Fixed Integration Tests to output VCF files with -NO_HEADER

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4548 348d0f76-0448-11de-a6fe-93d51630548a

java/test/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingPolymorphismsIntegrationTest.java

@@ -12,7 +12,8 @@ public class MergeSegregatingPolymorphismsIntegrationTest extends WalkerTest {
                 " -R " + reference +
                 " -B:variant,VCF " + validationDataLocation + VCF +
                 " --maxGenomicDistanceForMNP " + maxDistMNP +
-                " -o %s";
+                " -o %s" +
+                " -NO_HEADER";
     }
 
 
@@ -22,7 +23,7 @@ public class MergeSegregatingPolymorphismsIntegrationTest extends WalkerTest {
                 baseTestString(hg18Reference, "merging_test_chr20_556259_756570.vcf", 1)
                         + " -L chr20:556259-756570",
                 1,
-                Arrays.asList("f0e9796bc9866201aed0e97d76ed4a84"));
+                Arrays.asList("19d0b2361367024bb9a83b9c15ef2453"));
         executeTest("Merge MNP het sites within genomic distance of 1 [TEST ONE]", spec);
     }
 
@@ -32,7 +33,7 @@ public class MergeSegregatingPolymorphismsIntegrationTest extends WalkerTest {
                 baseTestString(hg18Reference, "merging_test_chr20_556259_756570.vcf", 10)
                         + " -L chr20:556259-756570",
                 1,
-                Arrays.asList("ab2b05dc6e7e4464e8f9e08d1d02f8ae"));
+                Arrays.asList("f25a6403579dab1395773b3ba365c327"));
         executeTest("Merge MNP het sites within genomic distance of 10 [TEST TWO]", spec);
     }
 
@@ -42,7 +43,7 @@ public class MergeSegregatingPolymorphismsIntegrationTest extends WalkerTest {
                 baseTestString(hg18Reference, "merging_test_chr20_556259_756570.vcf", 100)
                         + " -L chr20:556259-756570",
                 1,
-                Arrays.asList("d446a0076f9d3d13c128bc8402b087a4"));
+                Arrays.asList("a064955ffeea7fc4e09512f3e9cdbb9e"));
         executeTest("Merge MNP het sites within genomic distance of 100 [TEST THREE]", spec);
     }
 

java/test/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingIntegrationTest.java

@@ -15,7 +15,8 @@ public class ReadBackedPhasingIntegrationTest extends WalkerTest {
                 " --cacheWindowSize " + cacheWindowSize +
                 " --maxPhaseSites " + maxPhaseSites +
                 " --phaseQualityThresh " + phaseQualityThresh +
-                " -o %s";
+                " -o %s" +
+                " -NO_HEADER";
     }
 
 
@@ -25,7 +26,7 @@ public class ReadBackedPhasingIntegrationTest extends WalkerTest {
                 baseTestString(hg18Reference, "phasing_test_chr20_332341_1332503.bam", "phasing_test_chr20_332341_1332503.vcf", 20000, 10, 10)
                         + " -L chr20:332341-382503",
                 1,
-                Arrays.asList("2612b279cf651fba2b50c35373311642"));
+                Arrays.asList("cfa2a436008c0090ec03935b6efc6bb3"));
         executeTest("MAX 10 het sites [TEST ONE]; require PQ >= 10", spec);
     }
 
@@ -35,7 +36,7 @@ public class ReadBackedPhasingIntegrationTest extends WalkerTest {
                 baseTestString(hg18Reference, "phasing_test_chr20_332341_1332503.bam", "phasing_test_chr20_332341_1332503.vcf", 20000, 10, 10)
                         + " -L chr20:1232503-1332503",
                 1,
-                Arrays.asList("29bcc72f64088b39df20c0d1bfc9f5f7"));
+                Arrays.asList("60da5d2da66ae51bf42ad2b1c9505739"));
         executeTest("MAX 10 het sites [TEST TWO]; require PQ >= 10", spec);
     }
 
@@ -45,7 +46,7 @@ public class ReadBackedPhasingIntegrationTest extends WalkerTest {
                 baseTestString(hg18Reference, "phasing_test_chr20_332341_1332503.bam", "phasing_test_chr20_332341_1332503.vcf", 20000, 2, 30)
                         + " -L chr20:332341-382503",
                 1,
-                Arrays.asList("381eeedba5977edabec1a285b77df4a1"));
+                Arrays.asList("26befb1f5b11117f0ccb326fd05f9be7"));
         executeTest("MAX 2 het sites [TEST THREE]; require PQ >= 30", spec);
     }
 
@@ -55,7 +56,7 @@ public class ReadBackedPhasingIntegrationTest extends WalkerTest {
                 baseTestString(hg18Reference, "phasing_test_chr20_332341_1332503.bam", "phasing_test_chr20_332341_1332503.vcf", 20000, 5, 100)
                         + " -L chr20:332341-382503",
                 1,
-                Arrays.asList("513447f80b71a836bc99f569abeaa5d7"));
+                Arrays.asList("51ce38de72cf4163a272f00ba34832ff"));
         executeTest("MAX 5 het sites [TEST FOUR]; require PQ >= 100", spec);
     }
 
@@ -65,7 +66,7 @@ public class ReadBackedPhasingIntegrationTest extends WalkerTest {
                 baseTestString(hg18Reference, "phasing_test_chr20_332341_1332503.bam", "phasing_test_chr20_332341_1332503.vcf", 1000, 7, 10)
                         + " -L chr20:332341-482503",
                 1,
-                Arrays.asList("e10e370b0f2823cfc7efdac590abf93b"));
+                Arrays.asList("252964ea02d83ccf1e229e01fbfaaefa"));
         executeTest("MAX 7 het sites [TEST FIVE]; require PQ >= 10; cacheWindow = 1000", spec);
     }
 
@@ -75,7 +76,7 @@ public class ReadBackedPhasingIntegrationTest extends WalkerTest {
                 baseTestString(hg18Reference, "phasing_test_chr20_332341_1332503.bam", "phasing_test_chr20_332341_1332503.vcf", 20000, 10, 10)
                         + " -L chr20:652810-681757",
                 1,
-                Arrays.asList("adb46e988b27e13907d197bd058468bf"));
+                Arrays.asList("6983a121363ef4131b217805ae558313"));
         executeTest("MAX 10 het sites [TEST SIX]; require PQ >= 10; cacheWindow = 20000; has inconsistent sites", spec);
     }