Validation of sequence dictionaries from multiple BAMs now throws warning instead of exception in CNV workflows.

src/main/java/org/broadinstitute/hellbender/tools/copynumber/DetermineGermlineContigPloidy.java

@@ -318,11 +318,11 @@ private void writeSamplesByCoveragePerContig(final File samplesByCoveragePerCont
             logger.info(String.format("Aggregating read-count file %s (%d / %d)",
                     inputReadCountFile, sampleIndex + 1, numSamples));
             final SimpleCountCollection readCounts = SimpleCountCollection.read(inputReadCountFile);
-            Utils.validateArg(CopyNumberArgumentValidationUtils.isSameDictionary(
-                    readCounts.getMetadata().getSequenceDictionary(),
-                    metadata.getSequenceDictionary()),
-                    String.format("Sequence dictionary for read-count file %s does not match those " +
-                            "in other read-count files.", inputReadCountFile));
+            if (!CopyNumberArgumentValidationUtils.isSameDictionary(
+                    readCounts.getMetadata().getSequenceDictionary(), metadata.getSequenceDictionary())) {
+                logger.warn("Sequence dictionary for read-count file %s does not match that " +
+                        "in other read-count files.", inputReadCountFile);
+            }
             Utils.validateArg(readCounts.getIntervals().equals(intervals),
                     String.format("Intervals for read-count file %s do not match those in other " +
                             "read-count files.", inputReadCountFile));

src/main/java/org/broadinstitute/hellbender/tools/copynumber/GermlineCNVCaller.java

@@ -389,11 +389,11 @@ private List<File> writeIntervalSubsetReadCountFiles() {
             logger.info(String.format("Aggregating read-count file %s (%d / %d)",
                     inputReadCountFile, sampleIndex + 1, numSamples));
             final SimpleCountCollection readCounts = SimpleCountCollection.read(inputReadCountFile);
-            Utils.validateArg(CopyNumberArgumentValidationUtils.isSameDictionary(
-                    readCounts.getMetadata().getSequenceDictionary(),
-                    specifiedIntervals.getMetadata().getSequenceDictionary()),
-                    String.format("Sequence dictionary for read-count file %s does not match those in " +
-                            "other read-count files.", inputReadCountFile));
+            if (!CopyNumberArgumentValidationUtils.isSameDictionary(
+                    readCounts.getMetadata().getSequenceDictionary(), specifiedIntervals.getMetadata().getSequenceDictionary())) {
+                logger.warn("Sequence dictionary for read-count file %s does not match that " +
+                        "in other read-count files.", inputReadCountFile);
+            }
             Utils.validateArg(new HashSet<>(readCounts.getIntervals()).containsAll(intervalSubset),
                     String.format("Intervals for read-count file %s do not contain all specified intervals.",
                             inputReadCountFile));

src/main/java/org/broadinstitute/hellbender/tools/copynumber/ModelSegments.java

@@ -634,10 +634,11 @@ private AllelicCountCollection genotypeHets(final SampleLocatableMetadata metada
                         "Run CollectAllelicCounts using the same interval list of sites for both samples.");
             }
             final SampleLocatableMetadata normalMetadata = normalAllelicCounts.getMetadata();
-            Utils.validateArg(CopyNumberArgumentValidationUtils.isSameDictionary(
+            if (!CopyNumberArgumentValidationUtils.isSameDictionary(
                     normalMetadata.getSequenceDictionary(),
-                    metadata.getSequenceDictionary()),
-                    "Sequence dictionaries in allelic-count files do not match.");
+                    metadata.getSequenceDictionary())) {
+                logger.warn("Sequence dictionaries in allelic-count files do not match.");
+            }
 
             //filter on total count in matched normal
             logger.info(String.format("Filtering allelic counts in matched normal with total count less than %d...", minTotalAlleleCount));

src/main/java/org/broadinstitute/hellbender/tools/copynumber/arguments/CopyNumberArgumentValidationUtils.java

@@ -115,8 +115,9 @@ public static AnnotatedIntervalCollection validateAnnotatedIntervals(final File
         logger.info("Reading and validating GC-content annotations for intervals...");
         final AnnotatedIntervalCollection annotatedIntervals = new AnnotatedIntervalCollection(annotatedIntervalsFile);
         final SAMSequenceDictionary sequenceDictionary = locatableCollection.getMetadata().getSequenceDictionary();
-        Utils.validateArg(annotatedIntervals.getMetadata().getSequenceDictionary().isSameDictionary(sequenceDictionary),
-                "Annotated-intervals file contains incorrect sequence dictionary.");
+        if (!CopyNumberArgumentValidationUtils.isSameDictionary(annotatedIntervals.getMetadata().getSequenceDictionary(), sequenceDictionary)) {
+            logger.warn("Sequence dictionary in annotated-intervals file does not match the master sequence dictionary.");
+        }
         Utils.validateArg(annotatedIntervals.getIntervals().equals(locatableCollection.getIntervals()),
                 "Annotated intervals do not match provided intervals.");
         return annotatedIntervals;
@@ -140,8 +141,9 @@ public static AnnotatedIntervalCollection validateAnnotatedIntervalsSubset(final
         IOUtils.canReadFile(annotatedIntervalsFile);
         final AnnotatedIntervalCollection annotatedIntervals = new AnnotatedIntervalCollection(annotatedIntervalsFile);
         final SAMSequenceDictionary sequenceDictionary = locatableCollection.getMetadata().getSequenceDictionary();
-        Utils.validateArg(annotatedIntervals.getMetadata().getSequenceDictionary().isSameDictionary(sequenceDictionary),
-                "Annotated-intervals file contains incorrect sequence dictionary.");
+        if (!CopyNumberArgumentValidationUtils.isSameDictionary(annotatedIntervals.getMetadata().getSequenceDictionary(), sequenceDictionary)) {
+            logger.warn("Sequence dictionary in annotated-intervals file does not match the master sequence dictionary.");
+        }
         final Set<SimpleInterval> intervalsSubset = new HashSet<>(locatableCollection.getIntervals());
         Utils.validateArg(annotatedIntervals.getIntervals().containsAll(intervalsSubset),
                 "Annotated intervals do not contain all specified intervals.");

src/test/java/org/broadinstitute/hellbender/tools/copynumber/ModelSegmentsIntegrationTest.java

@@ -170,18 +170,6 @@ public void testMissingSites() {
         runCommandLine(argsBuilder);
     }
 
-    @Test(expectedExceptions = IllegalArgumentException.class)
-    public void testSequenceDictionaryMismatch() {
-        final File outputDir = createTempDir("testDir");
-        final String outputPrefix = "test";
-        final ArgumentsBuilder argsBuilder = new ArgumentsBuilder()
-                .addArgument(CopyNumberStandardArgument.ALLELIC_COUNTS_FILE_LONG_NAME, TUMOR_ALLELIC_COUNTS_FILE.getAbsolutePath())
-                .addArgument(CopyNumberStandardArgument.NORMAL_ALLELIC_COUNTS_FILE_LONG_NAME, NORMAL_ALLELIC_COUNTS_FILE_WITH_SEQUENCE_DICTIONARY_MISMATCH.getAbsolutePath())
-                .addOutput(outputDir)
-                .addArgument(CopyNumberStandardArgument.OUTPUT_PREFIX_LONG_NAME, outputPrefix);
-        runCommandLine(argsBuilder);
-    }
-
     @Test(expectedExceptions = UserException.class)
     public void testOutputDirExists() {
         final String outputPrefix = "test";