From d6e42d839cde59bc815e4a151fce912c638c15c9 Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Mon, 10 Sep 2012 16:39:49 -0400
Subject: [PATCH] Fixes GSA-558 GATK ReadShards don't handle unmapped reads
 correctly.

---
 .../sting/gatk/datasources/reads/ReadShard.java      | 12 ++++++++++--
 1 file changed, 10 insertions(+), 2 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/ReadShard.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/ReadShard.java
index fd1ee9859..def27b20d 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/ReadShard.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/ReadShard.java
@@ -8,7 +8,10 @@ import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
-import java.util.*;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.List;
+import java.util.Map;
 
 /**
  *
@@ -149,7 +152,12 @@ public class ReadShard extends Shard {
                 if ( read.getAlignmentEnd() > stop ) stop = read.getAlignmentEnd();
             }
 
-            return parser.createGenomeLoc(contig, start, stop);
+            assert contig != null;
+
+            if ( contig.equals("*") ) // all reads are unmapped
+                return GenomeLoc.UNMAPPED;
+            else
+                return parser.createGenomeLoc(contig, start, stop);
         }
     }
 }