a) Cleanups/bug fixes to previous commit to CombineVariants.

b) Change md5 to reflect records that are now merged correctly.
c) Change unit merge alleles test to reflect the fact that a null non-variant vc object is not valid and not supported because there's no way to codify such object in a vcf. The code correctly converts this to a non-variant single-base event with whatever the reference is at that location.

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

@@ -233,7 +233,7 @@ public class CombineVariants extends RodWalker<Integer, Integer> {
 
         if (minimumN > 1 && (vcs.size() - numFilteredRecords < minimumN))
             return 0;
-        
+
         List<VariantContext> mergedVCs = new ArrayList<VariantContext>();
         Map<VariantContext.Type, List<VariantContext>> VCsByType = VariantContextUtils.separateVariantContextsByType(vcs);
         // iterate over the types so that it's deterministic
@@ -248,7 +248,6 @@ public class CombineVariants extends RodWalker<Integer, Integer> {
             // only operate at the start of events
             if ( mergedVC == null )
                 continue;
-            System.out.println(mergedVC.toString());
 
             HashMap<String, Object> attributes = new HashMap<String, Object>(mergedVC.getAttributes());
             // re-compute chromosome counts

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

@@ -1495,7 +1495,7 @@ public class VariantContext implements Feature { // to enable tribble intergrati
 
             // Do not change the filter state if filters were not applied to this context
             Set<String> inputVCFilters = inputVC.filtersWereAppliedToContext ? inputVC.getFilters() : null;
-            return new VariantContext(inputVC.getSource(), inputVC.getChr(), inputVC.getStart(), inputVC.getEnd(), alleles, genotypes, inputVC.getNegLog10PError(), inputVCFilters, inputVC.getAttributes());
+            return new VariantContext(inputVC.getSource(), inputVC.getChr(), inputVC.getStart(), inputVC.getEnd(), alleles, genotypes, inputVC.getNegLog10PError(), inputVCFilters, inputVC.getAttributes(),refByte);
         }
         else
             return inputVC;

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

@@ -789,6 +789,7 @@ public class VariantContextUtils {
                         // vc has a type different than otherVC and its alleles are a subset of VC: add vc to otherVC's type list and don't add to its own
                         mappedVCs.get(type).add(vc);
                         addtoOwnList = false;
+                        break;
                     }
                 }
             }

public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java

@@ -110,7 +110,7 @@ public class CombineVariantsIntegrationTest extends WalkerTest {
                         " -priority NA19240_BGI,NA19240_ILLUMINA,NA19240_WUGSC,denovoInfo" +
                         " -genotypeMergeOptions UNIQUIFY -L 1"),
                 1,
-                Arrays.asList("212d9d3df10bb29e2c7fb226da422dc0"));
+                Arrays.asList("b14f8cbb5d03a2e613b12da4da9efd9a"));
         executeTest("threeWayWithRefs", spec);
     }
 

public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUtilsUnitTest.java

@@ -38,7 +38,7 @@ import java.io.FileNotFoundException;
 import java.util.*;
 
 public class VariantContextUtilsUnitTest extends BaseTest {
-    Allele Aref, T, C, delRef, ATC, ATCATC;
+    Allele Aref, T, C, delRef, Cref, ATC, ATCATC;
     private GenomeLocParser genomeLocParser;
 
     @BeforeSuite
@@ -54,6 +54,7 @@ public class VariantContextUtilsUnitTest extends BaseTest {
 
         // alleles
         Aref = Allele.create("A", true);
+        Cref = Allele.create("C", true);
         delRef = Allele.create("-", true);
         T = Allele.create("T");
         C = Allele.create("C");
@@ -94,7 +95,7 @@ public class VariantContextUtilsUnitTest extends BaseTest {
         int stop = start; // alleles.contains(ATC) ? start + 3 : start;
         return new VariantContext(source, "1", start, stop, alleles,
                 genotypes == null ? null : VariantContext.genotypeCollectionToMap(new TreeMap<String, Genotype>(), genotypes),
-                1.0, filters, null, (byte)'C');
+                1.0, filters, null, Cref.getBases()[0]);
     }
 
     // --------------------------------------------------------------------------------
@@ -148,8 +149,10 @@ public class VariantContextUtilsUnitTest extends BaseTest {
                 Arrays.asList(Aref, C),
                 Arrays.asList(Aref, C, T)); // sorted by allele
 
+        // The following is actually a pathological case - there's no way on a vcf to represent a null allele that's non-variant.
+        // The code converts this (correctly) to a single-base non-variant vc with whatever base was there as a reference.
         new MergeAllelesTest(Arrays.asList(delRef),
-                Arrays.asList(delRef)); // todo -- FIXME me GdA
+                Arrays.asList(Cref));
 
         new MergeAllelesTest(Arrays.asList(delRef),
                 Arrays.asList(delRef, ATC),
@@ -186,6 +189,14 @@ public class VariantContextUtilsUnitTest extends BaseTest {
                 inputs, priority,
                 VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED,
                 VariantContextUtils.GenotypeMergeType.PRIORITIZE, false, false, "set", false, false);
+        System.out.println("expected:");
+        System.out.println(cfg.expected.toString());
+        System.out.println("inputs");
+        for (VariantContext vc:inputs)
+            System.out.println(vc.toString());
+        System.out.println("merged:");
+        System.out.println(merged.toString());
+
         Assert.assertEquals(merged.getAlleles(), cfg.expected);
     }