Closing GSA-287:LocusReferenceView doesn't do very well in the case where contigs land off the end of the reference

-- Confirmed that reads spanning off the end of the chromosome don't cause an exception by adding integration test for a single read that starts 7 bases from the end of chromosome 1 and spans 90 bases or so off.  Added pileup integration test to ensure this behavior continues to work

public/java/test/org/broadinstitute/sting/gatk/walkers/PileupWalkerIntegrationTest.java

@@ -5,15 +5,7 @@ import org.testng.annotations.Test;
 
 import java.util.Arrays;
 
-/**
- * Created by IntelliJ IDEA.
- * User: chartl
- * Date: Dec 1, 2009
- * Time: 9:03:34 AM
- * To change this template use File | Settings | File Templates.
- */
 public class PileupWalkerIntegrationTest extends WalkerTest {
-
     @Test
     public void testGnarleyFHSPileup() {
         String gatk_args = "-T Pileup -I " + validationDataLocation + "FHS_Pileup_Test.bam "
@@ -23,4 +15,14 @@ public class PileupWalkerIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(gatk_args, 1, Arrays.asList(expected_md5));
         executeTest("Testing the standard (no-indel) pileup on three merged FHS pools with 27 deletions in 969 bases", spec);
     }
+
+    @Test
+    public void testSingleReadAligningOffChromosome1() {
+        String gatk_args = "-T Pileup "
+                + " -I " + privateTestDir + "readOffb37contig1.bam"
+                + " -R " + b37KGReference
+                + " -o %s";
+        WalkerTestSpec spec = new WalkerTestSpec(gatk_args, 1, Arrays.asList("4a45fe1f85aaa8c4158782f2b6dee2bd"));
+        executeTest("Testing single read spanning off chromosome 1", spec);
+    }
 }