Remove the extra trailing tab at the end of the VCF ## header line. Unfortunately, this meant updating every freaking integration test.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4806 348d0f76-0448-11de-a6fe-93d51630548a

java/test/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextIntegrationTest.java

@@ -49,7 +49,7 @@ public class VariantContextIntegrationTest extends WalkerTest {
 
         WalkerTestSpec spec = new WalkerTestSpec( cmdRoot + " -NO_HEADER -B:vcf,VCF " + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.500.vcf -L 1:1-1000000 -o %s --outputVCF %s",
                 2, // just one output file
-                Arrays.asList("e3c35d0c4b5d4935c84a270f9df0951f", "f4db5f7346792b1155693722bc190f63"));
+                Arrays.asList("e3c35d0c4b5d4935c84a270f9df0951f", "e6673737acbb6bfabfcd92c4b2268241"));
          executeTest("testToVCF", spec);
     }
 

java/test/org/broadinstitute/sting/gatk/walkers/VariantsToVCFIntegrationTest.java

@@ -20,7 +20,7 @@ public class VariantsToVCFIntegrationTest extends WalkerTest {
     @Test
     public void testVariantsToVCFUsingGeliInput() {
         List<String> md5 = new ArrayList<String>();
-        md5.add("b4f98bee580508637c88c421064936fc");
+        md5.add("bd15d98adc76b5798e3bbeff3f936feb");
 
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-R " + b36KGReference +
@@ -38,7 +38,7 @@ public class VariantsToVCFIntegrationTest extends WalkerTest {
     @Test
     public void testGenotypesToVCFUsingGeliInput() {
         List<String> md5 = new ArrayList<String>();
-        md5.add("0f310612c8609cba3dcf9cc97b2c1195");
+        md5.add("acd15d3f85bff5b545bc353e0e23cc6e");
 
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-R " + b36KGReference +
@@ -56,7 +56,7 @@ public class VariantsToVCFIntegrationTest extends WalkerTest {
     @Test
     public void testGenotypesToVCFUsingHapMapInput() {
         List<String> md5 = new ArrayList<String>();
-        md5.add("28728ad3a6af20a1e1aaaf185ffbff2b");
+        md5.add("946d53387d8048915f880101169620b4");
 
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-R " + b36KGReference +
@@ -73,7 +73,7 @@ public class VariantsToVCFIntegrationTest extends WalkerTest {
     @Test
     public void testGenotypesToVCFUsingVCFInput() {
         List<String> md5 = new ArrayList<String>();
-        md5.add("19371e6cfea5f29fb75d5a2be7fccd34");
+        md5.add("d8316fc1b9d8e954a58940354119a32e");
 
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-R " + b36KGReference +

java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java

@@ -15,7 +15,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testHasAnnotsNotAsking1() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -B:variant,VCF " + validationDataLocation + "vcfexample2.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("30ca0a572407f8f8d69ce83800db35ea"));
+                Arrays.asList("4cc077eb3d343e6b7ba12bff86ebe347"));
         executeTest("test file has annotations, not asking for annotations, #1", spec);
     }
 
@@ -23,7 +23,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testHasAnnotsNotAsking2() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -B:variant,VCF " + validationDataLocation + "vcfexample3.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1,
-                Arrays.asList("14e546fa7e819faeda3227c842fa92e7"));
+                Arrays.asList("1de8e943fbf55246ebd19efa32f22a58"));
         executeTest("test file has annotations, not asking for annotations, #2", spec);
     }
 
@@ -31,7 +31,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testHasAnnotsAsking1() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -G \"Standard\" -B:variant,VCF " + validationDataLocation + "vcfexample2.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("a7680de85e0b118415bcd032b3b49688"));
+                Arrays.asList("7ffa7d0ae9e4265eced1f793be9eba11"));
         executeTest("test file has annotations, asking for annotations, #1", spec);
     }
 
@@ -39,7 +39,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testHasAnnotsAsking2() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -G \"Standard\" -B:variant,VCF " + validationDataLocation + "vcfexample3.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1,
-                Arrays.asList("dcc7c522c4178b4fd9a0e5439bcdaebc"));
+                Arrays.asList("063235b9a98137902a77b6efbaffc618"));
         executeTest("test file has annotations, asking for annotations, #2", spec);
     }
 
@@ -47,7 +47,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testNoAnnotsNotAsking1() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -B:variant,VCF " + validationDataLocation + "vcfexample2empty.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("63fcabe0198b88a87ea645ffbf25165f"));
+                Arrays.asList("4b48e7d095ef73e3151542ea976ecd89"));
         executeTest("test file doesn't have annotations, not asking for annotations, #1", spec);
     }
 
@@ -55,7 +55,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testNoAnnotsNotAsking2() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -B:variant,VCF " + validationDataLocation + "vcfexample3empty.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1,
-                Arrays.asList("20b946924fffdf6700cd029424fb72b5"));
+                Arrays.asList("28dfbfd178aca071b948cd3dc2365357"));
         executeTest("test file doesn't have annotations, not asking for annotations, #2", spec);
     }
 
@@ -63,7 +63,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testNoAnnotsAsking1() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -G \"Standard\" -B:variant,VCF " + validationDataLocation + "vcfexample2empty.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("207a5af3647f1f0769fdd4dd6bd0c132"));
+                Arrays.asList("a20994036d2deeeff377a89d9b93a0c6"));
         executeTest("test file doesn't have annotations, asking for annotations, #1", spec);
     }
 
@@ -71,7 +71,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testNoAnnotsAsking2() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -G \"Standard\" -B:variant,VCF " + validationDataLocation + "vcfexample3empty.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1,
-                Arrays.asList("120fc0d4af1d370f1b306700258464b9"));
+                Arrays.asList("3677fd14ef2975afdca559a871f57a33"));
         executeTest("test file doesn't have annotations, asking for annotations, #2", spec);
     }
 
@@ -79,7 +79,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testOverwritingHeader() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -G \"Standard\" -B:variant,VCF " + validationDataLocation + "vcfexample4.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,001,292", 1,
-                Arrays.asList("10c31f8ab903843538a7604ed1e5405c"));
+                Arrays.asList("d4d33310e0280a9329efb8c6b39f7661"));
         executeTest("test overwriting header", spec);
     }
 
@@ -87,7 +87,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testNoReads() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -G \"Standard\" -B:variant,VCF " + validationDataLocation + "vcfexample3empty.vcf -BTI variant", 1,
-                Arrays.asList("a6ec667a656e7ba368de9dbae781eef3"));
+                Arrays.asList("04f677a7bed221037e8426c729641b65"));
         executeTest("not passing it any reads", spec);
     }
 
@@ -95,7 +95,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testDBTagWithDbsnp() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -D " + GATKDataLocation + "dbsnp_129_b36.rod -G \"Standard\" -B:variant,VCF " + validationDataLocation + "vcfexample3empty.vcf -BTI variant", 1,
-                Arrays.asList("8b4c309fe4900b5c8ae720c649715c7d"));
+                Arrays.asList("9180942ec0b93b93eb1c7a1b311e291b"));
         executeTest("getting DB tag with dbSNP", spec);
     }
 
@@ -103,7 +103,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testDBTagWithHapMap() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -B:compH3,VCF " + validationDataLocation + "fakeHM3.vcf -G \"Standard\" -B:variant,VCF " + validationDataLocation + "vcfexample3empty.vcf -BTI variant", 1,
-                Arrays.asList("ff6b3468f21b262de671e823349cbb3c"));
+                Arrays.asList("2ade14115912061c39bcbfcd788d5f6a"));
         executeTest("getting DB tag with HM3", spec);
     }
 
@@ -111,7 +111,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testUsingExpression() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -B:foo,VCF " + validationDataLocation + "targetAnnotations.vcf -G \"Standard\" -B:variant,VCF " + validationDataLocation + "vcfexample3empty.vcf -E foo.AF -BTI variant", 1,
-                Arrays.asList("9362ae272d5e2ff2cfe7db307a324b6d"));
+                Arrays.asList("6e87613ce2be9f97581396805c6f9173"));
         executeTest("using expression", spec);
     }
 

java/test/org/broadinstitute/sting/gatk/walkers/beagle/BeagleIntegrationTest.java

@@ -41,7 +41,7 @@ public class BeagleIntegrationTest extends WalkerTest {
                         "-B:beagleR2,BEAGLE " + beagleValidationDataLocation + "inttestbgl.r2 " +
                         "-B:beagleProbs,BEAGLE " + beagleValidationDataLocation + "inttestbgl.gprobs " +
                         "-B:beaglePhased,BEAGLE " + beagleValidationDataLocation + "inttestbgl.phased " +
-                        "-o %s -NO_HEADER", 1, Arrays.asList("e746763ade40edea56a051dc1dfd6165"));
+                        "-o %s -NO_HEADER", 1, Arrays.asList("6bccee48ad2f06ba5a8c774fed444478"));
         executeTest("test BeagleOutputToVCF", spec);
     }
    
@@ -60,7 +60,7 @@ public class BeagleIntegrationTest extends WalkerTest {
                 "-T ProduceBeagleInput -B:variant,VCF /humgen/gsa-hpprojects/GATK/data/Validation_Data/NA12878_HSQ_chr22_14-16m.vcf "+
                         "-B:validation,VCF /humgen/gsa-hpprojects/GATK/data/Validation_Data/NA12878_OMNI_chr22_14-16m.vcf "+
                         "-L 22:14000000-16000000 -o %s -bvcf %s -bs 0.8 -valp 0.98 -R /humgen/1kg/reference/human_g1k_v37.fasta -NO_HEADER ",2,
-                Arrays.asList("44d28b6b092d5f4c0ae59af442612ea3","481c58f8309916184a33ab1835e5cc48"));
+                Arrays.asList("44d28b6b092d5f4c0ae59af442612ea3","223fb977e8db567dcaf632c6ee51f294"));
         executeTest("test BeagleInputWithBootstrap",spec);
     }
 
@@ -72,7 +72,7 @@ public class BeagleIntegrationTest extends WalkerTest {
                 "-B:beagleR2,beagle /humgen/gsa-hpprojects/GATK/data/Validation_Data/EUR_beagle_in_test.r2 "+
                 "-B:beagleProbs,beagle /humgen/gsa-hpprojects/GATK/data/Validation_Data/EUR_beagle_in_test.gprobs.bgl "+
                 "-B:beaglePhased,beagle /humgen/gsa-hpprojects/GATK/data/Validation_Data/EUR_beagle_in_test.phased.bgl "+
-                "-L 20:1-70000 -o %s -NO_HEADER ",1,Arrays.asList("71e7ac1118ecef82a7de0b6543973a81"));
+                "-L 20:1-70000 -o %s -NO_HEADER ",1,Arrays.asList("e09d2cba18ab5c571e563085296cd514"));
 
         executeTest("testBeagleChangesSitesToRef",spec);
     }

java/test/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationIntegrationTest.java

@@ -16,7 +16,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
     public void testNoAction() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -B:variant,VCF " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("1faa4662400a1128b94d5f93d46eee1d"));
+                Arrays.asList("c9f49679f600c52e624c74cf65fd0a39"));
         executeTest("test no action", spec);
     }
 
@@ -24,7 +24,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
     public void testClusteredSnps() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -window 10 -B:variant,VCF " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("f09454e99562d839e5117f992f4eebef"));
+                Arrays.asList("559021b518503df2ca1cc5cd18642248"));
         executeTest("test clustered SNPs", spec);
     }
 
@@ -32,7 +32,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
     public void testMask() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -mask foo -B:mask,VCF " + validationDataLocation + "vcfexample2.vcf -B:variant,VCF " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("4b1d370e60c2bc0c763886c3adff473a"));
+                Arrays.asList("467480f5c2e840b68d8ef591f1c562c7"));
         executeTest("test mask", spec);
     }
 
@@ -40,7 +40,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
     public void testFilter1() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -filter 'DoC < 20 || FisherStrand > 20.0' -filterName foo -B:variant,VCF " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("3ea5495c6eace03971cb4c6cd1f84af4"));
+                Arrays.asList("b48b5965d05f2d0f02c6f7261e67e9d2"));
         executeTest("test filter #1", spec);
     }
 
@@ -48,7 +48,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
     public void testFilter2() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -filter 'AlleleBalance < 70.0 && FisherStrand == 1.4' -filterName bar -B:variant,VCF " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("b45f3ac20397ab4b64c963ce67cf9cca"));
+                Arrays.asList("42bfb7df7a83e5007a1d1da523a64d75"));
         executeTest("test filter #2", spec);
     }
 
@@ -56,7 +56,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
     public void testFilterWithSeparateNames() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " --filterName ABF -filter 'AlleleBalance < 0.7' --filterName FSF -filter 'FisherStrand == 1.4' -B:variant,VCF " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("d2484ea8f1d1b12b5586e9bab518d7fa"));
+                Arrays.asList("c2b1d53a50d99229b351470a39692eb6"));
         executeTest("test filter with separate names #2", spec);
     }
 
@@ -64,7 +64,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
     public void testGenotypeFilter1() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -G_filter 'GQ == 0.60' -G_filterName foo -B:variant,VCF " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("76a37ff57ae5c93f5abf341203f7af2c"));
+                Arrays.asList("6696e3f65a62ce912230d47cdb0c129b"));
         executeTest("test genotype filter #1", spec);
     }
 
@@ -72,7 +72,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
     public void testGenotypeFilter2() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -G_filter 'AF == 0.04 && isHomVar == 1' -G_filterName foo -B:variant,VCF " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("e8b80ce01f631c840336792cfbf35254"));
+                Arrays.asList("26e5b4ee954c9e0b5eb044afd4b88ee9"));
         executeTest("test genotype filter #2", spec);
     }
 }

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

@@ -25,7 +25,7 @@ public class
     public void testMultiSamplePilot1() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 baseCommand + " -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -o %s -L 1:10,022,000-10,025,000", 1,
-                Arrays.asList("aeef287589c010ff33ca5eee116c64f2"));
+                Arrays.asList("05359047d4d914c9740466c386a1addc"));
         executeTest("testMultiSamplePilot1", spec);
     }
 
@@ -33,7 +33,7 @@ public class
     public void testMultiSamplePilot2() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 baseCommand + " -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,050,000", 1,
-                Arrays.asList("59f2869835964eaa03fb9838b7d63bca"));
+                Arrays.asList("755f6abfca9db358a839b1ee2d35c5ca"));
         executeTest("testMultiSamplePilot2", spec);
     }
 
@@ -41,7 +41,7 @@ public class
     public void testSingleSamplePilot2() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,100,000", 1,
-                Arrays.asList("40b360318a7d0be8ae8f482816cb24c8"));
+                Arrays.asList("59d6bf8a5030119d1ef0a644a76b3212"));
         executeTest("testSingleSamplePilot2", spec);
     }
 
@@ -51,7 +51,7 @@ public class
     //
     // --------------------------------------------------------------------------------------------------------------
 
-    private final static String COMPRESSED_OUTPUT_MD5 = "c97fde4b21088eb0d3a5fa2136451ff7";
+    private final static String COMPRESSED_OUTPUT_MD5 = "6c4f8e5da47fc4346e8385c109ce731b";
 
     @Test
     public void testCompressedOutput() {
@@ -78,7 +78,7 @@ public class
 
     @Test
     public void testParallelization() {
-        String md5 = "376069f464f0e385c409bf6b5e67cc03";
+        String md5 = "f0d9f168a484d48b23b924f388f088b3";
 
         WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
                 baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,075,000", 1,
@@ -105,12 +105,12 @@ public class
     @Test
     public void testParameter() {
         HashMap<String, String> e = new HashMap<String, String>();
-        e.put( "-genotype", "707821d365ea146c74e512adfa315610" );
-        e.put( "-all_bases", "bf394fc7ee5d87bb7096a301a0a5ab0a" );
-        e.put( "--min_base_quality_score 26", "f0d3b8e337c9e7a00b457211f3739bda" );
-        e.put( "--min_mapping_quality_score 26", "f53db471200a23713e08ac4b357e090b" );
-        e.put( "--max_mismatches_in_40bp_window 5", "21b21d1c15d75db671821c4f119d6318" );
-        e.put( "--p_nonref_model GRID_SEARCH", "69879139904c2f51a20291bb73763def" );
+        e.put( "-genotype", "b4ed6bd0129088a9ab5effadcbbe8469" );
+        e.put( "-all_bases", "4bdfede52a766574ae9638ad3012bce5" );
+        e.put( "--min_base_quality_score 26", "8123a3ca9a7b83a4afacabb33f157613" );
+        e.put( "--min_mapping_quality_score 26", "6e79b6386624b537398e9971bdc5c6f4" );
+        e.put( "--max_mismatches_in_40bp_window 5", "b5f9af45dfc8e168bba619d158dd56a4" );
+        e.put( "--p_nonref_model GRID_SEARCH", "e57cfae0e2caf42172bc7c466d8ff004" );
 
         for ( Map.Entry<String, String> entry : e.entrySet() ) {
             WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
@@ -124,12 +124,12 @@ public class
     public void testConfidence() {
         WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
                 baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000 -stand_call_conf 10 ", 1,
-                Arrays.asList("69879139904c2f51a20291bb73763def"));
+                Arrays.asList("e57cfae0e2caf42172bc7c466d8ff004"));
         executeTest("testConfidence1", spec1);
 
         WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
                 baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000 -stand_emit_conf 10 ", 1,
-                Arrays.asList("b928c7c961d0fd7c8a2b6bc9c53be25e"));
+                Arrays.asList("4440f676bb27c345953b8aaa1e57a1ed"));
         executeTest("testConfidence2", spec2);
     }
 
@@ -141,8 +141,8 @@ public class
     @Test
     public void testHeterozyosity() {
         HashMap<Double, String> e = new HashMap<Double, String>();
-        e.put( 0.01, "73e350d0626a94d224de2f76e621d034" );
-        e.put( 1.0 / 1850, "81c1e24b956407a4e8d6385da8aadd82" );
+        e.put( 0.01, "f92075cf201ecfe7161b9646195348a5" );
+        e.put( 1.0 / 1850, "a428671a373246b20eabd66911e64612" );
 
         for ( Map.Entry<Double, String> entry : e.entrySet() ) {
             WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
@@ -161,7 +161,7 @@ public class
     @Test
     public void testOtherBaseCallModel() {
         HashMap<String, String> e = new HashMap<String, String>();
-        e.put( "three_state", "57906723c8d483d31504437269c9f59a" );
+        e.put( "three_state", "e06dd3becb9bfd083c4706bc0230b8e9" );
 
         for ( Map.Entry<String, String> entry : e.entrySet() ) {
             WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
@@ -184,7 +184,7 @@ public class
                         " -o %s" +
                         " -L 1:10,000,000-10,100,000",
                 1,
-                Arrays.asList("68bb882fba0d331c8f5bdf774e4e09a4"));
+                Arrays.asList("878a76dfd83f1c12dd68dc5a8bdfa483"));
 
         executeTest(String.format("testMultiTechnologies"), spec);
     }

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

@@ -23,7 +23,7 @@ public class MergeMNPsIntegrationTest extends WalkerTest {
                 baseTestString(hg18Reference, "merging_test_chr20_556259_756570.vcf", 1)
                         + " -L chr20:556259-756570",
                 1,
-                Arrays.asList("19d0b2361367024bb9a83b9c15ef2453"));
+                Arrays.asList("e312b7d3854d5b2834a370659514a813"));
         executeTest("Merge MNP sites within genomic distance of 1 [TEST ONE]", spec);
     }
 
@@ -33,7 +33,7 @@ public class MergeMNPsIntegrationTest extends WalkerTest {
                 baseTestString(hg18Reference, "merging_test_chr20_556259_756570.vcf", 10)
                         + " -L chr20:556259-756570",
                 1,
-                Arrays.asList("f25a6403579dab1395773b3ba365c327"));
+                Arrays.asList("681f50e45f1d697370d2c355df2e18bc"));
         executeTest("Merge MNP sites within genomic distance of 10 [TEST TWO]", spec);
     }
 
@@ -43,7 +43,7 @@ public class MergeMNPsIntegrationTest extends WalkerTest {
                 baseTestString(hg18Reference, "merging_test_chr20_556259_756570.vcf", 100)
                         + " -L chr20:556259-756570",
                 1,
-                Arrays.asList("a064955ffeea7fc4e09512f3e9cdbb9e"));
+                Arrays.asList("0bccb0ef928a108418246bec01098083"));
         executeTest("Merge MNP sites within genomic distance of 100 [TEST THREE]", spec);
     }
 

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

@@ -23,7 +23,7 @@ public class MergeSegregatingAlternateAllelesIntegrationTest extends WalkerTest
                 baseTestString(hg18Reference, "merging_test_chr20_556259_756570.vcf", 1)
                         + " -L chr20:556259-756570",
                 1,
-                Arrays.asList("e6a14fc97dbd0aaa8e6a4d9a7f1616a6"));
+                Arrays.asList("e16f957d888054ae0518e25660295241"));
         executeTest("Merge sites within genomic distance of 1 [TEST ONE]", spec);
     }
 
@@ -33,7 +33,7 @@ public class MergeSegregatingAlternateAllelesIntegrationTest extends WalkerTest
                 baseTestString(hg18Reference, "merging_test_chr20_556259_756570.vcf", 10)
                         + " -L chr20:556259-756570",
                 1,
-                Arrays.asList("cc2b45c85a51b4998e30758c48f61940"));
+                Arrays.asList("122a482090677c7619c2105d44e00d11"));
         executeTest("Merge sites within genomic distance of 10 [TEST TWO]", spec);
     }
 
@@ -43,7 +43,7 @@ public class MergeSegregatingAlternateAllelesIntegrationTest extends WalkerTest
                 baseTestString(hg18Reference, "merging_test_chr20_556259_756570.vcf", 100)
                         + " -L chr20:556259-756570",
                 1,
-                Arrays.asList("47300cc7a5a7d84b3c279f04c4567739"));
+                Arrays.asList("bc6a8c8a42bb2601db98e88e9ad74748"));
         executeTest("Merge sites within genomic distance of 100 [TEST THREE]", spec);
     }
 

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

@@ -26,7 +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("ce29d2e84ab6e4f4ed3a81467f19694d"));
+                Arrays.asList("6020a68bbec97fcd87819c10cd4e2470"));
         executeTest("MAX 10 het sites [TEST ONE]; require PQ >= 10", spec);
     }
 
@@ -36,7 +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("4f4773bb7463c0892d427c2a3db385d7"));
+                Arrays.asList("712c2145df4756c9a15758865d8007b5"));
         executeTest("MAX 10 het sites [TEST TWO]; require PQ >= 10", spec);
     }
 
@@ -46,7 +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("92d5b82dd0fa9268a5067ae633cb1a65"));
+                Arrays.asList("297e0896e4761529d979f40f5ad694db"));
         executeTest("MAX 2 het sites [TEST THREE]; require PQ >= 30", spec);
     }
 
@@ -56,7 +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("33d390ff7b6009f1bc767dac985e3aac"));
+                Arrays.asList("52a17f14692d726d3b726cf0ae7f2a09"));
         executeTest("MAX 5 het sites [TEST FOUR]; require PQ >= 100", spec);
     }
 
@@ -66,7 +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("f1cd792644664330d19bd8be11154450"));
+                Arrays.asList("af768f7958b8f4599c2374f1cc2fc613"));
         executeTest("MAX 7 het sites [TEST FIVE]; require PQ >= 10; cacheWindow = 1000", spec);
     }
 
@@ -76,7 +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("699e02c132b08fa4e572f1ead3045e3e"));
+                Arrays.asList("3dd886672f59a47908b94136d0427bb0"));
         executeTest("MAX 10 het sites [TEST SIX]; require PQ >= 10; cacheWindow = 20000; has inconsistent sites", spec);
     }
 

java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java

@@ -124,7 +124,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
         for (String tests : testsEnumerations) {
             WalkerTestSpec spec = new WalkerTestSpec(tests + " " + extraArgs + " -o %s -outputVCF %s -NO_HEADER",
                     2,
-                    Arrays.asList("50321436a65ef7d574286cb0a1c55f7e", "989bc30dea6c8a4cf771cd1b9fdab488"));
+                    Arrays.asList("50321436a65ef7d574286cb0a1c55f7e", "d4bdd06ed5cb1aff1dfee8b69d5d17b8"));
             executeTestParallel("testVEWriteVCF", spec);
             //executeTest("testVEWriteVCF", spec);
         }

java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java

@@ -31,14 +31,14 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
     VRTest yriTrio = new VRTest("yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf",
             "4eeffa7a1965ce0c25c5edd0bae76290",  // in vcf
             "7407987a0148284ed910e1858116dd8d",  // tranches
-            "15ab55be5b2f62627aea8546a4728d77",  // recalVCF
-            "9435f1aed7313fbfff540a4d6d19d0c4"); // cut VCF
+            "f34b36c1da8bcb080a584592d1f6dae7",  // recalVCF
+            "1296ebde7dd61c1c58c11b07b31fd61b"); // cut VCF
 
     VRTest lowPass = new VRTest("lowpass.N3.chr1.raw.vcf",
             "8937a3ae7f176dacf47b8ee6c0023416",  // in vcf
             "2896657b5c30bfd8e82e62e58d94ef4e",  // tranches
-            "a5fe2ee50144ef61121c42daf430381c",  // recalVCF
-            "9a35b69bed93894306c87bc9a0bcc116"); // cut VCF
+            "ae6a1e0874c966312e891b5a3c47b0e3",  // recalVCF
+            "5eed2030d513fae05e45468fa0bb1538"); // cut VCF
 
     @DataProvider(name = "VRTest")
     public Object[][] createData1() {

java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java

@@ -60,21 +60,21 @@ public class CombineVariantsIntegrationTest extends WalkerTest {
     }
 
 
-    @Test public void test1SNP() { test1InOut("pilot2.snps.vcf4.genotypes.vcf", "b9a1887dc8ff20a63a2bae07ea1131f4"); }
-    @Test public void test2SNP() { test1InOut("pilot2.snps.vcf4.genotypes.vcf", "1dc8fedba840de1335d23300446c1c07", " -setKey foo"); }
-    @Test public void test3SNP() { test1InOut("pilot2.snps.vcf4.genotypes.vcf", "33afd1b97340dfa192e5f886fcadd76f", " -setKey null"); }
-    @Test public void testOfficialCEUPilotCalls() { test1InOut("CEU.trio.2010_03.genotypes.vcf.gz", "99796c731462d5a60dd2789a8074fbc0"); } // official project VCF files in tabix format
+    @Test public void test1SNP() { test1InOut("pilot2.snps.vcf4.genotypes.vcf", "2117fff6e0d182cd20be508e9661829c"); }
+    @Test public void test2SNP() { test1InOut("pilot2.snps.vcf4.genotypes.vcf", "2cfaf7af3dd119df08b8a9c1f72e2f93", " -setKey foo"); }
+    @Test public void test3SNP() { test1InOut("pilot2.snps.vcf4.genotypes.vcf", "1474ac0fde2ce42a3c24f1c97eab333e", " -setKey null"); }
+    @Test public void testOfficialCEUPilotCalls() { test1InOut("CEU.trio.2010_03.genotypes.vcf.gz", "7fc66df048a0ab08cf507906e1d4a308"); } // official project VCF files in tabix format
 
-    @Test public void test1Indel1() { test1InOut("CEU.dindel.vcf4.trio.2010_06.indel.genotypes.vcf", "79566b450a71b295aef0285c73f36d6c"); }
-    @Test public void test1Indel2() { test1InOut("CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "0b08098d0519b26e58137c8b337a5119"); }
+    @Test public void test1Indel1() { test1InOut("CEU.dindel.vcf4.trio.2010_06.indel.genotypes.vcf", "ec9715f53dbf4531570557c212822f12"); }
+    @Test public void test1Indel2() { test1InOut("CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "f1072be5f5c6ee810276d9ca6537224d"); }
 
-    @Test public void combineTrioCalls() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "YRI.trio.2010_03.genotypes.vcf.gz", "", "f1749a11f05b383a8df52c98670b2d9a"); } // official project VCF files in tabix format
-    @Test public void combineTrioCallsMin() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "YRI.trio.2010_03.genotypes.vcf.gz", " -minimalVCF", "460bdbeaf7e9641395ac2ce6e1afc106"); } // official project VCF files in tabix format
-    @Test public void combine2Indels() { combine2("CEU.dindel.vcf4.trio.2010_06.indel.genotypes.vcf", "CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "", "67001f987e8d4aab237c506d6813970e"); }
+    @Test public void combineTrioCalls() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "YRI.trio.2010_03.genotypes.vcf.gz", "", "b77a1eec725201d9d8e74ee0c45638d3"); } // official project VCF files in tabix format
+    @Test public void combineTrioCallsMin() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "YRI.trio.2010_03.genotypes.vcf.gz", " -minimalVCF", "802977fdfd2f4905b501bb06800f60af"); } // official project VCF files in tabix format
+    @Test public void combine2Indels() { combine2("CEU.dindel.vcf4.trio.2010_06.indel.genotypes.vcf", "CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "", "a67157287dd2b24b5cdf7ebf8fcbbe9a"); }
 
-    @Test public void combineSNPsAndIndels() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "", "96e473ce30b3aca3e5f6c51b8fc562ea"); }
+    @Test public void combineSNPsAndIndels() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "", "e1f4718a179f1196538a33863da04f53"); }
 
-    @Test public void uniqueSNPs() { combine2("pilot2.snps.vcf4.genotypes.vcf", "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf", "", "0e6379c4a8c6ddc47ddc8059cf72d7bc"); }
+    @Test public void uniqueSNPs() { combine2("pilot2.snps.vcf4.genotypes.vcf", "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf", "", "b3783384b7c8e877b971033e90beba48"); }
 
     @Test public void threeWayWithRefs() {
         WalkerTestSpec spec = new WalkerTestSpec(
@@ -87,7 +87,7 @@ public class CombineVariantsIntegrationTest extends WalkerTest {
                         " -priority NA19240_BGI,NA19240_ILLUMINA,NA19240_WUGSC,denovoInfo" +
                         " -genotypeMergeOptions UNIQUIFY -L 1"),
                 1,
-                Arrays.asList("070dd17f49231576e4f8713e384c8026"));
+                Arrays.asList("00c431243201e7dec99c2c1a1a863438"));
         executeTest("threeWayWithRefs", spec);
         
     }

java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariantsIntegrationTest.java

@@ -40,7 +40,7 @@ public class LiftoverVariantsIntegrationTest extends WalkerTest {
          WalkerTestSpec spec = new WalkerTestSpec(
                  "-T LiftoverVariants -o %s -R " + b36KGReference + " -B:variant,vcf " + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.500.noheader.vcf -chain " + validationDataLocation + "b36ToHg19.broad.over.chain -dict /seq/references/Homo_sapiens_assembly19/v0/Homo_sapiens_assembly19.dict",
                  1,
-                 Arrays.asList("cc1b1ccb800b16abce2d177c181ede56"));
+                 Arrays.asList("37e23efd7d6471fc0f807b31ccafe0eb"));
          executeTest("test b36 to hg19", spec);
     }
 
@@ -49,7 +49,7 @@ public class LiftoverVariantsIntegrationTest extends WalkerTest {
          WalkerTestSpec spec = new WalkerTestSpec(
                  "-T LiftoverVariants -o %s -R " + hg18Reference + " -B:variant,vcf " + validationDataLocation + "liftover_test.vcf -chain " + validationDataLocation + "hg18ToHg19.broad.over.chain -dict /seq/references/Homo_sapiens_assembly19/v0/Homo_sapiens_assembly19.dict",
                  1,
-                 Arrays.asList("22d4cd78d72da55f2423b9ab06f467b2"));
+                 Arrays.asList("3275373b3c44ad14a270b50664b3f8a3"));
          executeTest("test hg18 to hg19, unsorted", spec);
     }
 }

java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java

@@ -18,7 +18,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
             baseTestString(" -sn A -sn '[CDH]' -sn " + samplesFile + " -env -ef -select 'DP < 250' -B:variant,VCF " + testfile + " -NO_HEADER"),
             1,
-            Arrays.asList("e22db73fd99fd4f28d472d407e40ead5")
+            Arrays.asList("1df84e2b755cce19f1876710ec38dd2c")
         );
 
         executeTest("testComplexSelection--" + testfile, spec);
@@ -31,7 +31,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString(" -sn A -sn B -sn C -B:variant,VCF " + testfile + " -NO_HEADER"),
                 1,
-                Arrays.asList("fae9822d5f7ad6c76b411e8ca0886409")
+                Arrays.asList("fe6963e5fea1d3854634dcf3defd7b92")
         );
 
         executeTest("testRepeatedLineSelection--" + testfile, spec);