Merged bug fix from Stable into Unstable

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

@@ -798,11 +798,11 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
 
     private void generateAlternateConsensesFromKnownIndels(final Set<Consensus> altConsensesToPopulate, final int leftmostIndex, final byte[] reference) {
         for ( VariantContext knownIndel : knownIndelsToTry ) {
-            if ( knownIndel == null || !knownIndel.isIndel() )
+            if ( knownIndel == null || !knownIndel.isIndel() || knownIndel.isComplexIndel() )
                 continue;
             byte[] indelStr = knownIndel.isInsertion() ? knownIndel.getAlternateAllele(0).getBases() : Utils.dupBytes((byte)'-', knownIndel.getReference().length());
             int start = knownIndel.getStart() - leftmostIndex + 1;
-            Consensus c = createAlternateConsensus(start, reference, indelStr, knownIndel.isDeletion());
+            Consensus c = createAlternateConsensus(start, reference, indelStr, knownIndel);
             if ( c != null )
                 altConsensesToPopulate.add(c);
         }
@@ -988,7 +988,7 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
     }
 
     // create a Consensus from just the indel string that falls on the reference
-    private Consensus createAlternateConsensus(final int indexOnRef, final byte[] reference, final byte[] indelStr, final boolean isDeletion) {
+    private Consensus createAlternateConsensus(final int indexOnRef, final byte[] reference, final byte[] indelStr, final VariantContext indel) {
         if ( indexOnRef < 0 || indexOnRef >= reference.length )
             return null;
 
@@ -1002,11 +1002,11 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
         if ( indexOnRef > 0 )
             cigar.add(new CigarElement(indexOnRef, CigarOperator.M));
 
-        if ( isDeletion ) {
+        if ( indel.isDeletion() ) {
             refIdx += indelStr.length;
             cigar.add(new CigarElement(indelStr.length, CigarOperator.D));
         }
-        else {
+        else if ( indel.isInsertion() ) {
             for ( byte b : indelStr )
                 sb.append((char)b);
             cigar.add(new CigarElement(indelStr.length, CigarOperator.I));

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

@@ -161,7 +161,7 @@ public class AnnotateMNPsWalker extends RodWalker<Integer, Integer> {
             boolean atStartOfVc = curLocus.getStart() == vcLoc.getStart();
             boolean atEndOfVc = curLocus.getStart() == vcLoc.getStop();
 
-            if (vc.getType() == VariantContext.Type.MNP) {
+            if (vc.isMNP()) {
                 logger.debug("Observed MNP at " + vcLoc);
 
                 if (isChrM(vc)) {

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

@@ -209,7 +209,7 @@ public class PickSequenomProbes extends RodWalker<String, String> {
             String assay_sequence;
             if ( vc.isSNP() )
                 assay_sequence = leading_bases + "[" + (char)ref.getBase() + "/" + vc.getAlternateAllele(0).toString() + "]" + trailing_bases;
-            else if ( vc.getType() == VariantContext.Type.MNP )
+            else if ( vc.isMNP() )
                 assay_sequence = leading_bases + "[" + new String(vc.getReference().getBases()) + "/" + new String(vc.getAlternateAllele(0).getBases())+"]"+trailing_bases.substring(vc.getReference().length()-1);
             else if ( vc.isInsertion() )
                 assay_sequence = leading_bases + (char)ref.getBase() + "[-/" + vc.getAlternateAllele(0).toString() + "]" + trailing_bases;

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

@@ -113,7 +113,7 @@ public class ValidateVariants extends RodWalker<Integer, Integer> {
             observedRefAllele = Allele.create(Allele.NULL_ALLELE_STRING);
         }
         // deletions
-        else if ( vc.isDeletion() || vc.isMixed() || vc.getType() == VariantContext.Type.MNP ) {
+        else if ( vc.isDeletion() || vc.isMixed() || vc.isMNP() ) {
             // we can't validate arbitrarily long deletions
             if ( reportedRefAllele.length() > 100 ) {
                 logger.info(String.format("Reference allele is too long (%d) at position %s:%d; skipping that record.", reportedRefAllele.length(), vc.getChr(), vc.getStart()));
@@ -123,7 +123,7 @@ public class ValidateVariants extends RodWalker<Integer, Integer> {
             // deletions are associated with the (position of) the last (preceding) non-deleted base;
             // hence to get actually deleted bases we need offset = 1
             int offset = 1 ;
-            if ( vc.getType() == VariantContext.Type.MNP ) offset = 0; // if it's an MNP, the reported position IS the first modified base
+            if ( vc.isMNP() ) offset = 0; // if it's an MNP, the reported position IS the first modified base
             byte[] refBytes = ref.getBases();
             byte[] trueRef = new byte[reportedRefAllele.length()];
             for (int i = 0; i < reportedRefAllele.length(); i++)

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

@@ -566,10 +566,21 @@ public class VariantContext implements Feature { // to enable tribble intergrati
         return getType() == Type.INDEL && getAlternateAllele(0).isNull();
     }
 
+    /**
+     * @return true if the alleles indicate neither a simple deletion nor a simple insertion
+     */
+    public boolean isComplexIndel() {
+        return isIndel() && !isDeletion() && !isInsertion();
+    }
+
     public boolean isSymbolic() {
         return getType() == Type.SYMBOLIC;
     }
 
+    public boolean isMNP() {
+        return getType() == Type.MNP;
+    }
+
     /**
      * convenience method for indels
      *