Fixing up GATKtool edits

broadinstitute · Aug 5, 2015 · 568fad7 · 568fad7
1 parent 01bea98
commit 568fad7
Showing 1 changed file with 11 additions and 5 deletions.
diff --git a/src/main/java/org/broadinstitute/hellbender/engine/GATKTool.java b/src/main/java/org/broadinstitute/hellbender/engine/GATKTool.java
@@ -85,22 +85,28 @@ void initializeReference() {
      * Package-private so that engine classes can access it, but concrete tool child classes cannot.
      * May be overridden by traversals that require custom initialization of the reads data source.
      */
-    void initializeReads() throws UserException {
+    void initializeReads() {
         SamReaderFactory factory = null;
         if (hasReference()){
             // pass in reference if available, because CRAM files need it
             factory = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT).referenceSequence(referenceArguments.getReferenceFile());
+        } else if (hasCramInput()) {
+            throw new UserException("A reference file is required when using CRAM files.");
         }
         reads = ! readArguments.getReadFiles().isEmpty() ? new ReadsDataSource(readArguments.getReadFiles(), factory) : null;
+    }
+
+    /**
+     * Helper method that simply returns a boolean regarding whether the input has CRAM files or not.
+     */
+    private boolean hasCramInput() {
         boolean hasCram = false;
         for (File inputFile : readArguments.getReadFiles()) {
-            if (FilenameUtils.getExtension(inputFile.getName()).equals("cram")) {
+            if (FilenameUtils.getExtension(inputFile.getName()).equalsIgnoreCase("cram")) {
                 hasCram = true;
             }
         }
-        if (hasCram && ! hasReference()) {
-            throw new UserException("A reference file is required when using CRAM files.");
-        }
+        return hasCram;
     }
 
     /**