From 58debd7e566fe43606b6a21399ad347ce997bc40 Mon Sep 17 00:00:00 2001
From: asivache <asivache@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 2 Sep 2009 17:00:39 +0000
Subject: [PATCH] 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
---
 .../broadinstitute/sting/utils/AlignmentUtils.java | 14 ++++++++++++++
 1 file changed, 14 insertions(+)

diff --git a/java/src/org/broadinstitute/sting/utils/AlignmentUtils.java b/java/src/org/broadinstitute/sting/utils/AlignmentUtils.java
index dd4edf521..a9c3f289d 100644
--- a/java/src/org/broadinstitute/sting/utils/AlignmentUtils.java
+++ b/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;
+    }
 }