diff --git a/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java b/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java
index c49f3a28a..b8705bd0c 100644
--- a/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java
+++ b/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java
@@ -52,7 +52,7 @@ import java.util.regex.Pattern;
 public class GenomeLocParser {
     private static Logger logger = Logger.getLogger(GenomeLocParser.class);
 
-    private static final Pattern mPattern = Pattern.compile("([\\w&&[^:]]+):([\\d,]+)?(\\+)?(-)?([\\d,]+)?$");  // matches case 3
+    private static final Pattern mPattern = Pattern.compile("([\\w&&[^:]]+):*([\\d,]+)?([\\+-])?([\\d,]+)?$");  // matches case 3
 
 
     // --------------------------------------------------------------------------------------------------------------
@@ -154,45 +154,39 @@ public class GenomeLocParser {
         
         String contig = null;
         long start = 1;
-        long stop = Integer.MAX_VALUE;
+        long stop = -1;
         boolean bad = false;
 
         Matcher match = mPattern.matcher(str);
-
-        try {
-            if (match.matches()) {
-                contig = match.group(1);
-                if (match.groupCount() == 5) {
-                    start = parsePosition(match.group(2));
-                    if (match.group(3) != null && match.group(3).equals("+") && match.group(5) == null) {
-                        // do nothing
-                    } else if (match.group(5) != null)
-                        stop = parsePosition(match.group(5));
-                    else if (match.group(5) == null && match.group(4) == null && match.group(3) == null)
-                        stop = start;
-                    else
-                        bad = true;
-                } else {
-                    bad = true;
-                }
-            }
+		try {
+			if (match.matches() && match.groupCount() == 4) {
+				if (match.group(1) != null) contig = match.group(1);
+				if (match.group(2) != null) start = parsePosition(match.group(2));
+				if ((match.group(3) != null && match.group(3).equals("+")) ||							// chr:1+
+					(match.group(3) == null && match.group(4) == null && match.group(2) == null)) 		// chr1
+					stop = Integer.MAX_VALUE;
+				else if (match.group(3) != null && match.group(3).equals("-")) 							// chr1:1-1
+					stop = parsePosition(match.group(4));
+				else if (match.group(3) == null && match.group(4) == null)								// chr1:1
+					stop = start;
+				else {
+					bad = true;
+				}
+			}			
+		} catch (Exception e) {
+			bad = true;
         }
 
-        catch (Exception e) {
-            bad = true;
-        }
+        if (bad || start < 0 || stop < 0 || contig == null)
+		    throw new StingException("Invalid Genome Location string: " + str);
+		
+		if (!isContigValid(contig))
+            throw new StingException("Contig " + contig + " does not match any contig in the GATK sequence dictionary derived from the reference.");
 
-        if (bad)
-            throw new StingException("Invalid Genome Location string: "); // + str);
-
-
-        if (stop == Integer.MAX_VALUE && hasKnownContigOrdering())
+		if (stop == Integer.MAX_VALUE && hasKnownContigOrdering())
             // lookup the actually stop position!
             stop = getContigInfo(contig).getSequenceLength();
-
-        if (!isContigValid(contig))
-            throw new MalformedGenomeLocException("Contig " + contig + " does not match any contig in the GATK sequence dictionary derived from the reference.");
-
+        
         GenomeLoc loc = parseGenomeLoc(contig, start, stop);
         return loc;
     }
diff --git a/java/test/org/broadinstitute/sting/utils/GenomeLocParserTest.java b/java/test/org/broadinstitute/sting/utils/GenomeLocParserTest.java
index afe1427dc..abda2d95a 100644
--- a/java/test/org/broadinstitute/sting/utils/GenomeLocParserTest.java
+++ b/java/test/org/broadinstitute/sting/utils/GenomeLocParserTest.java
@@ -7,7 +7,7 @@ import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
 import static org.junit.Assert.assertEquals;
 import org.junit.BeforeClass;
 import org.junit.Test;
-
+import java.util.Arrays;
 
 /**
  * @author aaron
@@ -158,11 +158,43 @@ public class GenomeLocParserTest extends BaseTest {
         assertEquals(1, loc.getStart());
     }
 
-    @Test(expected = RuntimeException.class)
+	@Test
+    public void testGenomeLocParseOnlyChrome() {
+		GenomeLoc loc = GenomeLocParser.parseGenomeLoc("chr1");
+        assertEquals(0, loc.getContigIndex());
+        assertEquals(10, loc.getStop()); // the size
+        assertEquals(1, loc.getStart());
+    }
+	
+	@Test(expected = StingException.class)
+    public void testGenomeLocParseOnlyBadChrome() {
+		GenomeLoc loc = GenomeLocParser.parseGenomeLoc("chr12");
+        assertEquals(0, loc.getContigIndex());
+        assertEquals(10, loc.getStop()); // the size
+        assertEquals(1, loc.getStart());
+    }
+	
+    @Test(expected = StingException.class)
     public void testGenomeLocBad() {
         GenomeLoc loc = GenomeLocParser.parseGenomeLoc("chr1:1-");
         assertEquals(0, loc.getContigIndex());
         assertEquals(10, loc.getStop()); // the size
         assertEquals(1, loc.getStart());
     }
+	
+	@Test(expected = StingException.class)
+    public void testGenomeLocBad2() {
+        GenomeLoc loc = GenomeLocParser.parseGenomeLoc("chr1:1-500-0");
+        assertEquals(0, loc.getContigIndex());
+        assertEquals(10, loc.getStop()); // the size
+        assertEquals(1, loc.getStart());
+    }
+	
+	@Test(expected = StingException.class)
+    public void testGenomeLocBad3() {
+        GenomeLoc loc = GenomeLocParser.parseGenomeLoc("chr1:1--0");
+        assertEquals(0, loc.getContigIndex());
+        assertEquals(10, loc.getStop()); // the size
+        assertEquals(1, loc.getStart());
+    }
 }