Fix setting of CommandLineProgram REFERENCE_SEQUENCE.

src/main/java/picard/cmdline/CommandLineProgram.java

@@ -342,9 +342,7 @@ protected boolean parseArgs(final String[] argv) {
         // the tool tries to access REFERENCE_SEQUENCE directly (such tools will subsequently fail given
         // a non-local file anyway, but this prevents them from immediately throwing an NPE).
         final PicardHtsPath picardHtsPath = referenceSequence.getHtsPath();
-        REFERENCE_SEQUENCE = picardHtsPath == null ?
-                null :
-                new File(picardHtsPath.getURI().getPath()); // Must remove the "file://" prefix
+        REFERENCE_SEQUENCE = ReferenceArgumentCollection.getFileSafe(picardHtsPath, Log.getInstance(this.getClass()));
 
         // The TMP_DIR setting section below was moved from instanceMain() to here due to timing issues
         // related to checking whether R is installed. Certain programs, such as CollectInsertSizeMetrics