Update MD5s due to new QualityUtils calculations

-- Increase the allowed runtime of one UG integration test
-- The GGA indels mode runs two UG commands, and was barely under the 10 minute limit before.  Some updates can push this right over the edge.  Increased limit
-- CalibrateGenotypeLikelihoods runs on a small data set now, so it's faster
-- Updating MD5s due to more correct quality utils.  DuplicatesWalkers quality estimates have changed.  One UG test has different FS and rank sum tests because the conversion to phred scores are slightly (second decimal place) different

protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java

@@ -387,7 +387,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
         executeTest("test MultiSample Pilot2 indels with alleles passed in and emitting all sites", spec);
     }
 
-    @Test
+    @Test(timeOut = 20*1000*60) // this guy can take a long time because it's two steps, so give it 12 minutes
     public void testMultiSampleIndels1() {
         // since we're going to test the MD5s with GGA only do one here
         WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
@@ -397,7 +397,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
 
         WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
                 baseCommandIndels + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + result.get(0).getAbsolutePath() + " -I " + validationDataLocation +
-                        "low_coverage_CEU.chr1.10k-11k.bam -o %s -L 1:10450700-10551000", 1,
+                        "low_coverage_CEU.chr1.10k-11k.bam -o %s -L " + result.get(0).getAbsolutePath(), 1,
                 Arrays.asList("08b3a85be00c8f6a4fefd3c671463ecf"));
         executeTest("test MultiSample Pilot1 CEU indels using GENOTYPE_GIVEN_ALLELES", spec2);
     }