Misc changes and cleanup from all previous commits in this push.

1. By default, do not include the UG CEU callset for assessment.
2. Updated md5s that are different now with all the HC changes.

protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest.java

@@ -64,7 +64,7 @@ public class HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest extends Wa
 
     @Test
     public void testHaplotypeCallerMultiSampleComplex1() {
-        HCTestComplexVariants(privateTestDir + "AFR.complex.variants.bam", "", "8d7728909b1b8eb3f30f2f1583f054a8");
+        HCTestComplexVariants(privateTestDir + "AFR.complex.variants.bam", "", "d21f15a5809fe5259af41ae6774af6f1");
     }
 
     private void HCTestSymbolicVariants(String bam, String args, String md5) {
@@ -88,12 +88,12 @@ public class HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest extends Wa
     @Test
     public void testHaplotypeCallerMultiSampleGGAComplex() {
         HCTestComplexGGA(NA12878_CHR20_BAM, "-L 20:119673-119823 -L 20:121408-121538",
-                "db71826dc798ff1cdf0c5d05b0ede976");
+                "d4a0797c2fd4c103bf9a137633376156");
     }
 
     @Test
     public void testHaplotypeCallerMultiSampleGGAMultiAllelic() {
         HCTestComplexGGA(NA12878_CHR20_BAM, "-L 20:133041-133161 -L 20:300207-300337",
-                "42831d5463552911b7da9de0b4a27289");
+                "a9872228d0275a30f5a1f7e070a9c9f4");
     }
 }

protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java

@@ -78,12 +78,12 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
 
     @Test
     public void testHaplotypeCallerMultiSample() {
-        HCTest(CEUTRIO_BAM, "", "1b15e4647013ab2c3ce7073c420d8640");
+        HCTest(CEUTRIO_BAM, "", "e9167a1bfc0fc276586788d1ce1be408");
     }
 
     @Test
     public void testHaplotypeCallerSingleSample() {
-        HCTest(NA12878_BAM, "", "423be27dc2cf7fd10baf465cf93e18e2");
+        HCTest(NA12878_BAM, "", "b1d46afb9659ac3b92a3d131b58924ef");
     }
 
     @Test(enabled = false) // can't annotate the rsID's yet
@@ -94,7 +94,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
     @Test
     public void testHaplotypeCallerMultiSampleGGA() {
         HCTest(CEUTRIO_BAM, "--max_alternate_alleles 3 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles " + validationDataLocation + "combined.phase1.chr20.raw.indels.sites.vcf",
-                "a28e6f14e28708283d61c1e423bbdcb1");
+                "d83856b8136776bd731a8037c16b71fa");
     }
 
     @Test
@@ -110,7 +110,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
 
     @Test
     public void testHaplotypeCallerSingleSampleIndelQualityScores() {
-        HCTestIndelQualityScores(NA12878_RECALIBRATED_BAM, "", "8344d86751b707c53b296c297eba4bfa");
+        HCTestIndelQualityScores(NA12878_RECALIBRATED_BAM, "", "70c4476816f5d35c9978c378dbeac09b");
     }
 
     private void HCTestNearbySmallIntervals(String bam, String args, String md5) {
@@ -147,7 +147,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
 
     @Test
     public void testHaplotypeCallerNearbySmallIntervals() {
-        HCTestNearbySmallIntervals(NA12878_BAM, "", "dea98f257d39fa1447a12c36a6bbf4a3");
+        HCTestNearbySmallIntervals(NA12878_BAM, "", "947aae309ecab7cd3f17ff9810884924");
     }
 
     // This problem bam came from a user on the forum and it spotted a problem where the ReadClipper
@@ -157,14 +157,14 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
     @Test
     public void HCTestProblematicReadsModifiedInActiveRegions() {
         final String base = String.format("-T HaplotypeCaller --disableDithering -R %s -I %s", REF, privateTestDir + "haplotype-problem-4.bam") + " --no_cmdline_in_header -o %s -minPruning 3 -L 4:49139026-49139965";
-        final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("7cd1c5e2642ae8ddf38932aba1f51d69"));
+        final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("0689d2c202849fd05617648eaf429b9a"));
         executeTest("HCTestProblematicReadsModifiedInActiveRegions: ", spec);
     }
 
     @Test
     public void HCTestStructuralIndels() {
         final String base = String.format("-T HaplotypeCaller --disableDithering -R %s -I %s", REF, privateTestDir + "AFR.structural.indels.bam") + " --no_cmdline_in_header -o %s -minPruning 6 -L 20:8187565-8187800 -L 20:18670537-18670730";
-        final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("ee55ff4c6ec1bbef88e21cc0f45d4c47"));
+        final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("91717e5e271742c2c9b67223e58f1320"));
         executeTest("HCTestStructuralIndels: ", spec);
     }
 
@@ -186,7 +186,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
     public void HCTestReducedBam() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-T HaplotypeCaller --disableDithering -R " + b37KGReference + " --no_cmdline_in_header -I " + privateTestDir + "bamExample.ReducedRead.ADAnnotation.bam -o %s -L 1:67,225,396-67,288,518", 1,
-                Arrays.asList("4886a98bf699f4e7f4491160749ada6a"));
+                Arrays.asList("0124c4923d96ec0f8222b596dd4ef534"));
         executeTest("HC calling on a ReducedRead BAM", spec);
     }
 
@@ -194,7 +194,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
     public void testReducedBamWithReadsNotFullySpanningDeletion() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-T HaplotypeCaller --disableDithering -R " + b37KGReference + " --no_cmdline_in_header -I " + privateTestDir + "reduced.readNotFullySpanningDeletion.bam -o %s -L 1:167871297", 1,
-                Arrays.asList("86bdd07a3ac4f6ce239c30efea8bf5ba"));
+                Arrays.asList("0e020dcfdf249225714f5cd86ed3869f"));
         executeTest("test calling on a ReducedRead BAM where the reads do not fully span a deletion", spec);
     }
 
@@ -208,7 +208,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
     public void HCTestDBSNPAnnotationWGS() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-T HaplotypeCaller --disableDithering -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_PCRFREE + " -o %s -L 20:10,000,000-10,100,000 -D " + b37dbSNP132, 1,
-                Arrays.asList("7b23a288a31cafca3946f14f2381e7cb"));
+                Arrays.asList("446a786bb539f3ec2084dd75167568aa"));
         executeTest("HC calling with dbSNP ID annotation on WGS intervals", spec);
     }
 

protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerParallelIntegrationTest.java

@@ -61,7 +61,7 @@ public class HaplotypeCallerParallelIntegrationTest extends WalkerTest {
         List<Object[]> tests = new ArrayList<Object[]>();
 
         for ( final int nct : Arrays.asList(1, 2, 4) ) {
-            tests.add(new Object[]{nct, "c277fd65365d59b734260dd8423313bb"});
+            tests.add(new Object[]{nct, "ef42a438b82681d1c0f921c57e16ff12"});
         }
 
         return tests.toArray(new Object[][]{});