address final reviewer comments

src/main/java/org/broadinstitute/hellbender/engine/MultiFeatureWalker.java

@@ -25,8 +25,8 @@
  */
 public abstract class MultiFeatureWalker<F extends Feature> extends WalkerBase {
 
-    SAMSequenceDictionary dictionary;
-    final Set<String> samples = new TreeSet<>();
+    private SAMSequenceDictionary dictionary;
+    private final Set<String> samples = new TreeSet<>();
 
     @Override
     public boolean requiresFeatures(){
@@ -84,6 +84,8 @@ public void traverse() {
      *
      * @param feature Current Feature being processed.
      * @param header Header object for the source from which the feature was drawn (may be null)
+     * @param readsContext An object that allows querying for the reads the overlap the feature
+     * @param referenceContext An object that allows querying for the reference sequence associated with the feature
      */
     public abstract void apply( final F feature,
                                 final Object header,
@@ -98,7 +100,7 @@ public abstract void apply( final F feature,
     /**
      * Get the list of sample names we accumulated
      */
-    public Set<String> getSampleNames() { return samples; }
+    public Set<String> getSampleNames() { return Collections.unmodifiableSet(samples); }
 
     /**
      * Choose the most comprehensive dictionary available (see betterDictionary method below),
@@ -111,68 +113,95 @@ public abstract void apply( final F feature,
      * dictionaries available.)
      */
     private void setDictionaryAndSamples() {
-        dictionary = getMasterSequenceDictionary();
+        DictSource dictSource = new DictSource(getMasterSequenceDictionary(),
+                                        StandardArgumentDefinitions.SEQUENCE_DICTIONARY_NAME);
         if ( hasReference() ) {
-            dictionary = betterDictionary(reference.getSequenceDictionary(), dictionary);
+            final DictSource refDictSource = new DictSource(reference.getSequenceDictionary(),
+                                                  StandardArgumentDefinitions.REFERENCE_LONG_NAME);
+            dictSource = betterDictionary(refDictSource, dictSource);
         }
         if ( hasReads() ) {
-            dictionary = betterDictionary(reads.getSequenceDictionary(), dictionary);
+            final DictSource readsDictSource = new DictSource(reads.getSequenceDictionary(), "read-source");
+            dictSource = betterDictionary(readsDictSource, dictSource);
         }
         for ( final FeatureInput<? extends Feature> input : features.getAllInputs() ) {
             final Object header = features.getHeader(input);
             if ( header instanceof SVFeaturesHeader ) {
                 final SVFeaturesHeader svFeaturesHeader = (SVFeaturesHeader)header;
-                dictionary = betterDictionary(svFeaturesHeader.getDictionary(), dictionary);
+                final DictSource featureDictSource = new DictSource(svFeaturesHeader.getDictionary(),
+                                                                    input.getName());
+                dictSource = betterDictionary(featureDictSource, dictSource);
                 final List<String> sampleNames = svFeaturesHeader.getSampleNames();
                 if ( sampleNames != null ) {
                     samples.addAll(svFeaturesHeader.getSampleNames());
                 }
             } else if (header instanceof VCFHeader ) {
                 final VCFHeader vcfHeader = (VCFHeader)header;
-                dictionary = betterDictionary(vcfHeader.getSequenceDictionary(), dictionary);
+                final DictSource featureDictSource = new DictSource(vcfHeader.getSequenceDictionary(),
+                                                                        input.getName());
+                dictSource = betterDictionary(featureDictSource, dictSource);
                 samples.addAll(vcfHeader.getSampleNamesInOrder());
             }
         }
-        if ( dictionary == null ) {
+        if ( dictSource.getDictionary() == null ) {
             throw new UserException("No dictionary found.  Provide one as --" +
                     StandardArgumentDefinitions.SEQUENCE_DICTIONARY_NAME + " or --" +
                     StandardArgumentDefinitions.REFERENCE_LONG_NAME + ".");
         }
+        dictionary = dictSource.getDictionary();
     }
 
     /**
      * Makes sure that the two dictionaries are consistent with regard to contig names and order.
      * Returns the more comprehensive (larger) dictionary if they're consistent.
      */
-    private static SAMSequenceDictionary betterDictionary( final SAMSequenceDictionary newDict,
-                                                           final SAMSequenceDictionary curDict ) {
-        if ( curDict == null ) return newDict;
-        if ( newDict == null ) return curDict;
-        final SAMSequenceDictionary smallDict;
-        final SAMSequenceDictionary largeDict;
-        if ( newDict.size() <= curDict.size() ) {
+    private static DictSource betterDictionary( final DictSource newDict,
+                                                final DictSource curDict ) {
+        if ( curDict.getDictionary() == null ) return newDict;
+        if ( newDict.getDictionary() == null ) return curDict;
+        final DictSource smallDict;
+        final DictSource largeDict;
+        if ( newDict.getDictionary().size() <= curDict.getDictionary().size() ) {
             smallDict = newDict;
             largeDict = curDict;
         } else {
             smallDict = curDict;
             largeDict = newDict;
         }
         int lastIdx = -1;
-        for ( final SAMSequenceRecord rec : smallDict.getSequences() ) {
-            final int newIdx = largeDict.getSequenceIndex(rec.getContig());
+        final SAMSequenceDictionary largeDictionary = largeDict.getDictionary();
+        for ( final SAMSequenceRecord rec : smallDict.getDictionary().getSequences() ) {
+            final int newIdx = largeDictionary.getSequenceIndex(rec.getContig());
             if ( newIdx == -1 ) {
-                throw new UserException("Contig " + rec.getContig() +
-                                        " not found in the larger dictionary");
+                throw new UserException("Contig " + rec.getContig() + " in the dictionary read from " +
+                        smallDict.getSource() + " does not appear in the larger dictionary read from " +
+                        largeDict.getSource());
             }
             if ( newIdx <= lastIdx ) {
-                throw new UserException("Contig " + rec.getContig() +
-                                        " not in same order as in larger dictionary");
+                final String prevContig = largeDictionary.getSequence(lastIdx).getContig();
+                throw new UserException("Contigs out of order: Contig " + rec.getContig() +
+                        " comes before contig " + prevContig + " in the dictionary read from " +
+                        largeDict.getSource() + ", but follows it in the dictionary read from " +
+                        smallDict.getSource());
             }
             lastIdx = newIdx;
         }
         return largeDict;
     }
 
+    public static final class DictSource {
+        private final SAMSequenceDictionary dictionary;
+        private final String source;
+
+        public DictSource( final SAMSequenceDictionary dictionary, final String source ) {
+            this.dictionary = dictionary;
+            this.source = source;
+        }
+
+        public SAMSequenceDictionary getDictionary() { return dictionary; }
+        public String getSource() { return source; }
+    }
+
     public static final class MergingIterator<F extends Feature> implements Iterator<PQEntry<F>> {
         final SAMSequenceDictionary dictionary;
         final PriorityQueue<PQEntry<F>> priorityQueue;

src/main/java/org/broadinstitute/hellbender/tools/examples/ExampleMultiFeatureWalker.java

@@ -42,5 +42,7 @@ public class ExampleMultiFeatureWalker extends MultiFeatureWalker<Feature> {
                                  final ReferenceContext referenceContext ) {
         // We'll just keep track of the Features we see, in the order that we see them.
         features.add(feature);
+        // And print them
+        System.out.println(feature);
     }
 }

src/main/java/org/broadinstitute/hellbender/tools/sv/BafEvidence.java

@@ -67,4 +67,8 @@ public boolean equals(Object o) {
     public int hashCode() {
         return Objects.hash(sample, contig, position, value);
     }
+
+    @Override public String toString() {
+        return contig + "\t" + position + "\t" + sample + "\t" + value;
+    }
 }

src/main/java/org/broadinstitute/hellbender/tools/sv/DepthEvidence.java

@@ -75,4 +75,13 @@ public int hashCode() {
         result = 31 * result + Arrays.hashCode(counts);
         return result;
     }
+
+    @Override public String toString() {
+        final StringBuilder sb = new StringBuilder(contig + "\t" + start + "\t" + end);
+        for ( final int count : counts ) {
+            sb.append("\t");
+            sb.append(count);
+        }
+        return  sb.toString();
+    }
 }

src/main/java/org/broadinstitute/hellbender/tools/sv/DiscordantPairEvidence.java

@@ -98,4 +98,9 @@ public boolean equals(Object o) {
     public int hashCode() {
         return Objects.hash(sample, startContig, endContig, start, end, startStrand, endStrand);
     }
+
+    @Override public String toString() {
+        return startContig + "\t" + start + "\t" + end + "\t" + sample + "\t" + endContig + "\t" +
+                startStrand + "\t" + endStrand;
+    }
 }

src/main/java/org/broadinstitute/hellbender/tools/sv/SplitReadEvidence.java

@@ -82,4 +82,8 @@ public boolean equals(Object o) {
     public int hashCode() {
         return Objects.hash(sample, contig, position, count, strand);
     }
-}
+
+    @Override public String toString() {
+        return contig + "\t" + position + "\t" + sample + "\t" + count + "\t" + strand;
+    }
+}