Better error messages for missing contigs in reference

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

@@ -445,7 +445,7 @@ void initializeReads() {
                 factory = factory.referenceSequence(referenceArguments.getReferencePath());
             }
             else if (hasCramInput()) {
-                throw new UserException.MissingReference("A reference file is required when using CRAM files.");
+                throw UserException.MISSING_REFERENCE_FOR_CRAM;
             }
 
             if(bamIndexCachingShouldBeEnabled()) {
@@ -823,7 +823,7 @@ public final SAMFileGATKReadWriter createSAMWriter(final File outputFile, final
     public final SAMFileGATKReadWriter createSAMWriter(final Path outputPath, final boolean preSorted) {
         final boolean isCramFile = IOUtils.isCramFile(outputPath);
         if (!hasReference() && isCramFile) {
-            throw new UserException.MissingReference("A reference file is required for writing CRAM files");
+            throw UserException.MISSING_REFERENCE_FOR_CRAM;
         }
 
         return new SAMFileGATKReadWriter(

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

@@ -198,20 +198,4 @@ protected final void onShutdown() {
         super.onShutdown();
     }
 
-    /**
-     *  The emit empty loci parameter comes with several pitfalls when used incorrectly.  Here we check and either give
-     *   warnings or errors.
-     */
-    protected void validateEmitEmptyLociParameters() {
-        if (emitEmptyLoci()) {
-            if (getBestAvailableSequenceDictionary() == null) {
-                throw new UserException.MissingReference("Could not create a sequence dictionary nor find a reference.  Therefore, emitting empty loci is impossible and this tool cannot be run.  The easiest fix here is to specify a reference dictionary.");
-            }
-            if (!hasReference() && !hasUserSuppliedIntervals()) {
-                logger.warn("****************************************");
-                logger.warn("* Running this tool without a reference nor intervals can yield unexpected results, since it will emit results for loci with no reads.  A sequence dictionary has been found.  The easiest way avoid this message is to specify a reference.");
-                logger.warn("****************************************");
-            }
-        }
-    }
 }

src/main/java/org/broadinstitute/hellbender/engine/spark/GATKSparkTool.java

@@ -336,7 +336,7 @@ protected JavaRDD<GATKRead> getGatkReadJavaRDD(TraversalParameters traversalPara
 
         } else {
             if (hasCramInput() && !hasReference()){
-                throw new UserException.MissingReference("A reference file is required when using CRAM files.");
+                throw UserException.MISSING_REFERENCE_FOR_CRAM;
             }
             final String refPath = hasReference() ?  referenceArguments.getReferenceFileName() : null;
             output = source.getParallelReads(input, refPath, traversalParameters, bamPartitionSplitSize, useNio);

src/main/java/org/broadinstitute/hellbender/exceptions/UserException.java

@@ -103,8 +103,14 @@ public static class MissingReference extends UserException {
         private static final long serialVersionUID = 0L;
 
         public MissingReference(String message) { super(message); }
+
+        public MissingReference(final String message, final boolean commandLine) {
+            super(message + (commandLine ? String.format("  A reference is specified with the -%s command line argument.", StandardArgumentDefinitions.REFERENCE_SHORT_NAME) : ""));
+        }
     }
 
+    public static final MissingReference MISSING_REFERENCE_FOR_CRAM = new MissingReference("A reference file is required when using CRAM files.", true);
+
     public static class MissingIndex extends UserException {
         private static final long serialVersionUID = 0L;
 

src/main/java/org/broadinstitute/hellbender/tools/walkers/rnaseq/SplitNCigarReads.java

@@ -192,7 +192,7 @@ public void closeTool() {
         if (outputWriter != null ) { outputWriter.close(); }
         try {if (referenceReader != null) { referenceReader.close(); } }
         catch (IOException ex) {
-            throw new UserException.MissingReference("Could not find reference file");
+            throw new UserException.MissingReference("Could not find reference file.", true);
         }
     }
 

src/main/java/org/broadinstitute/hellbender/tools/walkers/variantutils/ValidateVariants.java

@@ -335,7 +335,7 @@ private Collection<ValidationType> calculateValidationTypesToApply(final List<Va
             final Set<ValidationType> result = new LinkedHashSet<>(ValidationType.CONCRETE_TYPES);
             result.removeAll(excludeTypeSet);
             if (result.contains(ValidationType.REF) && !hasReference()) {
-                throw new UserException.MissingReference("Validation type " + ValidationType.REF.name() + " was selected but no reference was provided.");
+                throw new UserException.MissingReference("Validation type " + ValidationType.REF.name() + " was selected but no reference was provided.", true);
             }
             return result;
         }

src/main/java/org/broadinstitute/hellbender/utils/SequenceDictionaryUtils.java

@@ -156,7 +156,12 @@ public static void validateDictionaries( final String name1,
                 return;
             case COMMON_SUBSET:
                 if ( requireSuperset ) {
-                    throw new UserException.IncompatibleSequenceDictionaries(String.format("Dictionary %s is missing contigs found in dictionary %s", name1, name2), name1, dict1, name2, dict2);
+                    final Set<String> contigs1 = dict1.getSequences().stream().map(SAMSequenceRecord::getSequenceName).collect(Collectors.toSet());
+                    final List<String> missingContigs = dict2.getSequences().stream()
+                            .map(SAMSequenceRecord::getSequenceName)
+                            .filter(contig -> !contigs1.contains(contig))
+                            .collect(Collectors.toList());
+                    throw new UserException.IncompatibleSequenceDictionaries(String.format("Dictionary %s is missing contigs found in dictionary %s.  Missing contigs: \n %s \n", name1, name2, String.join(", ", missingContigs)), name1, dict1, name2, dict2);
                 }
                 return;
             case SUPERSET:

src/main/java/org/broadinstitute/hellbender/utils/read/ReadUtils.java

@@ -1193,7 +1193,7 @@ public static SAMFileWriter createCommonSAMWriterFromFactory(
         Utils.nonNull(header);
 
         if (null == referenceFile && outputPath.toString().endsWith(FileExtensions.CRAM)) {
-            throw new UserException("A reference file is required for writing CRAM files");
+            throw new UserException.MissingReference("A reference file is required for writing CRAM files");
         }
 
         return factory.makeWriter(header.clone(), preSorted, outputPath, referenceFile);