A convenience shortcut isReadUnmapped() added: thanks to SAM format specification, 'read unmapped' flag is not always required to be set for an unmapped read; this method checks both the flag and the alignment reference index/start (if those are set to '*' the flag is not required according to the spec!)

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1506 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/utils/AlignmentUtils.java

@@ -258,4 +258,18 @@ public class AlignmentUtils {
         refLine.append('\n');
         return refLine.toString();
     }
+
+    /**
+     * Due to (unfortunate) multiple ways to indicate that read is unmapped allowed by SAM format
+     * specification, one may need this convenience shortcut. Checks both 'read unmapped' flag and
+     * alignment reference index/start.
+     * @param r
+     * @return
+     */
+    public static boolean isReadUnmapped(final SAMRecord r) {
+        if ( r.getReadUnmappedFlag() ) return true;
+        if ( r.getReferenceIndex() == SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX ||
+             r.getAlignmentStart() == SAMRecord.NO_ALIGNMENT_START ) return true;
+        return false;
+    }
 }