Wow, symbolic alleles were all busted internally and this finally bubbled up after my previous commit. For some reason we were inconsistently forcing allele trimming/padding if one was present. Not anymore.

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

@@ -341,9 +341,7 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec {
             } catch (Exception e) {
                 generateException("the END value in the INFO field is not valid");
             }
-        }
+        } else if ( !isSingleNucleotideEvent(alleles) ) {
-        // handle multi-positional events
-        else if ( !isSingleNucleotideEvent(alleles) ) {
             ArrayList<Allele> newAlleles = new ArrayList<Allele>();
             stop = clipAlleles(pos, ref, alleles, newAlleles, lineNo);
             alleles = newAlleles;
@@ -611,11 +609,14 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec {
 
     public static int computeForwardClipping(List<Allele> unclippedAlleles, String ref) {
         boolean clipping = true;
+        int symbolicAlleleCount = 0;
         final byte ref0 = (byte)ref.charAt(0);
 
         for ( Allele a : unclippedAlleles ) {
-            if ( a.isSymbolic() )
+            if ( a.isSymbolic() ) {
+                symbolicAlleleCount++;
                 continue;
+            }
 
             if ( a.length() < 1 || (a.getBases()[0] != ref0) ) {
                 clipping = false;
@@ -623,7 +624,8 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec {
             }
         }
 
-        return (clipping) ? 1 : 0;
+        // don't clip if all alleles are symbolic
+        return (clipping && symbolicAlleleCount != unclippedAlleles.size()) ? 1 : 0;
     }
 
     protected static int computeReverseClipping(List<Allele> unclippedAlleles, String ref, int forwardClipping, int lineNo) {

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

@@ -1040,7 +1040,7 @@ public class VariantContext implements Feature { // to enable tribble intergrati
     }
 
     private void validateReferencePadding() {
-        if (hasSymbolicAlleles()) // symbolic alleles don't need padding...
+        if ( hasSymbolicAlleles() ) // symbolic alleles don't need padding...
             return;
 
         boolean needsPadding = (getReference().length() == getEnd() - getStart()); // off by one because padded base was removed
@@ -1078,7 +1078,7 @@ public class VariantContext implements Feature { // to enable tribble intergrati
 //            if ( getReference().length() != (getLocation().size()-1) ) {
         long length = (stop - start) + 1;
         if ( (getReference().isNull() && length != 1 ) ||
-                (getReference().isNonNull() && (length - getReference().length()  > 1))) {
+                (!isSymbolic() && getReference().isNonNull() && (length - getReference().length()  > 1))) {
             throw new IllegalStateException("BUG: GenomeLoc " + contig + ":" + start + "-" + stop + " has a size == " + length + " but the variation reference allele has length " + getReference().length() + " this = " + this);
         }
     }

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

@@ -140,22 +140,22 @@ public class VariantContextUtils {
 
     public static VariantContext createVariantContextWithPaddedAlleles(VariantContext inputVC, boolean refBaseShouldBeAppliedToEndOfAlleles) {
         // see if we need to pad common reference base from all alleles
-        boolean padVC;
+        boolean padVC = false;
 
         // We need to pad a VC with a common base if the length of the reference allele is less than the length of the VariantContext.
         // This happens because the position of e.g. an indel is always one before the actual event (as per VCF convention).
-        long locLength = (inputVC.getEnd() - inputVC.getStart()) + 1;
+        final int recordLength = inputVC.getEnd() - inputVC.getStart() + 1;
-        if (inputVC.hasSymbolicAlleles())
+        final int referenceLength = inputVC.getReference().length();
-            padVC = true;
+        if ( referenceLength == recordLength )
-        else if (inputVC.getReference().length() == locLength)
             padVC = false;
-        else if (inputVC.getReference().length() == locLength-1)
+        else if ( referenceLength == recordLength - 1 )
             padVC = true;
-        else throw new IllegalArgumentException("Badly formed variant context at location " + String.valueOf(inputVC.getStart()) +
+        else if ( !inputVC.hasSymbolicAlleles() )
+            throw new IllegalArgumentException("Badly formed variant context at location " + String.valueOf(inputVC.getStart()) +
                     " in contig " + inputVC.getChr() + ". Reference length must be at most one base shorter than location size");
 
         // nothing to do if we don't need to pad bases
-        if (padVC) {
+        if ( padVC ) {
             if ( !inputVC.hasReferenceBaseForIndel() )
                 throw new ReviewedStingException("Badly formed variant context at location " + inputVC.getChr() + ":" + inputVC.getStart() + "; no padded reference base is available.");
 
@@ -506,6 +506,7 @@ public class VariantContextUtils {
         final VariantContext first = VCs.get(0);
         final String name = first.getSource();
         final Allele refAllele = determineReferenceAllele(VCs);
+        Byte referenceBaseForIndel = null;
 
         final Set<Allele> alleles = new LinkedHashSet<Allele>();
         final Set<String> filters = new TreeSet<String>();
@@ -530,7 +531,7 @@ public class VariantContextUtils {
         // cycle through and add info from the other VCs, making sure the loc/reference matches
 
         for ( final VariantContext vc : VCs ) {
-            if ( loc.getStart() != vc.getStart() ) // || !first.getReference().equals(vc.getReference()) )
+            if ( loc.getStart() != vc.getStart() )
                 throw new ReviewedStingException("BUG: attempting to merge VariantContexts with different start sites: first="+ first.toString() + " second=" + vc.toString());
 
             if ( getLocation(genomeLocParser,vc).size() > loc.size() )
@@ -550,6 +551,9 @@ public class VariantContextUtils {
 
             filters.addAll(vc.getFilters());
 
+            if ( referenceBaseForIndel == null )
+                referenceBaseForIndel = vc.getReferenceBaseForIndel();
+
             //
             // add attributes
             //
@@ -659,6 +663,7 @@ public class VariantContextUtils {
         builder.genotypes(genotypes);
         builder.log10PError(log10PError);
         builder.filters(filters).attributes(mergeInfoWithMaxAC ? attributesWithMaxAC : attributes);
+        builder.referenceBaseForIndel(referenceBaseForIndel);
 
         // Trim the padded bases of all alleles if necessary
         final VariantContext merged = createVariantContextWithTrimmedAlleles(builder.make());