diff --git a/public/java/src/org/broadinstitute/sting/gatk/iterators/VerifyingSamIterator.java b/public/java/src/org/broadinstitute/sting/gatk/iterators/VerifyingSamIterator.java
index f33dd414b..2763bca7c 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/iterators/VerifyingSamIterator.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/iterators/VerifyingSamIterator.java
@@ -48,9 +48,7 @@ public class VerifyingSamIterator implements StingSAMIterator {
             if(cur.getReferenceIndex() == SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX || cur.getAlignmentStart() == SAMRecord.NO_ALIGNMENT_START)
                 throw new UserException.MalformedBAM(last,String.format("read %s has inconsistent mapping information.",cur.format()));
 
-            GenomeLoc lastLoc = genomeLocParser.createGenomeLoc( last );
-            GenomeLoc curLoc = genomeLocParser.createGenomeLoc( cur );
-            return curLoc.compareTo(lastLoc) == -1;
+            return last.getAlignmentStart() > cur.getAlignmentStart();
         }
     }
 
diff --git a/public/java/src/org/broadinstitute/sting/utils/GenomeLoc.java b/public/java/src/org/broadinstitute/sting/utils/GenomeLoc.java
index 0b35dd599..6df9c9f1d 100644
--- a/public/java/src/org/broadinstitute/sting/utils/GenomeLoc.java
+++ b/public/java/src/org/broadinstitute/sting/utils/GenomeLoc.java
@@ -427,7 +427,10 @@ public class GenomeLoc implements Comparable<GenomeLoc>, Serializable, HasGenome
                 result = cmpContig;
             } else {
                 if ( this.getStart() < that.getStart() ) result = -1;
-                if ( this.getStart() > that.getStart() ) result = 1;
+                else if ( this.getStart() > that.getStart() ) result = 1;
+                // these have the same start, so check the ends
+                else if ( this.getStop() < that.getStop() ) result = -1;
+                else if ( this.getStop() > that.getStop() ) result = 1;
             }
         }
 
diff --git a/public/java/test/org/broadinstitute/sting/utils/GenomeLocUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/GenomeLocUnitTest.java
index 49778a4d8..122e0265f 100644
--- a/public/java/test/org/broadinstitute/sting/utils/GenomeLocUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/utils/GenomeLocUnitTest.java
@@ -16,6 +16,7 @@ import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
 
 import java.io.File;
 import java.io.FileNotFoundException;
+import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collections;
 import java.util.List;
@@ -211,4 +212,59 @@ public class GenomeLocUnitTest extends BaseTest {
             Assert.assertEquals(cfg.gl1.reciprocialOverlapFraction(cfg.gl2), cfg.overlapFraction);
         }
     }
+
+    // -------------------------------------------------------------------------------------
+    //
+    // testing comparison, hashcode, and equals
+    //
+    // -------------------------------------------------------------------------------------
+
+    @DataProvider(name = "GenomeLocComparisons")
+    public Object[][] createGenomeLocComparisons() {
+        List<Object[]> tests = new ArrayList<Object[]>();
+
+        final int start = 10;
+        for ( int stop = start; stop < start + 3; stop++ ) {
+            final GenomeLoc g1 = genomeLocParser.createGenomeLoc("chr2", start, stop);
+            for ( final String contig : Arrays.asList("chr1", "chr2", "chr3")) {
+                for ( int start2 = start - 1; start2 <= stop + 1; start2++ ) {
+                    for ( int stop2 = start2; stop2 < stop + 2; stop2++ ) {
+                        final GenomeLoc g2 = genomeLocParser.createGenomeLoc(contig, start2, stop2);
+
+                        ComparisonResult cmp = ComparisonResult.EQUALS;
+                        if ( contig.equals("chr3") ) cmp = ComparisonResult.LESS_THAN;
+                        else if ( contig.equals("chr1") ) cmp = ComparisonResult.GREATER_THAN;
+                        else if ( start < start2 ) cmp = ComparisonResult.LESS_THAN;
+                        else if ( start > start2 ) cmp = ComparisonResult.GREATER_THAN;
+                        else if ( stop < stop2 ) cmp = ComparisonResult.LESS_THAN;
+                        else if ( stop > stop2 ) cmp = ComparisonResult.GREATER_THAN;
+
+                        tests.add(new Object[]{g1, g2, cmp});
+                    }
+                }
+            }
+        }
+
+        return tests.toArray(new Object[][]{});
+    }
+
+    private enum ComparisonResult {
+        LESS_THAN(-1),
+        EQUALS(0),
+        GREATER_THAN(1);
+
+        final int cmp;
+
+        private ComparisonResult(int cmp) {
+            this.cmp = cmp;
+        }
+    }
+
+    @Test(dataProvider = "GenomeLocComparisons")
+    public void testGenomeLocComparisons(GenomeLoc g1, GenomeLoc g2, ComparisonResult expected) {
+        Assert.assertEquals(g1.compareTo(g2), expected.cmp, "Comparing genome locs failed");
+        Assert.assertEquals(g1.equals(g2), expected == ComparisonResult.EQUALS);
+        if ( expected == ComparisonResult.EQUALS )
+            Assert.assertEquals(g1.hashCode(), g2.hashCode(), "Equal genome locs don't have the same hash code");
+    }
 }