Several more walkers have been brought up to use the new Allele representation.

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

@@ -107,11 +107,11 @@ public class FastaAlternateReference extends FastaReference {
                 continue;
 
             if ( vc.isSimpleDeletion()) {
-                deletionBasesRemaining = vc.getReference().length();
+                deletionBasesRemaining = vc.getReference().length() - 1;
                 // delete the next n bases, not this one
                 return new Pair<GenomeLoc, String>(context.getLocation(), refBase);
             } else if ( vc.isSimpleInsertion()) {
-                return new Pair<GenomeLoc, String>(context.getLocation(), refBase.concat(vc.getAlternateAllele(0).toString()));
+                return new Pair<GenomeLoc, String>(context.getLocation(), vc.getAlternateAllele(0).toString());
             } else if (vc.isSNP()) {
                 return new Pair<GenomeLoc, String>(context.getLocation(), vc.getAlternateAllele(0).toString());
             }

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

@@ -872,7 +872,13 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
         for ( VariantContext knownIndel : knownIndelsToTry ) {
             if ( knownIndel == null || !knownIndel.isIndel() || knownIndel.isComplexIndel() )
                 continue;
-            byte[] indelStr = knownIndel.isSimpleInsertion() ? knownIndel.getAlternateAllele(0).getBases() : Utils.dupBytes((byte)'-', knownIndel.getReference().length());
+            final byte[] indelStr;
+            if ( knownIndel.isSimpleInsertion() ) {
+                final byte[] fullAllele = knownIndel.getAlternateAllele(0).getBases();
+                indelStr = Arrays.copyOfRange(fullAllele, 1, fullAllele.length); // remove ref padding
+            } else {
+                indelStr = Utils.dupBytes((byte)'-', knownIndel.getReference().length() - 1);
+            }
             int start = knownIndel.getStart() - leftmostIndex + 1;
             Consensus c = createAlternateConsensus(start, reference, indelStr, knownIndel);
             if ( c != null )

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

@@ -139,11 +139,11 @@ public class LeftAlignVariants extends RodWalker<Integer, Integer> {
         final byte[] refSeq = ref.getBases();
 
         // get the indel length
-        int indelLength;
+        final int indelLength;
         if ( vc.isSimpleDeletion() )
-            indelLength = vc.getReference().length();
+            indelLength = vc.getReference().length() - 1;
         else
-            indelLength = vc.getAlternateAllele(0).length();
+            indelLength = vc.getAlternateAllele(0).length() - 1;
 
         if ( indelLength > 200 ) {
             writer.add(vc);
@@ -151,7 +151,7 @@ public class LeftAlignVariants extends RodWalker<Integer, Integer> {
         }
 
         // create an indel haplotype
-        int originalIndex = ref.getLocus().getStart() - ref.getWindow().getStart() + 1;
+        final int originalIndex = ref.getLocus().getStart() - ref.getWindow().getStart() + 1;
         final byte[] originalIndel = makeHaplotype(vc, refSeq, originalIndex, indelLength);
 
         // create a CIGAR string to represent the event
@@ -170,11 +170,12 @@ public class LeftAlignVariants extends RodWalker<Integer, Integer> {
             VariantContext newVC = new VariantContextBuilder(vc).start(vc.getStart()-difference).stop(vc.getEnd()-difference).make();
             //System.out.println("Moving record from " + vc.getChr()+":"+vc.getStart() + " to " + vc.getChr()+":"+(vc.getStart()-difference));
 
-            int indelIndex = originalIndex-difference;
+            final int indelIndex = originalIndex-difference;
-            byte[] newBases = new byte[indelLength];
+            final byte[] newBases = new byte[indelLength + 1];
-            System.arraycopy((vc.isSimpleDeletion() ? refSeq : originalIndel), indelIndex, newBases, 0, indelLength);
+            newBases[0] = refSeq[indelIndex-1];
-            Allele newAllele = Allele.create(newBases, vc.isSimpleDeletion());
+            System.arraycopy((vc.isSimpleDeletion() ? refSeq : originalIndel), indelIndex, newBases, 1, indelLength);
-            newVC = updateAllele(newVC, newAllele, refSeq[indelIndex-1]);
+            final Allele newAllele = Allele.create(newBases, vc.isSimpleDeletion());
+            newVC = updateAllele(newVC, newAllele);
 
             writer.add(newVC);
             return 1;
@@ -195,7 +196,7 @@ public class LeftAlignVariants extends RodWalker<Integer, Integer> {
         if ( vc.isSimpleDeletion() ) {
             indexOfRef += indelLength;
         } else {
-            System.arraycopy(vc.getAlternateAllele(0).getBases(), 0, hap, currentPos, indelLength);
+            System.arraycopy(vc.getAlternateAllele(0).getBases(), 1, hap, currentPos, indelLength);
             currentPos += indelLength;
         }
 
@@ -205,14 +206,14 @@ public class LeftAlignVariants extends RodWalker<Integer, Integer> {
         return hap;
     }
 
-    public static VariantContext updateAllele(VariantContext vc, Allele newAllele, Byte refBaseForIndel) {
+    public static VariantContext updateAllele(final VariantContext vc, final Allele newAllele) {
         // create a mapping from original allele to new allele
         HashMap<Allele, Allele> alleleMap = new HashMap<Allele, Allele>(vc.getAlleles().size());
         if ( newAllele.isReference() ) {
             alleleMap.put(vc.getReference(), newAllele);
-            alleleMap.put(vc.getAlternateAllele(0), vc.getAlternateAllele(0));
+            alleleMap.put(vc.getAlternateAllele(0), Allele.create(newAllele.getBases()[0], false));
         } else {
-            alleleMap.put(vc.getReference(), vc.getReference());
+            alleleMap.put(vc.getReference(), Allele.create(newAllele.getBases()[0], true));
             alleleMap.put(vc.getAlternateAllele(0), newAllele);
         }
 

public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java

@@ -248,7 +248,6 @@ public abstract class AbstractVCFCodec extends AsciiFeatureCodec<VariantContext>
             builder.id(parts[2]);
 
         final String ref = getCachedString(parts[3].toUpperCase());
-        builder.stop(pos + ref.length() - 1);
         final String alts = getCachedString(parts[4].toUpperCase());
         builder.log10PError(parseQual(parts[5]));
 
@@ -257,6 +256,17 @@ public abstract class AbstractVCFCodec extends AsciiFeatureCodec<VariantContext>
         final Map<String, Object> attrs = parseInfo(parts[7]);
         builder.attributes(attrs);
 
+        if ( attrs.containsKey(VCFConstants.END_KEY) ) {
+            // update stop with the end key if provided
+            try {
+                builder.stop(Integer.valueOf(attrs.get(VCFConstants.END_KEY).toString()));
+            } catch (Exception e) {
+                generateException("the END value in the INFO field is not valid");
+            }
+        } else {
+            builder.stop(pos + ref.length() - 1);
+        }
+
         // get our alleles, filters, and setup an attribute map
         final List<Allele> alleles = parseAlleles(ref, alts, lineNo);
         builder.alleles(alleles);

public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java

@@ -496,7 +496,7 @@ public class VariantContext implements Feature { // to enable tribble integratio
      */
     public boolean isSimpleInsertion() {
         // can't just call !isSimpleDeletion() because of complex indels
-        return getType() == Type.INDEL && isBiallelic() && getReference().length() < getAlternateAllele(0).length();
+        return getType() == Type.INDEL && isBiallelic() && getReference().length() == 1;
     }
 
     /**
@@ -504,7 +504,7 @@ public class VariantContext implements Feature { // to enable tribble integratio
      */
     public boolean isSimpleDeletion() {
         // can't just call !isSimpleInsertion() because of complex indels
-        return getType() == Type.INDEL && isBiallelic() && getReference().length() > getAlternateAllele(0).length();
+        return getType() == Type.INDEL && isBiallelic() && getAlternateAllele(0).length() == 1;
     }
 
     /**
@@ -1120,8 +1120,7 @@ public class VariantContext implements Feature { // to enable tribble integratio
         if ( hasAttribute(VCFConstants.END_KEY) ) {
             final int end = getAttributeAsInt(VCFConstants.END_KEY, -1);
             assert end != -1;
-            if ( end != getEnd() && end != getEnd() + 1 ) {
+            if ( end != getEnd() ) {
-                // the end is allowed to 1 bigger because of the padding
                 final String message = "Badly formed variant context at location " + getChr() + ":"
                         + getStart() + "; getEnd() was " + getEnd()
                         + " but this VariantContext contains an END key with value " + end;

public/java/test/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceIntegrationTest.java

@@ -26,7 +26,7 @@ public class FastaAlternateReferenceIntegrationTest extends WalkerTest {
         WalkerTestSpec spec2 = new WalkerTestSpec(
                 "-T FastaAlternateReferenceMaker -R " + b36KGReference + " -V " + validationDataLocation + "NA12878.chr1_10mb_11mb.slx.indels.vcf4 --snpmask:vcf " + b36dbSNP129 + " -L 1:10,075,000-10,075,380 -L 1:10,093,447-10,093,847 -L 1:10,271,252-10,271,452 -o %s",
                  1,
-                 Arrays.asList("0567b32ebdc26604ddf2a390de4579ac"));
+                 Arrays.asList("ef481be9962e21d09847b8a1d4a4ff65"));
         executeTest("testFastaAlternateReferenceIndels", spec2);
 
         WalkerTestSpec spec3 = new WalkerTestSpec(