
             // make a mapping from sample to genotype

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

@@ -3,11 +3,13 @@ package org.broadinstitute.sting.gatk.traversals;
 import net.sf.samtools.SAMRecord;
 import org.apache.log4j.Logger;
 import org.broadinstitute.sting.gatk.WalkerManager;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.datasources.providers.*;
 import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.DataSource;
 import org.broadinstitute.sting.gatk.walkers.ReadWalker;
 import org.broadinstitute.sting.utils.GenomeLocParser;
+import org.broadinstitute.sting.utils.GenomeLoc;
 
 /*
  * Copyright (c) 2009 The Broad Institute
@@ -77,12 +79,12 @@ public class TraverseReads<M,T> extends TraversalEngine<M,T,ReadWalker<M,T>,Read
 
         // while we still have more reads
         for (SAMRecord read : reads) {
-            // an array of characters that represent the reference
+            // ReferenceContext -- the reference bases covered by the read
-            char[] refSeq = null;
+            ReferenceContext refContext = null;
 
             // get the array of characters for the reference sequence, since we're a mapped read
             if (needsReferenceBasesP && !read.getReadUnmappedFlag() && dataProvider.hasReference())
-                refSeq = reference.getReferenceBases(read);
+                refContext = reference.getReferenceContext(read);
 
             // update the number of reads we've seen
             TraversalStatistics.nRecords++;
@@ -91,9 +93,9 @@ public class TraverseReads<M,T> extends TraversalEngine<M,T,ReadWalker<M,T>,Read
             // if the read is mapped, create a metadata tracker
             ReadMetaDataTracker tracker = (read.getReferenceIndex() >= 0) ? rodView.getReferenceOrderedDataForRead(read) : null;
 
-            final boolean keepMeP = walker.filter(refSeq, read);
+            final boolean keepMeP = walker.filter(refContext, read);
             if (keepMeP) {
-                M x = walker.map(refSeq, read, tracker); // the tracker can be null
+                M x = walker.map(refContext, read, tracker); // the tracker can be null
                 sum = walker.reduce(x, sum);
             }
 

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

@@ -34,6 +34,7 @@ import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.utils.*;
 import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.gatk.io.StingSAMFileWriter;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 
 import java.util.*;
 import java.util.regex.Pattern;
@@ -168,7 +169,7 @@ public class ClipReadsWalker extends ReadWalker<ClipReadsWalker.ReadClipper, Cli
      * @param read the read itself, as a SAMRecord
      * @return the ReadClipper object describing what should be done to clip this read
      */
-    public ReadClipper map(char[] ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
+    public ReadClipper map(ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
         if ( onlyDoRead == null || read.getReadName().equals(onlyDoRead) ) {
             ReadClipper clipper = new ReadClipper(read);
 

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

@@ -38,6 +38,7 @@ package org.broadinstitute.sting.gatk.walkers;
  */
 
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
 import org.broadinstitute.sting.commandline.Argument;
 import net.sf.samtools.SAMFileWriter;
@@ -62,7 +63,7 @@ public class FixBAMSortOrderTag extends ReadWalker<SAMRecord, SAMFileWriter> {
     public SAMFileHeader.SortOrder SORT_ORDER=SAMFileHeader.SortOrder.coordinate;
 
     @Override
-    public SAMRecord map(char[] ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
+    public SAMRecord map(ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
         return read;
     }
 

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

@@ -2,6 +2,7 @@ package org.broadinstitute.sting.gatk.walkers;
 
 import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 
 import java.text.DecimalFormat;
 import java.text.NumberFormat;
@@ -113,7 +114,7 @@ public class FlagStatWalker extends ReadWalker<Integer, Integer> {
 
     private FlagStat myStat = new FlagStat();
 
-    public Integer map( char[] ref, SAMRecord read, ReadMetaDataTracker metaDataTracker ) {
+    public Integer map( ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker ) {
         myStat.readCount++;
         if (read.getReadFailsVendorQualityCheckFlag()) {
             myStat.QC_failure++;

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

@@ -89,7 +89,7 @@ public class PileupWalker extends LocusWalker<Integer, Integer> implements TreeR
             if(shouldShowSecondaryBasePileup(basePileup))
                 secondBasePileup = getSecondBasePileup(basePileup);
 
-            out.printf("%s%s %s%n", basePileup.getPileupString(ref.getBase()), secondBasePileup, rods);
+            out.printf("%s%s %s%n", basePileup.getPileupString(ref.getBaseAsChar()), secondBasePileup, rods);
         }
 
         if ( context.hasExtendedEventPileup() ) {

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

@@ -29,6 +29,7 @@ import net.sf.samtools.SAMFileWriter;
 import net.sf.samtools.SAMReadGroupRecord;
 import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.commandline.Argument;
 
 /**
@@ -63,7 +64,7 @@ public class PrintReadsWalker extends ReadWalker<SAMRecord, SAMFileWriter> {
      * @param read the read itself, as a SAMRecord
      * @return true if the read passes the filter, false if it doesn't
      */
-    public boolean filter(char[] ref, SAMRecord read) {
+    public boolean filter(ReferenceContext ref, SAMRecord read) {
         // check the read group
         if  ( readGroup != null ) {
             SAMReadGroupRecord myReadGroup = read.getReadGroup();
@@ -91,7 +92,7 @@ public class PrintReadsWalker extends ReadWalker<SAMRecord, SAMFileWriter> {
      * @param read the read itself, as a SAMRecord
      * @return the read itself
      */
-    public SAMRecord map( char[] ref, SAMRecord read, ReadMetaDataTracker metaDataTracker ) {
+    public SAMRecord map( ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker ) {
         return read;
     }
 

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

@@ -2,6 +2,7 @@ package org.broadinstitute.sting.gatk.walkers;
 
 import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 
 /**
  * Created by IntelliJ IDEA.
@@ -18,11 +19,11 @@ public abstract class ReadWalker<MapType, ReduceType> extends Walker<MapType, Re
     /** Must return true for reads that need to be processed. Reads, for which this method return false will
      * be skipped by the engine and never passed to the walker.
      */
-    public boolean filter(char[] ref, SAMRecord read) {
+    public boolean filter(ReferenceContext ref, SAMRecord read) {
         // We are keeping all the reads
         return true;
     }
 
     // Map over the org.broadinstitute.sting.gatk.contexts.AlignmentContext
-    public abstract MapType map(char[] ref, SAMRecord read, ReadMetaDataTracker metaDataTracker);
+    public abstract MapType map(ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker);
 }

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

@@ -27,6 +27,7 @@ package org.broadinstitute.sting.gatk.walkers;
 
 import net.sf.samtools.*;
 import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.utils.sam.ReadUtils;
 import org.apache.log4j.Logger;
@@ -53,7 +54,7 @@ public class SplitSamFileWalker extends ReadWalker<SAMRecord, Map<String, SAMFil
         logger.info("SplitSamFile version: " + VERSION);
     }
 
-    public SAMRecord map(char[] ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
+    public SAMRecord map(ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
         return read;
     }
 

java/src/org/broadinstitute/sting/gatk/walkers/annotator/GCContent.java

@@ -30,7 +30,7 @@ public class GCContent implements InfoFieldAnnotation, ExperimentalAnnotation {
     private static double computeGCContent(ReferenceContext ref) {
         int gc = 0, at = 0;
 
-        for ( char base : ref.getBases() ) {
+        for ( byte base : ref.getBases() ) {
             int baseIndex = BaseUtils.simpleBaseToBaseIndex(base);
             if ( baseIndex == BaseUtils.gIndex || baseIndex == BaseUtils.cIndex )
                 gc++;

java/src/org/broadinstitute/sting/gatk/walkers/annotator/HomopolymerRun.java

@@ -24,7 +24,7 @@ public class HomopolymerRun implements InfoFieldAnnotation, StandardAnnotation {
 
         int run;
         if ( vc.isSNP() ) {
-            run = computeHomopolymerRun(vc.getAlternateAllele(0).toString().charAt(0), ref);
+            run = computeHomopolymerRun(vc.getAlternateAllele(0).getBases()[0], ref);
         } else if ( vc.isIndel() && ANNOTATE_INDELS ) {
             run = computeIndelHomopolymerRun(vc,ref);
         } else {
@@ -42,12 +42,12 @@ public class HomopolymerRun implements InfoFieldAnnotation, StandardAnnotation {
 
     public boolean useZeroQualityReads() { return false; }
 
-    private static int computeHomopolymerRun(char altAllele, ReferenceContext ref) {
+    private static int computeHomopolymerRun(byte altAllele, ReferenceContext ref) {
 
         // TODO -- this needs to be computed in a more accurate manner
         // We currently look only at direct runs of the alternate allele adjacent to this position
 
-        char[] bases = ref.getBases();
+        byte[] bases = ref.getBases();
         GenomeLoc window = ref.getWindow();
         GenomeLoc locus = ref.getLocus();
 
@@ -71,13 +71,13 @@ public class HomopolymerRun implements InfoFieldAnnotation, StandardAnnotation {
      }
 
     private static int computeIndelHomopolymerRun(VariantContext vc, ReferenceContext ref) {
-        char[] bases = ref.getBases();
+        byte[] bases = ref.getBases();
         GenomeLoc locus = ref.getLocus();
         GenomeLoc window = ref.getWindow();
         int refBasePos = (int) (locus.getStart() - window.getStart())+1;
         if ( vc.isDeletion() ) {
             // check that deleted bases are the same
-            char dBase = bases[refBasePos];
+            byte dBase = bases[refBasePos];
             for ( int i = 0; i < vc.getAlternateAllele(0).length(); i ++ ) {
                 if ( bases[refBasePos+i] != dBase ) {
                     return 0;
@@ -87,7 +87,7 @@ public class HomopolymerRun implements InfoFieldAnnotation, StandardAnnotation {
             return computeHomopolymerRun(dBase,ref);
         } else {
             // check that inserted bases are the same
-            char insBase = (char) vc.getAlternateAllele(0).getBases()[0];
+            byte insBase = vc.getAlternateAllele(0).getBases()[0];
             for ( byte b : vc.getAlternateAllele(0).getBases() ) {
                 if ( insBase != (char) b ) {
                     return 0;

java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java

@@ -37,7 +37,7 @@ public abstract class RankSumTest implements InfoFieldAnnotation, WorkInProgress
                 if ( context == null )
                     continue;
 
-                fillQualsFromPileup(ref.getBase(), vc.getAlternateAllele(0).toString().charAt(0), context.getContext(StratifiedAlignmentContext.StratifiedContextType.COMPLETE).getBasePileup(), refQuals, altQuals);
+                fillQualsFromPileup(ref.getBaseAsChar(), vc.getAlternateAllele(0).toString().charAt(0), context.getContext(StratifiedAlignmentContext.StratifiedContextType.COMPLETE).getBasePileup(), refQuals, altQuals);
             }
         }
 

java/src/org/broadinstitute/sting/gatk/walkers/annotator/SecondBaseSkew.java

@@ -68,7 +68,7 @@ public class SecondBaseSkew implements InfoFieldAnnotation, ExperimentalAnnotati
         Pair<Integer, Integer> depth = new Pair<Integer, Integer>(0, 0);
         for ( String sample : stratifiedContexts.keySet() ) {
             //Pair<Integer,Integer> sampleDepth = getSecondaryPileupNonrefCount(ref.getBase(),stratifiedContexts.get(sample).getContext(StratifiedAlignmentContext.StratifiedContextType.COMPLETE).getPileup(), alternate);
-            Pair<Integer, Integer> sampleDepth = getSecondaryPileupNonrefCount(ref.getBase(), stratifiedContexts.get(sample).getContext(StratifiedAlignmentContext.StratifiedContextType.COMPLETE).getBasePileup(), alternate);
+            Pair<Integer, Integer> sampleDepth = getSecondaryPileupNonrefCount(ref.getBaseAsChar(), stratifiedContexts.get(sample).getContext(StratifiedAlignmentContext.StratifiedContextType.COMPLETE).getBasePileup(), alternate);
             depth.first += sampleDepth.first;
             depth.second += sampleDepth.second;
         }

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

@@ -171,7 +171,7 @@ public class VariantAnnotator extends LocusWalker<Integer, Integer> {
             return 0;
 
         Object variant = rods.get(0);
-        VariantContext vc = VariantContextAdaptors.toVariantContext("variant", variant);
+        VariantContext vc = VariantContextAdaptors.toVariantContext("variant", variant, ref);
         if ( vc == null )
             return 0;
 

java/src/org/broadinstitute/sting/gatk/walkers/concordance/IndelSubsets.java

@@ -77,12 +77,12 @@ public class IndelSubsets implements ConcordanceType {
     }
 
     private int homopolymerRunSize(ReferenceContext ref, VCFRecord indel) {
-        char[] bases = ref.getBases();
+        byte[] bases = ref.getBases();
         GenomeLoc window = ref.getWindow();
         GenomeLoc locus = ref.getLocus();
 
         int refBasePos = (int)(locus.getStart() - window.getStart());
-        char indelBase = indel.isDeletion() ? bases[refBasePos+1] : indel.getAlternateAlleleList().get(0).charAt(0);
+        byte indelBase = indel.isDeletion() ? bases[refBasePos+1] : (byte)indel.getAlternateAlleleList().get(0).charAt(0);
         int leftRun = 0;
         for ( int i = refBasePos; i >= 0; i--) {
             if ( bases[i] != indelBase )
@@ -90,7 +90,7 @@ public class IndelSubsets implements ConcordanceType {
             leftRun++;
         }
 
-        indelBase = indel.isDeletion() ? bases[Math.min(refBasePos+indel.getAlternateAlleleList().get(0).length(),bases.length-1)] : indel.getAlternateAlleleList().get(0).charAt(indel.getAlternateAlleleList().get(0).length()-1);
+        indelBase = indel.isDeletion() ? bases[Math.min(refBasePos+indel.getAlternateAlleleList().get(0).length(),bases.length-1)] : (byte)indel.getAlternateAlleleList().get(0).charAt(indel.getAlternateAlleleList().get(0).length()-1);
         int rightRun = 0;
         for ( int i = refBasePos + (indel.isDeletion() ? 1+indel.getAlternateAlleleList().get(0).length() : 1); i < bases.length; i++) {
             if ( bases[i] != indelBase )

java/src/org/broadinstitute/sting/gatk/walkers/concordance/SNPGenotypeConcordance.java

@@ -31,7 +31,7 @@ public class SNPGenotypeConcordance implements ConcordanceType {
     }
 
     public String computeConcordance(Map<String, VCFGenotypeRecord> samplesToRecords, ReferenceContext ref) {
-        char refBase = ref.getBase();
+        char refBase = ref.getBaseAsChar();
 
         VCFGenotypeRecord call1 = samplesToRecords.get(sample1);
         if ( call1 != null && call1.isNoCall() )
@@ -90,7 +90,7 @@ public class SNPGenotypeConcordance implements ConcordanceType {
             // are they the same genotype
             if ( genotype1.equals(genotype2) )
                 result.append("sameGenotype");
-            else if ( sameVariantAllele(genotype1, genotype2, ref.getBase()) )
+            else if ( sameVariantAllele(genotype1, genotype2, ref.getBaseAsChar()) )
                 result.append("differentGenotypeSameVariantAllele");
             else
                 result.append("differentVariantAllele");

java/src/org/broadinstitute/sting/gatk/walkers/coverage/CoarseCoverageWalker.java

@@ -29,6 +29,7 @@ import net.sf.samtools.SAMRecord;
 
 import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.ReadWalker;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.commandline.Argument;
 
 /**
@@ -54,7 +55,7 @@ public class CoarseCoverageWalker extends ReadWalker<Integer,Integer> {
     }
     
 	@Override
-	public Integer map(char[] ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
+	public Integer map(ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
 		
 		if ( read.getReadUnmappedFlag() ||
 			 read.getDuplicateReadFlag() ||

java/src/org/broadinstitute/sting/gatk/walkers/fasta/BamToFastqWalker.java

@@ -28,6 +28,7 @@ package org.broadinstitute.sting.gatk.walkers.fasta;
 import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.ReadWalker;
 import org.broadinstitute.sting.gatk.walkers.WalkerName;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.commandline.Argument;
 import net.sf.samtools.SAMRecord;
@@ -59,7 +60,7 @@ public class BamToFastqWalker extends ReadWalker<Integer, Integer> {
         }
     }
 
-	public Integer map(char[] ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
+	public Integer map(ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
         out.println("@" + read.getReadName());
         if ( !RE_REVERSE || !read.getReadNegativeStrandFlag() ) {
             out.println(read.getReadString());

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

@@ -53,7 +53,7 @@ public class FastaAlternateReferenceWalker extends FastaReferenceWalker {
             return new Pair<GenomeLoc, String>(context.getLocation(), "");
         }
 
-        String refBase = String.valueOf(ref.getBase());
+        String refBase = String.valueOf(ref.getBaseAsChar());
 
         for ( VariantContext vc : tracker.getAllVariantContexts(ref) ) {
             // if we have multiple variants at a locus, just take the first one we see

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

@@ -142,7 +142,7 @@ public class VariantFiltrationWalker extends RodWalker<Integer, Integer> {
         if ( rods.size() == 0 )
             return 0;
 
-        VariantContext vc = VariantContextAdaptors.toVariantContext("variant", rods.get(0));
+        VariantContext vc = VariantContextAdaptors.toVariantContext("variant", rods.get(0), ref);
         FiltrationContext varContext = new FiltrationContext(tracker, ref, vc);
 
         // if we're still initializing the context, do so

java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SimpleIndelCalculationModel.java

@@ -9,6 +9,8 @@ import org.broadinstitute.sting.gatk.contexts.variantcontext.*;
 
 import java.util.*;
 
+import net.sf.samtools.util.SequenceUtil;
+
 public class SimpleIndelCalculationModel extends GenotypeCalculationModel {
 
     private int MIN_COVERAGE = 6;
@@ -100,7 +102,7 @@ public class SimpleIndelCalculationModel extends GenotypeCalculationModel {
             // calculate the sum of quality scores for each base
             ReadBackedExtendedEventPileup pileup = context.getExtendedEventPileup();
 
-            List<Pair<String,Integer>> all_events = pileup.getEventStringsWithCounts(ref);
+            List<Pair<String,Integer>> all_events = pileup.getEventStringsWithCounts(BaseUtils.charSeq2byteSeq(ref));
             for ( Pair<String,Integer> p : all_events ) {
                 if ( p.second > bestIndelCount ) {
                     bestIndelCount = p.second;

java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java

@@ -159,7 +159,7 @@ public class UnifiedGenotyperEngine {
             gcm.set(GenotypeCalculationModelFactory.makeGenotypeCalculation(samples, logger, UAC, format, verboseWriter, beagleWriter));
         }
 
-        char ref = Character.toUpperCase(refContext.getBase());
+        char ref = Character.toUpperCase(refContext.getBaseAsChar());
         if ( !BaseUtils.isRegularBase(ref) )
             return null;
 

java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelGenotyperV2Walker.java

@@ -39,6 +39,7 @@ import org.broadinstitute.sting.gatk.refdata.utils.LocationAwareSeekableRODItera
 import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList;
 import org.broadinstitute.sting.gatk.walkers.ReadFilters;
 import org.broadinstitute.sting.gatk.walkers.ReadWalker;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.utils.*;
 import org.broadinstitute.sting.utils.sam.AlignmentUtils;
 import org.broadinstitute.sting.utils.collections.CircularArray;
@@ -178,7 +179,7 @@ public class IndelGenotyperV2Walker extends ReadWalker<Integer,Integer> {
 
 
 	@Override
-	public Integer map(char[] ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
+	public Integer map(ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
 
     //        if ( read.getReadName().equals("428EFAAXX090610:2:36:1384:639#0") ) System.out.println("GOT READ");
 
@@ -294,9 +295,9 @@ public class IndelGenotyperV2Walker extends ReadWalker<Integer,Integer> {
                 if ( rg == null ) throw new StingException("Read "+read.getReadName()+" has no read group in merged stream. RG is required for somatic calls.");
 
                 if ( normalReadGroups.contains(rg) ) {
-                    normal_context.add(read,ref);
+                    normal_context.add(read,ref.getBasesAsChars());
                 } else if ( tumorReadGroups.contains(rg) ) {
-                    tumor_context.add(read,ref);
+                    tumor_context.add(read,ref.getBasesAsChars());
                 } else {
                     throw new StingException("Unrecognized read group in merged stream: "+rg);
                 }
@@ -315,7 +316,7 @@ public class IndelGenotyperV2Walker extends ReadWalker<Integer,Integer> {
 
 
             } else {
-                normal_context.add(read, ref);
+                normal_context.add(read, ref.getBasesAsChars());
                 if ( normal_context.getReads().size() > MAX_READ_NUMBER ) {
                     System.out.println("WARNING: a count of "+MAX_READ_NUMBER+" reads reached in a window "+
                             refName+':'+normal_context.getStart()+'-'+normal_context.getStop()+". The whole window will be dropped");

java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java

@@ -30,6 +30,7 @@ import net.sf.samtools.util.StringUtil;
 import org.broadinstitute.sting.utils.interval.IntervalMergingRule;
 import org.broadinstitute.sting.utils.interval.IntervalUtils;
 import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.datasources.simpleDataSources.SAMReaderID;
 import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
 import org.broadinstitute.sting.gatk.refdata.VariantContextAdaptors;
@@ -283,7 +284,7 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
         }
     }
 
-    public Integer map(char[] ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
+    public Integer map(ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
         if ( currentInterval == null ) {
             emit(read);
             return 0;
@@ -314,9 +315,9 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
                  read.getAlignmentStart() == SAMRecord.NO_ALIGNMENT_START ) {
                 readsNotToClean.add(read);
             } else {
-                readsToClean.add(read, ref);
+                readsToClean.add(read, ref.getBasesAsChars());
                 // add the rods to the list of known variants
-                populateKnownIndels(metaDataTracker);
+                populateKnownIndels(metaDataTracker, null);     // todo -- fixme!
             }
 
             if ( readsToClean.size() + readsNotToClean.size() >= MAX_READS ) {
@@ -335,7 +336,7 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
         return 0;
     }
 
-    private void cleanAndCallMap(char[] ref, SAMRecord read, ReadMetaDataTracker metaDataTracker, GenomeLoc readLoc) {
+    private void cleanAndCallMap(ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker, GenomeLoc readLoc) {
         clean(readsToClean);
         knownIndelsToTry.clear();
 
@@ -403,7 +404,7 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
         }
     }
 
-    private void populateKnownIndels(ReadMetaDataTracker metaDataTracker) {
+    private void populateKnownIndels(ReadMetaDataTracker metaDataTracker, ReferenceContext ref) {
         for ( Collection<GATKFeature> rods : metaDataTracker.getContigOffsetMapping().values() ) {
             Iterator<GATKFeature> rodIter = rods.iterator();
             while ( rodIter.hasNext() ) {
@@ -411,7 +412,7 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
                 if ( knownIndelsToTry.containsKey(rod) )
                     continue;
                 if ( VariantContextAdaptors.canBeConvertedToVariantContext(rod))
-                    knownIndelsToTry.put(rod, VariantContextAdaptors.toVariantContext("", rod));
+                    knownIndelsToTry.put(rod, VariantContextAdaptors.toVariantContext("", rod, ref));
                 else
                     knownIndelsToTry.put(rod, null);
             }

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

@@ -123,7 +123,7 @@ public class RealignerTargetCreator extends LocusWalker<RealignerTargetCreator.E
         if ( pileup != null ) {
 
             int mismatchQualities = 0, totalQualities = 0;
-            char upperRef = Character.toUpperCase(ref.getBase());
+            char upperRef = Character.toUpperCase(ref.getBaseAsChar());
             for (PileupElement p : pileup ) {
                 // check the ends of the reads to see how far they extend
                 SAMRecord read = p.getRead();

java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReadsWalker.java

@@ -5,6 +5,7 @@ import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.Requires;
 import org.broadinstitute.sting.gatk.walkers.DataSource;
 import org.broadinstitute.sting.gatk.walkers.ReadWalker;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 
 /**
  * Walks over the input data set, calculating the number of reads seen for diagnostic purposes.
@@ -13,7 +14,7 @@ import org.broadinstitute.sting.gatk.walkers.ReadWalker;
  */
 @Requires({DataSource.READS, DataSource.REFERENCE})
 public class CountReadsWalker extends ReadWalker<Integer, Integer> {
-    public Integer map(char[] ref, SAMRecord read, ReadMetaDataTracker tracker) {
+    public Integer map(ReferenceContext ref, SAMRecord read, ReadMetaDataTracker tracker) {
         //System.out.println(read.format());
         return 1;
     }

java/src/org/broadinstitute/sting/gatk/walkers/qc/CycleQualityWalker.java

@@ -29,6 +29,7 @@ import org.broadinstitute.sting.gatk.walkers.Requires;
 import org.broadinstitute.sting.gatk.walkers.DataSource;
 import org.broadinstitute.sting.gatk.walkers.ReadWalker;
 import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.sam.AlignmentUtils;
 import org.broadinstitute.sting.commandline.Argument;
@@ -104,7 +105,7 @@ public class CycleQualityWalker extends ReadWalker<Integer,Integer> {
 
     }
 
-    public Integer map(char[] ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
+    public Integer map(ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
 
         if ( AlignmentUtils.isReadUnmapped(read) && MAPPED_ONLY) return 0;
 

java/src/org/broadinstitute/sting/gatk/walkers/qc/PrintLocusContextWalker.java

@@ -16,7 +16,7 @@ import net.sf.samtools.SAMRecord;
  */
 public class PrintLocusContextWalker extends LocusWalker<AlignmentContext, Integer> implements TreeReducible<Integer> {
     public AlignmentContext map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
-        out.printf( "In map: ref = %s, loc = %s, reads = %s%n", ref.getBase(),
+        out.printf( "In map: ref = %s, loc = %s, reads = %s%n", ref.getBaseAsChar(),
                                                                 context.getLocation(),
                                                                 Arrays.deepToString( getReadNames(context.getReads()) ) );
         return context;

java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadClippingStatsWalker.java

@@ -26,6 +26,7 @@ import org.broadinstitute.sting.gatk.walkers.Requires;
 import org.broadinstitute.sting.gatk.walkers.DataSource;
 import org.broadinstitute.sting.gatk.walkers.ReadWalker;
 import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.MathUtils;
@@ -67,7 +68,7 @@ public class ReadClippingStatsWalker extends ReadWalker<ReadClippingStatsWalker.
         int readLength, nClippingEvents, nClippedBases;
     }
 
-    public ReadClippingInfo map(char[] ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
+    public ReadClippingInfo map(ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
         if ( AlignmentUtils.isReadUnmapped(read) && MAPPED_ONLY)
             return null;
 

java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadValidationWalker.java

@@ -2,6 +2,7 @@ package org.broadinstitute.sting.gatk.walkers.qc;
 
 import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.ReadWalker;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.utils.StingException;
 import net.sf.samtools.SAMRecord;
 import net.sf.samtools.SAMFileWriter;
@@ -67,7 +68,7 @@ public class ReadValidationWalker extends ReadWalker<SAMRecord, SAMRecord> {
      * @param read the read itself, as a SAMRecord
      * @return true if the read passes the filter, false if it doesn't
      */
-    public boolean filter(char[] ref, SAMRecord read) {
+    public boolean filter(ReferenceContext ref, SAMRecord read) {
         return true;
 	}
 
@@ -77,7 +78,7 @@ public class ReadValidationWalker extends ReadWalker<SAMRecord, SAMRecord> {
      * @param read the read itself, as a SAMRecord
      * @return the read itself
      */
-    public SAMRecord map( char[] ref, SAMRecord read, ReadMetaDataTracker metaDataTracker ) {
+    public SAMRecord map( ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker ) {
         return read;
     }
 

java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupWalker.java

@@ -54,7 +54,7 @@ public class ValidatingPileupWalker extends LocusWalker<Integer, ValidationStats
         SAMPileupFeature truePileup = getTruePileup( tracker );
 
         if ( truePileup == null ) {
-            out.printf("No truth pileup data available at %s%n", pileup.getPileupString(ref.getBase()));
+            out.printf("No truth pileup data available at %s%n", pileup.getPileupString(ref.getBaseAsChar()));
             if ( ! CONTINUE_AFTER_AN_ERROR ) {
                 Utils.scareUser(String.format("No pileup data available at %s given GATK's output of %s -- this walker requires samtools pileup data over all bases",
                                 context.getLocation(), new String(pileup.getBases())));
@@ -62,7 +62,7 @@ public class ValidatingPileupWalker extends LocusWalker<Integer, ValidationStats
         } else {
             String pileupDiff = pileupDiff(pileup, truePileup, true);
             if ( pileupDiff != null ) {
-                out.printf("%s vs. %s%n", pileup.getPileupString(ref.getBase()), truePileup.getPileupString());
+                out.printf("%s vs. %s%n", pileup.getPileupString(ref.getBaseAsChar()), truePileup.getPileupString());
                 if ( ! CONTINUE_AFTER_AN_ERROR ) {
                     throw new RuntimeException(String.format("Pileups aren't equal: %s", pileupDiff));
                 }

java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CovariateCounterWalker.java

@@ -298,7 +298,7 @@ public class CovariateCounterWalker extends LocusWalker<Integer, PrintStream> {
                 if( gatkRead.getBaseQualities()[offset] > 0 ) {
 
                     bases = gatkRead.getReadBases();
-                    refBase = (byte)ref.getBase();
+                    refBase = ref.getBase();
 
                     // Skip if this base is an 'N' or etc.
                     if( BaseUtils.isRegularBase( (char)(bases[offset]) ) ) {
@@ -345,9 +345,9 @@ public class CovariateCounterWalker extends LocusWalker<Integer, PrintStream> {
      * @param context The AlignmentContext which holds the reads covered by this locus
      * @param ref The reference base
      */
-    private static void updateMismatchCounts(final Pair<Long, Long> counts, final AlignmentContext context, final char ref) {
+    private static void updateMismatchCounts(final Pair<Long, Long> counts, final AlignmentContext context, final byte ref) {
         for( PileupElement p : context.getBasePileup() ) {
-            final char readChar = (char)(p.getBase());
+            final byte readChar = p.getBase();
             final int readCharBaseIndex = BaseUtils.simpleBaseToBaseIndex(readChar);
             final int refCharBaseIndex  = BaseUtils.simpleBaseToBaseIndex(ref);
 

java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java

@@ -49,6 +49,7 @@ import org.broadinstitute.sting.gatk.walkers.DataSource;
 import org.broadinstitute.sting.gatk.walkers.ReadWalker;
 import org.broadinstitute.sting.gatk.walkers.Requires;
 import org.broadinstitute.sting.gatk.walkers.WalkerName;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.utils.classloader.JVMUtils;
 import org.broadinstitute.sting.utils.classloader.PackageUtils;
 import org.broadinstitute.sting.utils.collections.NestedHashMap;
@@ -316,7 +317,7 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
      * @param read The read to be recalibrated
      * @return The read with quality scores replaced
      */
-    public SAMRecord map( char[] refBases, SAMRecord read, ReadMetaDataTracker metaDataTracker  ) {
+    public SAMRecord map( ReferenceContext refBases, SAMRecord read, ReadMetaDataTracker metaDataTracker  ) {
 
         RecalDataManager.parseSAMRecord( read, RAC );
 
@@ -332,7 +333,7 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
                     return read; // can't recalibrate a SOLiD read with no calls in the color space, and the user wants to skip over them
                 }
             }
-            originalQuals = RecalDataManager.calcColorSpace( read, originalQuals, RAC.SOLID_RECAL_MODE, coinFlip, refBases );
+            originalQuals = RecalDataManager.calcColorSpace( read, originalQuals, RAC.SOLID_RECAL_MODE, coinFlip, refBases == null ? null : refBases.getBasesAsChars() );
         }
 
         //compute all covariate values for this read
@@ -360,9 +361,9 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
         if ( read.getAttribute(RecalDataManager.ORIGINAL_QUAL_ATTRIBUTE_TAG) == null ) { // Save the old qualities if the tag isn't already taken in the read
             read.setAttribute(RecalDataManager.ORIGINAL_QUAL_ATTRIBUTE_TAG, QualityUtils.phredToFastq(originalQuals));
         }
+
         if (read.getAttribute(SAMTag.UQ.name()) != null) {
-            // TODO - When refBases is switches to byte[], call the appropriate overload in SAM-JDK, and remove char[] overload from SAM-JDK.
+            read.setAttribute(SAMTag.UQ.name(), SequenceUtil.sumQualitiesOfMismatches(read, refBases.getBases(), read.getAlignmentStart() - 1, false));
-            read.setAttribute(SAMTag.UQ.name(), SequenceUtil.sumQualitiesOfMismatches(read, refBases, read.getAlignmentStart() - 1));
         }
 
         return read;

java/src/org/broadinstitute/sting/gatk/walkers/sequenom/PickSequenomProbes.java

@@ -92,8 +92,6 @@ public class PickSequenomProbes extends RodWalker<String, String> {
 
         logger.debug("Probing " + ref.getLocus() + " " + ref.getWindow());
 
-        String refBase = String.valueOf(ref.getBase());
-
         Collection<VariantContext> VCs = tracker.getAllVariantContexts(ref);
         if ( VCs.size() == 0 )
             return "";
@@ -128,7 +126,7 @@ public class PickSequenomProbes extends RodWalker<String, String> {
             }
         }
 
-		char[] context_bases = ref.getBases();
+		byte[] context_bases = ref.getBases();
 		for (int i = 0; i < 401; i++) {
 			if ( maskFlags[i] == 1 ) {
                 context_bases[i] = 'N';
@@ -140,11 +138,11 @@ public class PickSequenomProbes extends RodWalker<String, String> {
 
         String assay_sequence;
         if ( vc.isSNP() )
-            assay_sequence = leading_bases + "[" + refBase + "/" + vc.getAlternateAllele(0).toString() + "]" + trailing_bases;
+            assay_sequence = leading_bases + "[" + ref.getBaseAsChar() + "/" + vc.getAlternateAllele(0).toString() + "]" + trailing_bases;
         else if ( vc.isInsertion() )
-            assay_sequence = leading_bases + refBase + "[-/" + vc.getAlternateAllele(0).toString() + "]" + trailing_bases;
+            assay_sequence = leading_bases + ref.getBaseAsChar() + "[-/" + vc.getAlternateAllele(0).toString() + "]" + trailing_bases;
         else if ( vc.isDeletion() )
-            assay_sequence = leading_bases + refBase + "[" + new String(vc.getReference().getBases()) + "/-]" + trailing_bases.substring(vc.getReference().length());
+            assay_sequence = leading_bases + ref.getBaseAsChar() + "[" + new String(vc.getReference().getBases()) + "/-]" + trailing_bases.substring(vc.getReference().length());
         else
             return "";
 

java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java

@@ -441,7 +441,7 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> {
     public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
         //System.out.printf("map at %s with %d skipped%n", context.getLocation(), context.getSkippedBases());
 
-        Map<String, VariantContext> vcs = getVariantContexts(tracker, context);
+        Map<String, VariantContext> vcs = getVariantContexts(ref, tracker, context);
         //Collection<VariantContext> comps = getCompVariantContexts(tracker, context);
 
         // to enable walking over pairs where eval or comps have no elements
@@ -493,7 +493,7 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> {
         return 0;
     }
 
-    private void writeInterestingSite(List<String> interestingReasons, VariantContext vc, char ref) {
+    private void writeInterestingSite(List<String> interestingReasons, VariantContext vc, byte ref) {
         if ( vc != null && writer != null && interestingReasons.size() > 0 ) {
             // todo -- the vc == null check is because you can be interesting because you are a FN, and so VC == null
             MutableVariantContext mvc = new MutableVariantContext(vc);
@@ -576,21 +576,21 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> {
 //
 //logger.info(String.format("Ignore second+ events at locus %s in rod %s => rec is %s", context.getLocation(), rodList.getName(), rec));
 
-    private Map<String, VariantContext> getVariantContexts(RefMetaDataTracker tracker, AlignmentContext context) {
+    private Map<String, VariantContext> getVariantContexts(ReferenceContext ref, RefMetaDataTracker tracker, AlignmentContext context) {
         // todo -- we need to deal with dbSNP where there can be multiple records at the same start site.  A potential solution is to
         // todo -- allow the variant evaluation to specify the type of variants it wants to see and only take the first such record at a site
         Map<String, VariantContext> bindings = new HashMap<String, VariantContext>();
         if ( tracker != null ) {
-            bindVariantContexts(bindings, evalNames, tracker, context, false);
+            bindVariantContexts(ref, bindings, evalNames, tracker, context, false);
-            bindVariantContexts(bindings, compNames, tracker, context, true);
+            bindVariantContexts(ref, bindings, compNames, tracker, context, true);
         }
         return bindings;
     }
 
-    private void bindVariantContexts(Map<String, VariantContext> map, Collection<String> names,
+    private void bindVariantContexts(ReferenceContext ref, Map<String, VariantContext> map, Collection<String> names,
                                      RefMetaDataTracker tracker, AlignmentContext context, boolean allowExcludes ) {
         for ( String name : names ) {
-            Collection<VariantContext> contexts = tracker.getVariantContexts(name, ALLOW_VARIANT_CONTEXT_TYPES, context.getLocation(), true, true);
+            Collection<VariantContext> contexts = tracker.getVariantContexts(ref, name, ALLOW_VARIANT_CONTEXT_TYPES, context.getLocation(), true, true);
             if ( contexts.size() > 1 )
                 throw new StingException("Found multiple variant contexts at " + context.getLocation());
 

java/src/org/broadinstitute/sting/gatk/walkers/vcf/FilterLiftedVCF.java

@@ -80,7 +80,7 @@ public class FilterLiftedVCF extends RodWalker<Integer, Integer> {
         List<Object> rods = tracker.getReferenceMetaData("vcf");
 
         for ( Object rod : rods )
-            filterAndWrite(ref.getBase(), (VCFRecord)rod);
+            filterAndWrite(ref.getBaseAsChar(), (VCFRecord)rod);
 
         return 0;
     }

java/src/org/broadinstitute/sting/oneoffprojects/multisamplecaller/MultiSampleCaller.java

@@ -350,14 +350,14 @@ public class MultiSampleCaller extends LocusWalker<MultiSampleCaller.MultiSample
 
 		context = filter_each_read(context);
 
-		if (ref.getBase() == 'N') { return null; }
+		if (ref.getBaseAsChar() == 'N') { return null; }
 		if (BaseUtils.simpleBaseToBaseIndex(ref.getBase()) == -1) { return null; }
 		if (context.getReads().size() <= 0) { return null; }
         if (context.getReads().size() >= 10000) { return null; }     // to deal with big piles -- totally arbitrary threshold
 
-		this.ref = ref.getBase();
+		this.ref = ref.getBaseAsChar();
-		MultiSampleCallResult result = this.MultiSampleCall(tracker, ref.getBase(), context, sample_names);
+		MultiSampleCallResult result = this.MultiSampleCall(tracker, ref.getBaseAsChar(), context, sample_names);
-        if ( INCLUDE_STATS ) stats_output_file.println(DepthStats.Row(ref.getBase(), context));
+        if ( INCLUDE_STATS ) stats_output_file.println(DepthStats.Row(ref.getBaseAsChar(), context));
 		return result;
 	}
 

java/src/org/broadinstitute/sting/oneoffprojects/walkers/AlignedReadsHistoWalker.java

@@ -4,6 +4,7 @@ import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.ReadWalker;
 import org.broadinstitute.sting.gatk.walkers.WalkerName;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 
 /**
  * Created by IntelliJ IDEA.
@@ -28,7 +29,7 @@ public class AlignedReadsHistoWalker extends ReadWalker<Integer, Integer> {
 	    return !read.getReadUnmappedFlag();
     }
 
-    public Integer map(char[] ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
+    public Integer map(ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
         //System.out.println(read.getAttribute("NM"));
         int editDist = Integer.parseInt(read.getAttribute("NM").toString());
         if (editDist <= 50)

java/src/org/broadinstitute/sting/oneoffprojects/walkers/AlleleBalanceHistogramWalker.java

@@ -104,7 +104,7 @@ public class AlleleBalanceHistogramWalker extends LocusWalker<Map<String,Double>
         }
         
         for ( PileupElement e : alicon.getBasePileup() ) {
-            if ( BaseUtils.basesAreEqual( e.getBase(), (byte) ref.getBase() ) ) {
+            if ( BaseUtils.basesAreEqual( e.getBase(), ref.getBase() ) ) {
                 refBases++;
             } else if ( BaseUtils.basesAreEqual(e.getBase(), (byte) snpBase ) ) {
                 altBases++;

java/src/org/broadinstitute/sting/oneoffprojects/walkers/BaseTransitionTableCalculatorJavaWalker.java

@@ -230,7 +230,7 @@ public class BaseTransitionTableCalculatorJavaWalker extends LocusWalker<Set<Bas
     public void updateTable(BaseTransitionTable t, SAMRecord r, int o, ReferenceContext ref) {
         // System.out.println("Update Table");
         if ( r.getReadNegativeStrandFlag() ) {
-            t.update(BaseUtils.simpleComplement((char) r.getReadBases()[o]),BaseUtils.simpleComplement(ref.getBase()));
+            t.update((byte)BaseUtils.simpleComplement((char) r.getReadBases()[o]), (byte)BaseUtils.simpleComplement(ref.getBaseAsChar()));
         } else {
             t.update(r.getReadBases()[o], ref.getBase());
         }
@@ -353,7 +353,7 @@ public class BaseTransitionTableCalculatorJavaWalker extends LocusWalker<Set<Bas
         return String.format("%s\t%s%n",header,"Counts");
     }
 
-    public int countMismatches(char ref, ReadBackedPileup p) {
+    public int countMismatches(byte ref, ReadBackedPileup p) {
         int refM = p.getBaseCounts()[BaseUtils.simpleBaseToBaseIndex(ref)];
         return p.size()-refM;
     }
@@ -477,7 +477,7 @@ class BaseTransitionTable implements Comparable {
         out.print(s.toString());
     }
 
-    public void update(char observedBase, char refBase ) {
+    public void update(byte observedBase, byte refBase ) {
         //if ( observedBase == refBase ) {
         //    throw new StingException("BaseTransitionTable received equal observed and reference bases, which should not happen.");
         //}
@@ -485,10 +485,6 @@ class BaseTransitionTable implements Comparable {
         table[BaseUtils.simpleBaseToBaseIndex(observedBase)][BaseUtils.simpleBaseToBaseIndex(refBase)]++;
     }
 
-    public void update(byte observed, char ref) {
-        update( (char) observed, ref);
-    }
-
     public int numConditions() {
         return conditions.size();
     }

java/src/org/broadinstitute/sting/oneoffprojects/walkers/DSBWalkerV3.java

@@ -27,6 +27,7 @@ package org.broadinstitute.sting.oneoffprojects.walkers;
 
 import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.ReadWalker;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.utils.*;
 import org.broadinstitute.sting.utils.sam.AlignmentUtils;
@@ -353,7 +354,7 @@ public class DSBWalkerV3 extends ReadWalker<Integer,Integer> {
     }
 
 
-    public Integer map(char[] ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
+    public Integer map(ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
 
         if ( AlignmentUtils.isReadUnmapped(read) ) return 0;
 

java/src/org/broadinstitute/sting/oneoffprojects/walkers/IOCrusherWalker.java

@@ -27,6 +27,7 @@ package org.broadinstitute.sting.oneoffprojects.walkers;
 
 import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.ReadWalker;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.utils.sam.ReadUtils;
 import net.sf.samtools.SAMRecord;
@@ -63,7 +64,7 @@ public class IOCrusherWalker extends ReadWalker<SAMRecord, ArrayList<SAMFileWrit
     /**
      *
      */
-    public SAMRecord map(char[] ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
+    public SAMRecord map(ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
         nReadsRead++;
         return read;
     }

java/src/org/broadinstitute/sting/oneoffprojects/walkers/IndelDBRateWalker.java

@@ -95,7 +95,7 @@ public class IndelDBRateWalker extends RodWalker<OverlapTable,OverlapTabulator>
                       tracker.getReferenceMetaData("comp").size() != 0 ? tracker.getReferenceMetaData("comp").get(0) : null;
         VariantContext compContext;
         if ( comp != null ) {
-            compContext = VariantContextAdaptors.toVariantContext("comp",comp);
+            compContext = VariantContextAdaptors.toVariantContext("comp",comp, ref);
         } else {
             compContext = null;
         }
@@ -142,12 +142,12 @@ public class IndelDBRateWalker extends RodWalker<OverlapTable,OverlapTabulator>
         if ( vcfWriter != null ) {
             int i = 0;
             while ( i < compContexts.size() && compContexts.get(i).getLocation().isBefore(evalContexts.get(0).getLocation())) {
-                vcfWriter.addRecord(VariantContextAdaptors.toVCF(compContexts.get(i),(char)compContexts.get(i).getReference().getBases()[0]));
+                vcfWriter.addRecord(VariantContextAdaptors.toVCF(compContexts.get(i),compContexts.get(i).getReference().getBases()[0]));
                 i++;
             }
             vcfWriter.addRecord(VariantContextAdaptors.toVCF(evalContexts.get(0),ref.getBase()));
             while ( i < compContexts.size() && compContexts.get(i).getLocation().distance(evalContexts.get(0).getLocation()) <= indelWindow) {
-                vcfWriter.addRecord(VariantContextAdaptors.toVCF(compContexts.get(i),(char) compContexts.get(i).getReference().getBases()[0]));
+                vcfWriter.addRecord(VariantContextAdaptors.toVCF(compContexts.get(i),compContexts.get(i).getReference().getBases()[0]));
                 i++;
             }
         }

java/src/org/broadinstitute/sting/oneoffprojects/walkers/MismatchCounterWalker.java

@@ -4,24 +4,25 @@ import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.ReadWalker;
 import org.broadinstitute.sting.gatk.walkers.WalkerName;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.utils.Utils;
 
 import java.util.List;
 
 @WalkerName("CountMismatches")
 public class MismatchCounterWalker extends ReadWalker<Integer, Integer> {
-    public Integer map(char[] ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
+    public Integer map(ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
         int nMismatches = 0;
         
         int start = read.getAlignmentStart()-1;
         int stop  = read.getAlignmentEnd();
         // sometimes BWA outputs screwy reads
-        if ( stop - start > ref.length )
+        if ( stop - start > ref.getBases().length )
             return 0;
 
         if ( read.getAlignmentBlocks().size() == 1 ) {
             // No indels
-            List<Byte> refSeq = Utils.subseq(ref);
+            List<Byte> refSeq = Utils.subseq(ref.getBases());
             List<Byte> readBases = Utils.subseq(read.getReadBases());
 
             assert(refSeq.size() == readBases.size());

java/src/org/broadinstitute/sting/oneoffprojects/walkers/MismatchHistoWalker.java

@@ -4,6 +4,7 @@ import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.ReadWalker;
 import org.broadinstitute.sting.gatk.walkers.WalkerName;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.utils.Utils;
 
 import java.util.List;
@@ -17,12 +18,12 @@ public class MismatchHistoWalker extends ReadWalker<Integer, Integer> {
     protected final int MAX_TARGET_EDIT_DISTANCE = 10;
 
     // Do we actually want to operate on the context?
-    public boolean filter(char[] ref, SAMRecord read) {
+    public boolean filter(ReferenceContext ref, SAMRecord read) {
 	    // we only want aligned reads
 	    return !read.getReadUnmappedFlag();
     }
 
-    public Integer map(char[] ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
+    public Integer map(ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
 
         int editDist = Integer.parseInt(read.getAttribute("NM").toString());
 
@@ -34,15 +35,15 @@ public class MismatchHistoWalker extends ReadWalker<Integer, Integer> {
             int start = read.getAlignmentStart()-1;
             int stop  = read.getAlignmentEnd();
             // sometimes BWA outputs screwy reads
-            if ( stop - start > ref.length )
+            if ( stop - start > ref.getBases().length )
                 return 0;
 
-            List<Byte> refSeq = Utils.subseq(ref);
+            List<Byte> refSeq = Utils.subseq(ref.getBases());
             List<Byte> readBases = Utils.subseq(read.getReadBases());
             assert(refSeq.size() == readBases.size());
 
             // it's actually faster to reallocate a resized array than to use ArrayLists...
-            if ( ref.length > mismatchCounts.length ) {
+            if ( ref.getBases().length > mismatchCounts.length ) {
                 int oldLength = mismatchCounts.length;
                 mismatchCounts = (long[])resizeArray(mismatchCounts, refSeq.size());
                 for ( int i = oldLength; i < refSeq.size(); i++ )

java/src/org/broadinstitute/sting/oneoffprojects/walkers/PairedQualityScoreCountsWalker.java

@@ -27,6 +27,7 @@ package org.broadinstitute.sting.oneoffprojects.walkers;
 
 import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.ReadWalker;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.QualityUtils;
 import org.broadinstitute.sting.utils.BaseUtils;
@@ -61,7 +62,7 @@ public class PairedQualityScoreCountsWalker extends ReadWalker<Pair<byte[],Boole
         return reduceCounts;
     }
 
-    public Pair<byte[],Boolean> map( char[] ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
+    public Pair<byte[],Boolean> map( ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
         if ( canUseRead(read) ) {
             return getCorrectlyOrientedBaseQualities(read);
         } else {

java/src/org/broadinstitute/sting/oneoffprojects/walkers/ReadErrorRateWalker.java

@@ -27,6 +27,7 @@ package org.broadinstitute.sting.oneoffprojects.walkers;
 
 import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.ReadWalker;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.utils.QualityUtils;
 import org.broadinstitute.sting.utils.BaseUtils;
@@ -56,8 +57,8 @@ public class ReadErrorRateWalker extends ReadWalker<boolean[], ReadErrorRateColl
      * @param read     the read to assess
      * @return true if the read can be processed, false if it should be ignored
      */
-    public boolean filter(char[] ref, SAMRecord read) {
+    public boolean filter(ReferenceContext ref, SAMRecord read) {
-        return (read.getCigar().numCigarElements() == 1 && read.getReadLength() <= ref.length && (!useNonNextBestBase || read.getAttribute("SQ") != null));
+        return (read.getCigar().numCigarElements() == 1 && read.getReadLength() <= ref.getBases().length && (!useNonNextBestBase || read.getAttribute("SQ") != null));
     }
 
     /**
@@ -71,7 +72,7 @@ public class ReadErrorRateWalker extends ReadWalker<boolean[], ReadErrorRateColl
      *         Last element is for internal use so the reduce() function can figure out how
      *         many reads we processed.
      */
-    public boolean[] map(char[] ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
+    public boolean[] map(ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
         boolean[] errorsPerCycle = new boolean[read.getReadLength() + 1];
 
         byte[] bases  = read.getReadBases();
@@ -85,7 +86,7 @@ public class ReadErrorRateWalker extends ReadWalker<boolean[], ReadErrorRateColl
             System.out.println();
 
             for (int cycle = 0; cycle < bases.length; cycle++) {
-                byte compBase = convertIUPACBaseToSimpleBase((byte)ref[cycle]);
+                byte compBase = convertIUPACBaseToSimpleBase(ref.getBases()[cycle]);
 
                 System.out.print((char) compBase);
             }
@@ -93,7 +94,7 @@ public class ReadErrorRateWalker extends ReadWalker<boolean[], ReadErrorRateColl
         }
 
         for (int cycle = 0; cycle < bases.length; cycle++) {
-            byte compBase = convertIUPACBaseToSimpleBase((byte)ref[cycle]);
+            byte compBase = convertIUPACBaseToSimpleBase(ref.getBases()[cycle]);
 
             if (compBase != '.') {
                 if (useNextBestBase || useNextRandomBase || useNonNextBestBase) {

java/src/org/broadinstitute/sting/oneoffprojects/walkers/ReadQualityScoreWalker.java

@@ -27,6 +27,7 @@ package org.broadinstitute.sting.oneoffprojects.walkers;
 
 import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.ReadWalker;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
@@ -70,7 +71,7 @@ public class ReadQualityScoreWalker extends ReadWalker<SAMRecord, SAMFileWriter>
     protected static BufferedReader inputReader = null;
     protected static String line = null;
 
-    public SAMRecord map( char[] ref, SAMRecord read, ReadMetaDataTracker metaDataTracker ) {
+    public SAMRecord map( ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker ) {
         return read; // all the work is done in the reduce step for this walker
     }
 

java/src/org/broadinstitute/sting/oneoffprojects/walkers/ReplaceQuals.java

@@ -27,6 +27,7 @@ package org.broadinstitute.sting.oneoffprojects.walkers;
 
 import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.ReadWalker;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.utils.collections.Pair;
 import net.sf.samtools.*;
@@ -90,7 +91,7 @@ public class ReplaceQuals extends ReadWalker<SAMRecord, SAMFileWriter> {
     /**
      *
      */
-    public SAMRecord map(char[] ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
+    public SAMRecord map(ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
         final String name = read.getReadName();
 
         if ( readNameToPairs.containsKey(name) ) {

java/src/org/broadinstitute/sting/oneoffprojects/walkers/TestReadFishingWalker.java

@@ -27,6 +27,7 @@ package org.broadinstitute.sting.oneoffprojects.walkers;
 
 import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.ReadWalker;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.alignment.bwa.BWAAligner;
 import org.broadinstitute.sting.alignment.bwa.BWAConfiguration;
 import org.broadinstitute.sting.alignment.bwa.c.BWACAligner;
@@ -130,7 +131,7 @@ public class TestReadFishingWalker extends ReadWalker<Integer,Long> {
     }
 
     @Override
-    public Integer map(char[] ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
+    public Integer map(ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
         Alignment bestAlignment = aligner.getBestAlignment(read.getReadBases());
         System.out.println("bestAlignment = " + bestAlignment);
         return 1;

java/src/org/broadinstitute/sting/oneoffprojects/walkers/VCFReferenceFixerWalker.java

@@ -46,7 +46,7 @@ public class VCFReferenceFixerWalker extends RodWalker<VCFRecord,Long> {
             vcfrod = (VCFRecord) rod;
         }
 
-        if (vcfrod != null) vcfrod.setReferenceBase(new String(BaseUtils.charSeq2byteSeq(context.getBases())));
+        if (vcfrod != null) vcfrod.setReferenceBase(new String(context.getBases()));
         return vcfrod;
 
         /*

java/src/org/broadinstitute/sting/oneoffprojects/walkers/annotator/ProportionOfNonrefBasesSupportingSNP.java

@@ -62,7 +62,7 @@ public class ProportionOfNonrefBasesSupportingSNP implements InfoFieldAnnotation
         Pair<Integer,Integer> totalNonref_totalSNP = new Pair<Integer,Integer>(0,0);
         for ( String sample : context.keySet() ) {
             ReadBackedPileup pileup = context.get(sample).getContext(StratifiedAlignmentContext.StratifiedContextType.COMPLETE).getBasePileup();
-            totalNonref_totalSNP = getNonrefAndSNP(pileup, ref.getBase(), vc.getAlternateAllele(0).toString().charAt(0), totalNonref_totalSNP);
+            totalNonref_totalSNP = getNonrefAndSNP(pileup, ref.getBaseAsChar(), vc.getAlternateAllele(0).toString().charAt(0), totalNonref_totalSNP);
 
         }
         if ( totalNonref_totalSNP.equals(new Pair<Integer,Integer>(0,0)) )

java/src/org/broadinstitute/sting/oneoffprojects/walkers/annotator/ProportionOfRefSecondBasesSupportingSNP.java

@@ -59,7 +59,7 @@ public class ProportionOfRefSecondBasesSupportingSNP implements InfoFieldAnnotat
         Pair<Integer,Integer> totalAndSNPSupporting = new Pair<Integer,Integer>(0,0);
         for ( String sample : context.keySet() ) {
             ReadBackedPileup pileup = context.get(sample).getContext(StratifiedAlignmentContext.StratifiedContextType.COMPLETE).getBasePileup();
-            totalAndSNPSupporting = getTotalRefAndSNPSupportCounts(pileup, ref.getBase(), vc.getAlternateAllele(0).toString().charAt(0), totalAndSNPSupporting);
+            totalAndSNPSupporting = getTotalRefAndSNPSupportCounts(pileup, ref.getBaseAsChar(), vc.getAlternateAllele(0).toString().charAt(0), totalAndSNPSupporting);
 
         }
         if ( totalAndSNPSupporting.equals(new Pair<Integer,Integer>(0,0)) )

java/src/org/broadinstitute/sting/oneoffprojects/walkers/annotator/ProportionOfSNPSecondBasesSupportingRef.java

@@ -62,7 +62,7 @@ public class ProportionOfSNPSecondBasesSupportingRef implements InfoFieldAnnotat
         Pair<Integer,Integer> totalAndSNPSupporting = new Pair<Integer,Integer>(0,0);
         for ( String sample : context.keySet() ) {
             ReadBackedPileup pileup = context.get(sample).getContext(StratifiedAlignmentContext.StratifiedContextType.COMPLETE).getBasePileup();
-            totalAndSNPSupporting = getTotalSNPandRefSupporting(pileup, ref.getBase(), vc.getAlternateAllele(0).toString().charAt(0), totalAndSNPSupporting);
+            totalAndSNPSupporting = getTotalSNPandRefSupporting(pileup, ref.getBaseAsChar(), vc.getAlternateAllele(0).toString().charAt(0), totalAndSNPSupporting);
 
         }
         if ( totalAndSNPSupporting.equals(new Pair<Integer,Integer>(0,0)) )

java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/multisample/LocusConcordanceInfo.java

@@ -54,7 +54,7 @@ class LocusConcordanceInfo {
     }
 
     public byte getReferenceBase() {
-        return (byte) reference.getBase();
+        return reference.getBase();
     }
 
     public boolean isTruthOnly () {
@@ -63,7 +63,7 @@ class LocusConcordanceInfo {
 
     public boolean isVariantSite() {
         for ( VCFGenotypeRecord g : truthVCFRecord.getVCFGenotypeRecords() ) {
-            if ( g.isVariant(reference.getBase()) ) {
+            if ( g.isVariant(reference.getBaseAsChar()) ) {
                 return true;
             }
         }

java/src/org/broadinstitute/sting/oneoffprojects/walkers/vcftools/BeagleTrioToVCFWalker.java

@@ -73,7 +73,7 @@ public class BeagleTrioToVCFWalker extends RodWalker<VariantContext, Long> {
         VariantContext vc = null;
 
         if ( ref != null ) {
-            vc = tracker.getVariantContext(TRACK_NAME, null, context.getLocation(), false);
+            vc = tracker.getVariantContext(ref, TRACK_NAME, null, context.getLocation(), false);
             BeagleROD beagle = tracker.lookup(BEAGLE_NAME,BeagleROD.class);
 
             if ( vc != null ) {

java/src/org/broadinstitute/sting/oneoffprojects/walkers/vcftools/VCFToBeagleWalker.java

@@ -67,7 +67,7 @@ public class VCFToBeagleWalker extends RodWalker<Integer, VCFToBeagleWalker.Resu
         if ( ref != null ) {
             EnumSet<VariantContext.Type> allowedTypes = EnumSet.of(VariantContext.Type.SNP);
 
-            VariantContext vc = tracker.getVariantContext("variants", allowedTypes, context.getLocation(), false);
+            VariantContext vc = tracker.getVariantContext(ref, "variants", allowedTypes, context.getLocation(), false);
 
             if ( vc != null && vc.isBiallelic() && vc.isNotFiltered() ) {
                 if ( trio != null ) { // we are emitting a trio file

java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/CalculateAlleleLikelihoodsWalker.java

@@ -28,6 +28,7 @@ package org.broadinstitute.sting.playground.gatk.walkers.HLAcaller;
 import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.*;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.commandline.Argument;
 
 import java.util.ArrayList;
@@ -106,7 +107,7 @@ public class CalculateAlleleLikelihoodsWalker extends ReadWalker<Integer, Intege
         return 0;
     }
 
-    public Integer map(char[] ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
+    public Integer map(ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
         HLAnamesAL.add(read.getReadName());
         HLAreadsAL.add(formatter.FormatRead(read.getCigarString(), read.getReadString()));
         HLAstartposAL.add(read.getAlignmentStart());

java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/CalculatePhaseLikelihoodsWalker.java

@@ -29,6 +29,7 @@ import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.commandline.Argument;
 
 import java.util.ArrayList;
@@ -180,7 +181,7 @@ public class CalculatePhaseLikelihoodsWalker extends ReadWalker<Integer, Integer
         return isWithinInterval;
     }
 
-    public Integer map(char[] ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
+    public Integer map(ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
         if (!ReadsToDiscard.contains(read.getReadName())){
             UpdateCorrelation(read);
         }else{

java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/CallHLAWalker.java

@@ -408,7 +408,7 @@ public class CallHLAWalker extends LocusWalker<Integer, Pair<Long, Long>>{
                 }
 
                 //Get likelihood score for homozygous ref: used to normalize likelihoood scores at 0.
-                String homref = String.valueOf(ref.getBase())+String.valueOf(ref.getBase());
+                String homref = String.valueOf(ref.getBaseAsChar())+String.valueOf(ref.getBaseAsChar());
                 Double homreflikelihood = Double.parseDouble((String) Scores.get(homref).toString());
 
                 //Add SNP if it is a SNP and hasn't been added before

java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/ClusterReadsWalker.java

@@ -3,6 +3,7 @@ package org.broadinstitute.sting.playground.gatk.walkers.HLAcaller;
 import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.commandline.Argument;
 
 import java.util.ArrayList;
@@ -89,7 +90,7 @@ public class ClusterReadsWalker extends ReadWalker<Integer, Integer> {
         return 0;
     }
 
-    public Integer map(char[] ref, SAMRecord read, ReadMetaDataTracker tracker) {
+    public Integer map(ReferenceContext ref, SAMRecord read, ReadMetaDataTracker tracker) {
         //Calculate concordance for this read and all overlapping reads
         if (!ReadsToDiscard.contains(read.getReadName())){
             AlignedReads.add(read);

java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/CreateHaplotypesWalker.java

@@ -3,6 +3,8 @@ package org.broadinstitute.sting.playground.gatk.walkers.HLAcaller;
 import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.*;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+
 import java.util.Hashtable;
 /**
  * Creates a haplotype file given reads (for SNP analysis, imputation, etc)
@@ -37,7 +39,7 @@ public class CreateHaplotypesWalker extends ReadWalker<Integer, Integer> {
 
 
     
-    public Integer map(char[] ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
+    public Integer map(ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
 
         int readstart = read.getAlignmentStart();
         int readstop = read.getAlignmentEnd();

java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/CreatePedFileWalker.java

@@ -28,6 +28,7 @@ package org.broadinstitute.sting.playground.gatk.walkers.HLAcaller;
 import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.*;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.commandline.Argument;
 
 import java.util.ArrayList;
@@ -209,7 +210,7 @@ public class CreatePedFileWalker extends ReadWalker<Integer, Integer> {
         }
     }
 
-    public Integer map(char[] ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
+    public Integer map(ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
         HLAnamesAL.add(read.getReadName());
         HLAreadsAL.add(formatter.FormatRead(read.getCigarString(), read.getReadString()));
         HLAstartposAL.add(read.getAlignmentStart());

java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/FindClosestAlleleWalker.java

@@ -28,6 +28,7 @@ package org.broadinstitute.sting.playground.gatk.walkers.HLAcaller;
 import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.*;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.commandline.Argument;
 
 import java.util.ArrayList;
@@ -227,7 +228,7 @@ public class FindClosestAlleleWalker extends ReadWalker<Integer, Integer> {
         return maxFreq;
     }
 
-    public Integer map(char[] ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
+    public Integer map(ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
         //Calculate concordance for this read and all overlapping reads
         if (read.getMappingQuality() > 0){
             double maxConcordance = CalculateConcordance(read);

java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/FindPolymorphicSitesWalker.java

@@ -3,6 +3,7 @@ package org.broadinstitute.sting.playground.gatk.walkers.HLAcaller;
 import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.*;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.commandline.Argument;
 
 import java.util.ArrayList;
@@ -139,7 +140,7 @@ public class FindPolymorphicSitesWalker extends ReadWalker<Integer, Integer> {
         NonPolymorphicSites = nonpolymorphicsites.toArray(new Integer[nonpolymorphicsites.size()]);
     }
 
-    public Integer map(char[] ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
+    public Integer map(ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
         //Calculate concordance for this read and all overlapping reads
         return 1;
     }

java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/ImputeAllelesWalker.java

@@ -3,6 +3,7 @@ package org.broadinstitute.sting.playground.gatk.walkers.HLAcaller;
 import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.*;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 
 import java.io.FileInputStream;
 import java.io.BufferedReader;
@@ -161,7 +162,7 @@ public class ImputeAllelesWalker extends ReadWalker<Integer, Integer> {
     }
 
 
-    public Integer map(char[] ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
+    public Integer map(ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
         int readstart = read.getAlignmentStart();
         int readstop = read.getAlignmentEnd();
         int startimputation = 0, stopimputation = 0;

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

@@ -125,7 +125,7 @@ public class LocusMismatchWalker extends LocusWalker<String,Integer> implements
                 //System.out.printf("Using %s%n", e.getRead().getReadName());
                 baseCounts[e.getBaseIndex()] += 1;
                 usableDepth++;
-                if ( ! BaseUtils.basesAreEqual(e.getBase(), (byte)ref.getBase()) ) {
+                if ( ! BaseUtils.basesAreEqual(e.getBase(), ref.getBase()) ) {
                     nMismatches++;
                     qSumMismatches += e.getQual();
                 }
@@ -138,7 +138,7 @@ public class LocusMismatchWalker extends LocusWalker<String,Integer> implements
                 baseCountString += baseCounts[BaseUtils.simpleBaseToBaseIndex(b)] + " ";
             }
             return String.format("%s %c %10s %5.2f %d %d %d %s",
-                    pileup.getLocation(), ref.getBase(),
+                    pileup.getLocation(), ref.getBaseAsChar(),
                     getGenotypeClass(g), 10 * g.getNegLog10PError(),
                     usableDepth, nMismatches, qSumMismatches, baseCountString);
         }

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

@@ -90,7 +90,7 @@ public class TrioGenotyperWalker extends RefWalker<VariantContext, Integer>{
     }
 
     public VariantContext map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
-        VariantContext vc = tracker.getVariantContext("variants", EnumSet.of(VariantContext.Type.SNP), context.getLocation(), true);
+        VariantContext vc = tracker.getVariantContext(ref, "variants", EnumSet.of(VariantContext.Type.SNP), context.getLocation(), true);
         
         if ( vc != null && vc.isPolymorphic() ) {
             if ( ! vc.hasGenotypes(FAMILY_MEMBERS) )
@@ -179,7 +179,7 @@ public class TrioGenotyperWalker extends RefWalker<VariantContext, Integer>{
             if ( a == 0 )
                 writer.writeHeader(VariantContextAdaptors.createVCFHeader(null, vc));
 
-            writer.addRecord(VariantContextAdaptors.toVCF(vc, '.'));
+            writer.addRecord(VariantContextAdaptors.toVCF(vc, (byte)'.'));
             a++;
         }
 

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

@@ -31,8 +31,8 @@ public class VCFConcordance extends RodWalker<Integer, Integer> {
             VariantContext eval = null;
             VariantContext truth = null;
             try {
-                eval = tracker.getVariantContext("eval", vc, loc, true);
+                eval = tracker.getVariantContext(ref, "eval", vc, loc, true);
-                truth = tracker.getVariantContext("truth", vc, loc, true);
+                truth = tracker.getVariantContext(ref, "truth", vc, loc, true);
             } catch (java.util.NoSuchElementException e) {
                 return 0;
             }

java/src/org/broadinstitute/sting/playground/gatk/walkers/annotator/GenomicAnnotator.java

@@ -205,11 +205,11 @@ public class GenomicAnnotator extends RodWalker<Integer, Integer> {
             return 0;
 
         Object variant = rods.get(0);
-        if( ref.getBase() == 'N') {
+        if( BaseUtils.isNBase(ref.getBase()) ) {
             return 0; //TODO Currently, VariantContextAdaptors.toVCF(annotatedVC, ref.getBase()) fails when base is 'N'. is this right?
         }
 
-        VariantContext vc = VariantContextAdaptors.toVariantContext("variant", variant);
+        VariantContext vc = VariantContextAdaptors.toVariantContext("variant", variant, ref);
         if ( vc == null )
             return 0;
 

java/src/org/broadinstitute/sting/playground/gatk/walkers/annotator/TranscriptToInfo.java

@@ -261,7 +261,7 @@ public class TranscriptToInfo extends RodWalker<TreeMap<String, String>, TreeMap
             if(parsedTranscriptRod.positiveStrand) {
                 parsedTranscriptRod.txSequence.append(ref.getBase());
             } else {
-                final char complementBase = BaseUtils.simpleComplement(ref.getBase());
+                final char complementBase = BaseUtils.simpleComplement(ref.getBaseAsChar());
                 parsedTranscriptRod.txSequence.insert(0, complementBase);
             }
 
@@ -275,16 +275,16 @@ public class TranscriptToInfo extends RodWalker<TreeMap<String, String>, TreeMap
                 {
                     if(position < parsedTranscriptRod.cdsStart)
                     {
-                        parsedTranscriptRod.utr5Sequence.append(ref.getBase()); //within utr5
+                        parsedTranscriptRod.utr5Sequence.append(ref.getBaseAsChar()); //within utr5
                     }
                     else if(position >= parsedTranscriptRod.cdsStart && position <= parsedTranscriptRod.cdsEnd)
                     {
-                        parsedTranscriptRod.cdsSequence.append(ref.getBase()); //within CDS
+                        parsedTranscriptRod.cdsSequence.append(ref.getBaseAsChar()); //within CDS
                     }
                 }
                 else
                 {
-                    final char complementBase = BaseUtils.simpleComplement(ref.getBase());
+                    final char complementBase = BaseUtils.simpleComplement(ref.getBaseAsChar());
                     if(position > parsedTranscriptRod.cdsEnd)
                     {
                         //As we move left to right (aka. 3' to 5'), we do insert(0,..) to reverse the sequence so that it become 5' to 3' in parsedTranscriptRod.utr5Sequence.

java/src/org/broadinstitute/sting/playground/gatk/walkers/diagnostics/ComputeConfusionMatrix.java

@@ -81,7 +81,7 @@ public class ComputeConfusionMatrix extends LocusWalker<Integer, Integer> {
         int windowCenter = (windowLength - 1)/2;
 
         String fwRefBases = new String(ref.getBases());
-        String fwRefBase = String.format("%c", ref.getBase());
+        String fwRefBase = String.format("%c", ref.getBaseAsChar());
         String fwWindowLeft = fwRefBases.substring(windowCenter - WINDOW_SIZE, windowCenter);
 
         //String rcRefBases = new String(BaseUtils.simpleReverseComplement(ref.getBases()));

java/src/org/broadinstitute/sting/playground/gatk/walkers/diagnostics/MatePairLibrarySize.java

@@ -2,6 +2,7 @@ package org.broadinstitute.sting.playground.gatk.walkers.diagnostics;
 
 import org.broadinstitute.sting.gatk.walkers.ReadWalker;
 import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.utils.StingException;
 import net.sf.samtools.SAMRecord;
@@ -31,11 +32,11 @@ public class MatePairLibrarySize extends ReadWalker<Integer, Integer> {
         }
     }
 
-    public boolean filter(char[] ref, SAMRecord read) {
+    public boolean filter(ReferenceContext ref, SAMRecord read) {
         return (read.getReadPairedFlag() && read.getFirstOfPairFlag());
     }
 
-    public Integer map(char[] ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
+    public Integer map(ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
         int insert = read.getInferredInsertSize();
 
         Integer oldcount = matePairSize.get(read.getReadGroup().getLibrary()).get(insert);

java/src/org/broadinstitute/sting/playground/gatk/walkers/diagnostics/SNPDensity.java

@@ -67,7 +67,7 @@ public class SNPDensity extends RefWalker<Pair<VariantContext, GenomeLoc>, SNPDe
 
         VCFRecord vcf = tracker.lookup("eval",VCFRecord.class);
         if (vcf != null)
-            vc = VariantContextAdaptors.toVariantContext("eval", vcf);
+            vc = VariantContextAdaptors.toVariantContext("eval", vcf, ref);
         return new Pair<VariantContext, GenomeLoc>(vc, context.getLocation());
     }
 

java/src/org/broadinstitute/sting/playground/gatk/walkers/graphalign/GraphReferenceAssessor.java

@@ -27,6 +27,7 @@ package org.broadinstitute.sting.playground.gatk.walkers.graphalign;
 
 import org.broadinstitute.sting.gatk.refdata.*;
 import org.broadinstitute.sting.gatk.walkers.*;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.utils.*;
 import org.broadinstitute.sting.commandline.Argument;
 
@@ -176,7 +177,7 @@ public class GraphReferenceAssessor extends ReadWalker<Integer, Integer> {
         return minNMM;
     }
 
-    public Integer map(char[] refArg, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
+    public Integer map(ReferenceContext refArg, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
 
         if ( MAXREADS-- == 0 ) {
             System.exit(0);
@@ -184,7 +185,7 @@ public class GraphReferenceAssessor extends ReadWalker<Integer, Integer> {
             ;
         } else if ( ! read.getReadUnmappedFlag() && read.getCigar().numCigarElements() == 1 ) {
             try {
-                byte[] ref = BaseUtils.charSeq2byteSeq(refArg);
+                byte[] ref = refArg.getBases();
                 // we're all XM
                 int nMMFromRead = (Short)read.getAttribute("NM");
                 MismatchCounter nAlignedMM = countMismatches(ref, read.getReadBases(), read.getBaseQualities());

java/src/org/broadinstitute/sting/playground/gatk/walkers/papergenotyper/GATKPaperGenotyper.java

@@ -68,7 +68,7 @@ public class GATKPaperGenotyper extends LocusWalker<SimpleCall, Integer> impleme
         if (ref.getBase() == 'N' || ref.getBase() == 'n') return null; // we don't deal with the N ref base case
 
         ReadBackedPileup pileup = context.getPileup();
-        double likelihoods[] = DiploidGenotypePriors.getReferencePolarizedPriors(ref.getBase(),
+        double likelihoods[] = DiploidGenotypePriors.getReferencePolarizedPriors(ref.getBaseAsChar(),
                                                                                  DiploidGenotypePriors.HUMAN_HETEROZYGOSITY,
                                                                                  0.01);
         // get the bases and qualities from the pileup
@@ -97,7 +97,7 @@ public class GATKPaperGenotyper extends LocusWalker<SimpleCall, Integer> impleme
         return new SimpleCall(context.getLocation(),
                               GENOTYPE.values()[sortedList[9]].toString(),
                               likelihoods[sortedList[9]] - likelihoods[sortedList[8]],
-                              ref.getBase());
+                              ref.getBaseAsChar());
     }
 
     /**

java/src/org/broadinstitute/sting/playground/gatk/walkers/secondaryBases/SecondaryBaseTransitionTableWalker.java

@@ -39,14 +39,14 @@ public class SecondaryBaseTransitionTableWalker extends LocusWalker<Integer, Int
     }
 
     public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
-        char refBase = Character.toUpperCase(ref.getBase());
+        char refBase = Character.toUpperCase(ref.getBaseAsChar());
         ReadBackedPileup pileup = context.getBasePileup();
         int[] baseCounts = pileup.getBaseCounts();
         int length = 0;
         for (int i : baseCounts) {length += i;}
-        char[] contextBases = ref.getBases();
+        byte[] contextBases = ref.getBases();
-        char prevBase = Character.toUpperCase(contextBases[0]);
+        byte prevBase = (byte)Character.toUpperCase(contextBases[0]);
-        char nextBase = Character.toUpperCase(contextBases[contextBases.length - 1]);
+        byte nextBase = (byte)Character.toUpperCase(contextBases[contextBases.length - 1]);
 
         if (contextBases.length == 3 && refBase != 'N' && pileup.getBases() != null && pileup.getSecondaryBases() != null) {
             VariantCallContext ugResult = ug.runGenotyper(tracker,ref,context);
@@ -83,14 +83,14 @@ public class SecondaryBaseTransitionTableWalker extends LocusWalker<Integer, Int
                             if (!element.getRead().getReadNegativeStrandFlag()) {
                                 strandRef = Character.toString(refBase);
                                 strandPrimary = Character.toString(primaryBase);
-                                strandPrev = Character.toString(prevBase);
+                                strandPrev = Character.toString((char)prevBase);
                                 strandSecondary = Character.toString(secondaryBase);
                                 strandCall = call;
                             }
                             else {
                                 strandRef = Character.toString(BaseUtils.simpleComplement(refBase));
                                 strandPrimary = Character.toString(BaseUtils.simpleComplement(primaryBase));
-                                strandPrev = Character.toString(BaseUtils.simpleComplement(nextBase));
+                                strandPrev = Character.toString(BaseUtils.simpleComplement((char)nextBase));
                                 strandSecondary = Character.toString(BaseUtils.simpleComplement(secondaryBase));
                                 strandCall = BaseUtils.simpleReverseComplement(call);
                             }

java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/AnnotationDataManager.java

@@ -54,7 +54,7 @@ public class AnnotationDataManager {
         INDICATE_MEAN_NUM_VARS = _INDICATE_MEAN_NUM_VARS;
     }
 
-    public void addAnnotations( final VariantContext vc, final char ref, final String sampleName, final boolean isInTruthSet, final boolean isTrueVariant ) {
+    public void addAnnotations( final VariantContext vc, final byte ref, final String sampleName, final boolean isInTruthSet, final boolean isTrueVariant ) {
 
         if( sampleName != null ) { // Only process variants that are found in the sample with this sampleName
             if( vc.getGenotype(sampleName).isNoCall() ) { // This variant isn't found in this sample so break out

java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/ApplyVariantClustersWalker.java

@@ -172,7 +172,7 @@ public class ApplyVariantClustersWalker extends RodWalker<ExpandingArrayList<Var
                     boolean isKnown = !vc.getAttribute("ID").equals(".");
                     if(usingDBSNP) {
                         isKnown = false;
-                        for( VariantContext dbsnpVC : tracker.getVariantContexts(DbSNPHelper.STANDARD_DBSNP_TRACK_NAME, null, context.getLocation(), false, false) ) {
+                        for( VariantContext dbsnpVC : tracker.getVariantContexts(ref, DbSNPHelper.STANDARD_DBSNP_TRACK_NAME, null, context.getLocation(), false, false) ) {
                             if(dbsnpVC != null && dbsnpVC.isSNP()) {
                                 isKnown=true;
                             }

java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/VariantOptimizer.java

@@ -146,7 +146,7 @@ public class VariantOptimizer extends RodWalker<ExpandingArrayList<VariantDatum>
                     boolean isKnown = !vc.getAttribute("ID").equals(".");
                     if(usingDBSNP) {
                         isKnown = false;
-                        for( final VariantContext dbsnpVC : tracker.getVariantContexts(DbSNPHelper.STANDARD_DBSNP_TRACK_NAME, null, context.getLocation(), false, false) ) {
+                        for( final VariantContext dbsnpVC : tracker.getVariantContexts(ref, DbSNPHelper.STANDARD_DBSNP_TRACK_NAME, null, context.getLocation(), false, false) ) {
                             if(dbsnpVC != null && dbsnpVC.isSNP()) {
                                 isKnown = true;
                             }

java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFGenotypeWriterAdapter.java

@@ -89,7 +89,7 @@ public class VCFGenotypeWriterAdapter implements VCFGenotypeWriter {
         if ( mHeader == null )
             throw new IllegalStateException("The VCF Header must be written before records can be added");
 
-        VCFRecord call = VariantContextAdaptors.toVCF(vc, refAllele.charAt(0), allowedGenotypeFormatStrings, false, false);
+        VCFRecord call = VariantContextAdaptors.toVCF(vc, (byte)refAllele.charAt(0), allowedGenotypeFormatStrings, false, false);
 
         Set<Allele> altAlleles = vc.getAlternateAlleles();
         StringBuffer altAlleleCountString = new StringBuffer();

java/src/org/broadinstitute/sting/utils/pileup/ReadBackedExtendedEventPileup.java

@@ -346,7 +346,7 @@ public class ReadBackedExtendedEventPileup implements Iterable<ExtendedEventPile
      * @return list of distinct events; first element of a pair is a string representation of the event, second element
      * gives the number of reads, in which that event was observed
      */
-    public List<Pair<String,Integer>> getEventStringsWithCounts(char[] refBases) {
+    public List<Pair<String,Integer>> getEventStringsWithCounts(byte[] refBases) {
         Map<String, Integer> events = new HashMap<String,Integer>();
 
         for ( ExtendedEventPileupElement e : this ) {
@@ -385,7 +385,7 @@ public class ReadBackedExtendedEventPileup implements Iterable<ExtendedEventPile
      * @param refBases
      * @return
      */
-    private String getDeletionString(int length, char[] refBases) {
+    private String getDeletionString(int length, byte[] refBases) {
         if ( refBases == null ) {
             return  Integer.toString(length)+"D"; // if we do not have reference bases, we can only report something like "5D"
         } else {

java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java

@@ -156,7 +156,7 @@ public class AlignmentUtils {
 
         int windowStart = (int)ref.getWindow().getStart();
         int windowStop = (int)ref.getWindow().getStop();
-        char[] refBases = ref.getBases();
+        byte[] refBases = ref.getBases();
         byte[] readBases = p.getRead().getReadBases();
         byte[] readQualities = p.getRead().getBaseQualities();
         Cigar c = p.getRead().getCigar();
@@ -179,7 +179,7 @@ public class AlignmentUtils {
                         if ( currentPos < windowStart )
                             continue;
 
-                        char refChr = refBases[refIndex++];
+                        byte refChr = refBases[refIndex++];
 
                         // do we need to skip the target site?
                         if ( ignoreTargetSite && ref.getLocus().getStart() == currentPos )

java/src/org/broadinstitute/sting/utils/sam/ArtificialReadsTraversal.java

@@ -6,6 +6,7 @@ import org.broadinstitute.sting.gatk.walkers.Walker;
 import org.broadinstitute.sting.gatk.walkers.ReadWalker;
 import org.broadinstitute.sting.gatk.datasources.providers.ShardDataProvider;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.apache.log4j.Logger;
 
 import net.sf.samtools.SAMRecord;
@@ -102,14 +103,14 @@ public class ArtificialReadsTraversal<M,T> extends TraversalEngine<M,T,Walker<M,
             AlignmentContext alignment = null;
 
             // an array of characters that represent the reference
-            char[] refSeq = null;
+            ReferenceContext refSeq = null;
 
             // update the number of reads we've seen
             TraversalStatistics.nRecords++;
 
             final boolean keepMeP = readWalker.filter(refSeq, read);
             if (keepMeP) {
-                M x = readWalker.map(refSeq, read,null);  // TODO: fix me at some point, it would be nice to fake out ROD data too
+                M x = readWalker.map(refSeq, read, null);  // TODO: fix me at some point, it would be nice to fake out ROD data too
                 sum = readWalker.reduce(x, sum);
             }
 

java/test/org/broadinstitute/sting/gatk/datasources/providers/LocusReferenceViewUnitTest.java

@@ -61,7 +61,8 @@ public class LocusReferenceViewUnitTest extends ReferenceViewTemplate {
         LocusShardDataProvider dataProvider = new LocusShardDataProvider(shard, null, shard.getGenomeLocs().get(0), null, sequenceFile, null);
         LocusReferenceView view = new LocusReferenceView(dataProvider);
 
-        char[] results = view.getReferenceBases(GenomeLocParser.createGenomeLoc(0, sequenceFile.getSequence("chrM").length() - 10, sequenceFile.getSequence("chrM").length() + 9));
+        byte[] results = view.getReferenceBases(GenomeLocParser.createGenomeLoc(0, sequenceFile.getSequence("chrM").length() - 10, sequenceFile.getSequence("chrM").length() + 9));
+        System.out.printf("results are %s%n", new String(results));
         Assert.assertEquals(20, results.length);
         for (int x = 0; x < results.length; x++) {
             if (x <= 10) Assert.assertTrue(results[x] != 'X');
@@ -104,7 +105,7 @@ public class LocusReferenceViewUnitTest extends ReferenceViewTemplate {
 
             ReferenceSequence expectedAsSeq = sequenceFile.getSubsequenceAt(locus.getContig(), locus.getStart(), locus.getStop());
             char expected = StringUtil.bytesToString(expectedAsSeq.getBases()).charAt(0);
-            char actual = view.getReferenceContext(locus).getBase();
+            char actual = view.getReferenceContext(locus).getBaseAsChar();
 
             Assert.assertEquals(String.format("Value of base at position %s in shard %s does not match expected", locus.toString(), shard.getGenomeLocs()),
                     expected,

java/test/org/broadinstitute/sting/gatk/datasources/providers/ReadReferenceViewUnitTest.java

@@ -75,8 +75,9 @@ public class ReadReferenceViewUnitTest extends ReferenceViewTemplate {
 
         SAMRecord rec = buildSAMRecord(selectedContig.getSequenceName(),(int)contigStart,(int)contigStop);
         ReferenceSequence expectedAsSeq = sequenceFile.getSubsequenceAt(selectedContig.getSequenceName(),(int)contigStart,selectedContig.getSequenceLength());
-        char[] expected = StringUtil.bytesToString(expectedAsSeq.getBases()).toCharArray();
+        //char[] expected = StringUtil.bytesToString(expectedAsSeq.getBases()).toCharArray();
-        char[] actual = view.getReferenceBases(rec);
+        byte[] expected = expectedAsSeq.getBases();
+        byte[] actual = view.getReferenceBases(rec);
 
         Assert.assertEquals(expected.length, (readLength - overlap));
         Assert.assertEquals(actual.length, readLength);
@@ -101,8 +102,8 @@ public class ReadReferenceViewUnitTest extends ReferenceViewTemplate {
         ReadReferenceView view = new ReadReferenceView(dataProvider);
 
         ReferenceSequence expectedAsSeq = sequenceFile.getSubsequenceAt(loc.getContig(),loc.getStart(),loc.getStop());
-        char[] expected = StringUtil.bytesToString(expectedAsSeq.getBases()).toCharArray();
+        byte[] expected = expectedAsSeq.getBases();
-        char[] actual = view.getReferenceBases(read);
+        byte[] actual = view.getReferenceBases(read);
 
         Assert.assertArrayEquals(String.format("Base array at  in shard %s does not match expected",loc.toString()),
                                  expected,

java/test/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptorsUnitTest.java

@@ -84,7 +84,7 @@ public class VariantContextAdaptorsUnitTest extends BaseTest {
         while (glf.hasNext()) {
             glf.next();
             records.add((GLFSingleCall)glf.mRecord); // we know they're all single calls in the reference file
-            VariantContext vc = VariantContextAdaptors.toVariantContext("GLF",glf);
+            VariantContext vc = VariantContextAdaptors.toVariantContext("GLF",glf, null);
             gw.addCall(vc,null);
         }
         gw.close(); // close the file
@@ -148,7 +148,7 @@ public class VariantContextAdaptorsUnitTest extends BaseTest {
         while (line != null && line != "") {
             geliText = (GeliTextFeature)codec.decode(line);
             records.add(geliText); // we know they're all single calls in the reference file
-            VariantContext vc = VariantContextAdaptors.toVariantContext("Geli",geliText);
+            VariantContext vc = VariantContextAdaptors.toVariantContext("Geli",geliText, null);
             if (vc != null) gw.addCall(vc,null);
             line = readLine(reader);
         }
@@ -211,7 +211,7 @@ public class VariantContextAdaptorsUnitTest extends BaseTest {
         while (iterator.hasNext()) {
             rodGELI gel = new rodGELI("myROD",iterator.next());
             records.add(gel);
-            VariantContext vc = VariantContextAdaptors.toVariantContext("myROD",gel);
+            VariantContext vc = VariantContextAdaptors.toVariantContext("myROD",gel, null);
             if (vc != null) gw.addCall(vc,null);
         }
         iterator.close();

java/test/org/broadinstitute/sting/gatk/walkers/PrintReadsWalkerUnitTest.java

@@ -3,6 +3,7 @@ package org.broadinstitute.sting.gatk.walkers;
 import org.broadinstitute.sting.BaseTest;
 import org.broadinstitute.sting.gatk.datasources.shards.Shard;
 import org.broadinstitute.sting.gatk.datasources.providers.ShardDataProvider;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.utils.sam.ArtificialReadsTraversal;
 import org.broadinstitute.sting.utils.sam.ArtificialSAMFileWriter;
 import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
@@ -54,7 +55,9 @@ public class PrintReadsWalkerUnitTest extends BaseTest {
      */
     private ArtificialReadsTraversal trav;
     private int readTotal = 0;
-    private char bases[] = {'a', 't'};
+    //private char bases[] = {'a', 't'};
+    private ReferenceContext bases = null;
+    //private ReferenceContext ref = new ReferenceContext()
 
     @Before
     public void before() {