Merged bug fix from Stable into Unstable

public/java/src/org/broadinstitute/sting/gatk/iterators/MalformedBAMErrorReformatingIterator.java

@@ -1,6 +1,5 @@
 package org.broadinstitute.sting.gatk.iterators;
 
-import net.sf.samtools.SAMFormatException;
 import net.sf.samtools.SAMRecord;
 import net.sf.samtools.util.CloseableIterator;
 import org.broadinstitute.sting.utils.exceptions.UserException;
@@ -23,7 +22,7 @@ public class MalformedBAMErrorReformatingIterator implements CloseableIterator<S
     public boolean hasNext() {
         try {
             return this.it.hasNext();
-        } catch ( SAMFormatException e ) {
+        } catch ( RuntimeException e ) { // we need to catch RuntimeExceptions here because the Picard code is throwing them (among SAMFormatExceptions) sometimes
             throw new UserException.MalformedBAM(source, e.getMessage());
         }
     }
@@ -31,7 +30,7 @@ public class MalformedBAMErrorReformatingIterator implements CloseableIterator<S
     public SAMRecord next() {
         try {
             return it.next();
-        } catch ( SAMFormatException e ) {
+        } catch ( RuntimeException e ) { // we need to catch RuntimeExceptions here because the Picard code is throwing them (among SAMFormatExceptions) sometimes
             throw new UserException.MalformedBAM(source, e.getMessage());
         }
     }

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/LowMQ.java

@@ -31,8 +31,10 @@ public class LowMQ extends InfoFieldAnnotation {
 		double total = 0;
         for ( Map.Entry<String, AlignmentContext> sample : stratifiedContexts.entrySet() )
 		{
-            ReadBackedPileup pileup = sample.getValue().getBasePileup();
+            if ( !sample.getValue().hasBasePileup() )
-            for (PileupElement p : pileup ) 
+                continue;
+
+            for ( PileupElement p : sample.getValue().getBasePileup() )
 			{
                 if ( p.getMappingQual() == 0 )  { mq0 += 1; }
                 if ( p.getMappingQual() <= 10 ) { mq10 += 1; }

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

@@ -243,6 +243,19 @@ public class CombineVariants extends RodWalker<Integer, Integer> {
 
         if (multipleAllelesMergeType == VariantContextUtils.MultipleAllelesMergeType.BY_TYPE) {
             Map<VariantContext.Type, List<VariantContext>> VCsByType = VariantContextUtils.separateVariantContextsByType(vcs);
+
+            // TODO -- clean this up in a refactoring
+            // merge NO_VARIATION into another type of variant (based on the ordering in VariantContext.Type)
+            if ( VCsByType.containsKey(VariantContext.Type.NO_VARIATION) && VCsByType.size() > 1 ) {
+                final List<VariantContext> refs = VCsByType.remove(VariantContext.Type.NO_VARIATION);
+                for ( VariantContext.Type type : VariantContext.Type.values() ) {
+                    if ( VCsByType.containsKey(type) ) {
+                        VCsByType.get(type).addAll(refs);
+                        break;
+                    }
+                }
+            }
+
             // iterate over the types so that it's deterministic
             for (VariantContext.Type type : VariantContext.Type.values()) {
                 if (VCsByType.containsKey(type))

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("ab72f4bfb16d3894942149173a087647"));
+                Arrays.asList("ee43a558fd3faeaa447acab89f0001d5"));
         executeTest("threeWayWithRefs", spec);
     }