diff --git a/protected/java/test/org/broadinstitute/sting/utils/SWPairwiseAlignmentUnitTest.java b/protected/java/test/org/broadinstitute/sting/utils/SWPairwiseAlignmentUnitTest.java
index 6d3c310b7..c55b4147d 100644
--- a/protected/java/test/org/broadinstitute/sting/utils/SWPairwiseAlignmentUnitTest.java
+++ b/protected/java/test/org/broadinstitute/sting/utils/SWPairwiseAlignmentUnitTest.java
@@ -72,22 +72,22 @@ public class SWPairwiseAlignmentUnitTest extends BaseTest {
         Assert.assertEquals(sw.getCigar().toString(), expectedCigar);
     }
 
-    // TODO
-    // TODO
-    // TODO this example demonstrates some kind of failure mode of SW that results in the read not being aligned
-    // TODO to the reference at all.  It has something to do with the specific parameters provided to the
-    // TODO SW code.  With the default parameters the result is the one expected.  With the specified parameters
-    // TODO the code fails
-    // TODO
-    // TODO
-    @Test(enabled = false)
-    public void testOddNoAlignment() {
-        final String reference = "AAAGACTACTG";
-        final String read = "AACGGACACTG";
-        final int expectedStart = 0;
-        final String expectedCigar = "11M";
-        final SWPairwiseAlignment sw = new SWPairwiseAlignment(reference.getBytes(), read.getBytes(), 5.0, -10.0, -22.0, -1.2);
-        sw.printAlignment(reference.getBytes(), read.getBytes());
+    @DataProvider(name = "OddNoAlignment")
+    public Object[][] makeOddNoAlignment() {
+        List<Object[]> tests = new ArrayList<Object[]>();
+
+        final String ref1     = "AAAGACTACTG";
+        final String read1    = "AACGGACACTG";
+        tests.add(new Object[]{ref1, read1, 5.0, -10.0, -22.0, -1.2, 1, "2M2I3M1D4M"});
+        tests.add(new Object[]{ref1, read1, 20.0, -5.0, -30.0, -2.2, 0, "11M"});
+
+        return tests.toArray(new Object[][]{});
+    }
+
+    @Test(dataProvider = "OddNoAlignment", enabled = true)
+    public void testOddNoAlignment(final String reference, final String read, final double match, final double mismatch, final double gap, final double gap_extend,
+                                   final int expectedStart, final String expectedCigar) {
+        final SWPairwiseAlignment sw = new SWPairwiseAlignment(reference.getBytes(), read.getBytes(), match, mismatch, gap, gap_extend);
         Assert.assertEquals(sw.getAlignmentStart2wrt1(), expectedStart);
         Assert.assertEquals(sw.getCigar().toString(), expectedCigar);
     }
diff --git a/public/java/src/org/broadinstitute/sting/utils/SWPairwiseAlignment.java b/public/java/src/org/broadinstitute/sting/utils/SWPairwiseAlignment.java
index e501cf40a..6c8beb32d 100644
--- a/public/java/src/org/broadinstitute/sting/utils/SWPairwiseAlignment.java
+++ b/public/java/src/org/broadinstitute/sting/utils/SWPairwiseAlignment.java
@@ -205,10 +205,9 @@ public final class SWPairwiseAlignment {
 
     private void calculateCigar(int n, int m, double [] sw, int [] btrack) {
         // p holds the position we start backtracking from; we will be assembling a cigar in the backwards order
-        //PrimitivePair.Int p = new PrimitivePair.Int();
         int p1 = 0, p2 = 0;
 
-        double maxscore = 0.0;
+        double maxscore = Double.NEGATIVE_INFINITY; // sw scores are allowed to be negative
         int segment_length = 0; // length of the segment (continuous matches, insertions or deletions)
 
         // look for largest score. we use >= combined with the traversal direction
@@ -259,7 +258,7 @@ public final class SWPairwiseAlignment {
 
             // move to next best location in the sw matrix:
             switch( new_state ) {
-                case MSTATE: data_offset -= (m+2); p1--; p2--; break; // move back along the diag in th esw matrix
+                case MSTATE: data_offset -= (m+2); p1--; p2--; break; // move back along the diag in the sw matrix
                 case ISTATE: data_offset -= step_length; p2 -= step_length; break; // move left
                 case DSTATE: data_offset -= (m+1)*step_length; p1 -= step_length; break; // move up
             }
diff --git a/public/java/test/org/broadinstitute/sting/utils/haplotypeBAMWriter/HaplotypeBAMWriterUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/haplotypeBAMWriter/HaplotypeBAMWriterUnitTest.java
index 89d87a3c3..db16582b8 100644
--- a/public/java/test/org/broadinstitute/sting/utils/haplotypeBAMWriter/HaplotypeBAMWriterUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/utils/haplotypeBAMWriter/HaplotypeBAMWriterUnitTest.java
@@ -127,12 +127,6 @@ public class HaplotypeBAMWriterUnitTest extends BaseTest {
             }
         }
 
-        // test that reads without a good alignment to hap get excluded
-        {
-            final GATKSAMRecord read = makeRead("NNNNN");
-            tests.add(new Object[]{read, allM, 10, -1, null});
-        }
-
         // example case of bad alignment because SW doesn't necessarily left-align indels
         {
             final String hap = "ACTGTGGGTTCCTCTTATTTTATTTCTACATCAATGTTCATATTTAACTTATTATTTTATCTTATTTTTAAATTTCTTTTATGTTGAGCCTTGATGAAAGCCATAGGTTCTCTCATATAATTGTATGTGTATGTATGTATATGTACATAATATATACATATATGTATATGTATGTGTATGTACATAATATATACGTATATGTATGTGTATGTACATAATATATACGTATATGTATGTGTATGTACATAATATATACGTATATGTATGTGTATGTACATAATATATACGTATATGTATGTGTATGTACATAATATATACGTATATGTATGTGTATGTGTATTACATAATATATACATATATGTATATATTATGTATATGTACATAATATATACATATATG";