- Fix our private repository of bwa reference support files.

- Update the test to point to our repository.
- Update the md5 to reflect new Picard tag ordering.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4247 348d0f76-0448-11de-a6fe-93d51630548a

java/test/org/broadinstitute/sting/alignment/AlignerIntegrationTest.java

@@ -14,9 +14,9 @@ import java.util.Arrays;
 public class AlignerIntegrationTest extends WalkerTest {
     @Test
     public void testBasicAlignment() {
-        String md5 = "c6d95d8ae707e78fefdaa7375f130995";
+        String md5 = "34eb4323742999d6d250a0aaa803c6d5";
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
-                        "-R " + b36KGReference +
+                "-R /humgen/gsa-scr1/GATK_Data/bwa/human_b36_both.fasta" +
                         " -T Align" +
                         " -I " + validationDataLocation + "NA12878_Pilot1_20.trimmed.unmapped.bam" +
                         " -ob %s",