Updating many MD5s to reflect correct fixed headers

-- Previous bugfix ensures that header fixing is always on in the GATK by default, even after integration tests that failed and when through the VCFDiffableReader.  Updating md5s to reflect this.

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

@@ -16,7 +16,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testHasAnnotsNotAsking1() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " --variant " + privateTestDir + "vcfexample2.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("55785745fe13ad81a2c4a14373d091f0"));
+                Arrays.asList("360610e4990860bb5c45249b8ac31e5b"));
         executeTest("test file has annotations, not asking for annotations, #1", spec);
     }
 
@@ -24,7 +24,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testHasAnnotsNotAsking2() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " --variant " + privateTestDir + "vcfexample3.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1,
-                Arrays.asList("d6f749f8dbeb2d42c9effaff9fe571d7"));
+                Arrays.asList("d69a3c92a0e8f44e09e7377e3eaed4e8"));
         executeTest("test file has annotations, not asking for annotations, #2", spec);
     }
 
@@ -32,7 +32,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testHasAnnotsAsking1() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -G Standard --variant " + privateTestDir + "vcfexample2.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("9084e6c7b1cec0f3a2c6d96711844d5e"));
+                Arrays.asList("e0a08416249515ea18bd0663c90c9330"));
         executeTest("test file has annotations, asking for annotations, #1", spec);
     }
 
@@ -40,7 +40,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testHasAnnotsAsking2() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -G Standard --variant " + privateTestDir + "vcfexample3.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1,
-                Arrays.asList("3dfabdcaa2648ac34380fb71860c42d3"));
+                Arrays.asList("0b60da46ba0eabb3abe5e0288937f9b0"));
         executeTest("test file has annotations, asking for annotations, #2", spec);
     }
 
@@ -48,7 +48,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testNoAnnotsNotAsking1() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " --variant " + privateTestDir + "vcfexample2empty.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("b85c1ea28194484b327fbe0add1b5685"));
+                Arrays.asList("540a9be8a8cb85b0f675fea1184bf78c"));
         executeTest("test file doesn't have annotations, not asking for annotations, #1", spec);
     }
 
@@ -58,7 +58,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
         // they don't get reordered.  It's a good test of the genotype ordering system.
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " --variant " + privateTestDir + "vcfexample3empty.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1,
-                Arrays.asList("fe4d4e2484c4cf8b1cd50ad42cfe468e"));
+                Arrays.asList("f900e65b65ff0f9d9eb0891ef9b28c73"));
         executeTest("test file doesn't have annotations, not asking for annotations, #2", spec);
     }
 
@@ -66,7 +66,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testNoAnnotsAsking1() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -G Standard --variant " + privateTestDir + "vcfexample2empty.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("043fc6205b0633edcd3fadc9e044800c"));
+                Arrays.asList("5eb576d0234c912d8efea184492691d0"));
         executeTest("test file doesn't have annotations, asking for annotations, #1", spec);
     }
 
@@ -74,7 +74,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testNoAnnotsAsking2() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -G Standard --variant " + privateTestDir + "vcfexample3empty.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1,
-                Arrays.asList("6fafb42d374a67ba4687a23078a126af"));
+                Arrays.asList("8860524d793d24b2e32f318433fcf527"));
         executeTest("test file doesn't have annotations, asking for annotations, #2", spec);
     }
 
@@ -82,7 +82,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testExcludeAnnotations() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -G Standard -XA FisherStrand -XA ReadPosRankSumTest --variant " + privateTestDir + "vcfexample2empty.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("639462a0e0fa79e33def5f011fe55961"));
+                Arrays.asList("f33f417fad98c05d9cd08ffa22943b0f"));
         executeTest("test exclude annotations", spec);
     }
 
@@ -98,7 +98,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testNoReads() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -G Standard --variant " + privateTestDir + "vcfexample3empty.vcf -L " + privateTestDir + "vcfexample3empty.vcf", 1,
-                Arrays.asList("afe6c9d3b4b80635a541cdfcfa48db2f"));
+                Arrays.asList("1c423b7730b9805e7b885ece924286e0"));
         executeTest("not passing it any reads", spec);
     }
 
@@ -106,7 +106,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testDBTagWithDbsnp() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " --dbsnp " + b36dbSNP129 + " -G Standard --variant " + privateTestDir + "vcfexample3empty.vcf -L " + privateTestDir + "vcfexample3empty.vcf", 1,
-                Arrays.asList("21d696ea8c55d2fd4cbb4dcd5f7f7db6"));
+                Arrays.asList("54d7d5bb9404652857adf5e50d995f30"));
         executeTest("getting DB tag with dbSNP", spec);
     }
 
@@ -114,7 +114,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testMultipleIdsWithDbsnp() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " --alwaysAppendDbsnpId --dbsnp " + b36dbSNP129 + " -G Standard --variant " + privateTestDir + "vcfexample3withIDs.vcf -L " + privateTestDir + "vcfexample3withIDs.vcf", 1,
-                Arrays.asList("ef95394c14d5c16682a322f3dfb9000c"));
+                Arrays.asList("5fe63e511061ed4f91d938e72e7e3c39"));
         executeTest("adding multiple IDs with dbSNP", spec);
     }
 
@@ -122,7 +122,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testDBTagWithHapMap() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " --comp:H3 " + privateTestDir + "fakeHM3.vcf -G Standard --variant " + privateTestDir + "vcfexample3empty.vcf -L " + privateTestDir + "vcfexample3empty.vcf", 1,
-                Arrays.asList("e6e276b7d517d57626c8409589cd286f"));
+                Arrays.asList("cc7184263975595a6e2473d153227146"));
         executeTest("getting DB tag with HM3", spec);
     }
 
@@ -130,7 +130,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testNoQuals() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " --variant " + privateTestDir + "noQual.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L " + privateTestDir + "noQual.vcf -A QualByDepth", 1,
-                Arrays.asList("a99e8315571ed1b6bce942451b3d8612"));
+                Arrays.asList("aea983adc01cd059193538cc30adc17d"));
         executeTest("test file doesn't have QUALs", spec);
     }
 
@@ -138,7 +138,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testUsingExpression() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " --resource:foo " + privateTestDir + "targetAnnotations.vcf -G Standard --variant " + privateTestDir + "vcfexample3empty.vcf -E foo.AF -L " + privateTestDir + "vcfexample3empty.vcf", 1,
-                Arrays.asList("7d6ea3b54210620cbc7e14dad8836bcb"));
+                Arrays.asList("2b0e8cdfd691779befc5ac123d1a1887"));
         executeTest("using expression", spec);
     }
 
@@ -146,13 +146,13 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testUsingExpressionWithID() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " --resource:foo " + privateTestDir + "targetAnnotations.vcf -G Standard --variant " + privateTestDir + "vcfexample3empty.vcf -E foo.ID -L " + privateTestDir + "vcfexample3empty.vcf", 1,
-                Arrays.asList("35ce4fb0288dfc5c01ec6ce8b14c6157"));
+                Arrays.asList("3de1d1998203518098ffae233f3e2352"));
         executeTest("using expression with ID", spec);
     }
 
     @Test
     public void testTabixAnnotations() {
-        final String MD5 = "5aebcf8f76c649d645708b1262185c80";
+        final String MD5 = "99938d1e197b8f10c408cac490a00a62";
         for ( String file : Arrays.asList("CEU.exon.2010_03.sites.vcf", "CEU.exon.2010_03.sites.vcf.gz")) {
             WalkerTestSpec spec = new WalkerTestSpec(
                     baseTestString() + " -A HomopolymerRun --variant:vcf " + validationDataLocation + file + " -L " + validationDataLocation + "CEU.exon.2010_03.sites.vcf --no_cmdline_in_header", 1,
@@ -168,7 +168,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
             validationDataLocation + "1kg_exomes_unfiltered.AFR.unfiltered.vcf --snpEffFile  " + validationDataLocation +
             "snpEff2.0.5.AFR.unfiltered.vcf -L 1:1-1,500,000 -L 2:232,325,429",
             1,
-            Arrays.asList("0c20cda1cf0b903a287f1807ae5bee02")
+            Arrays.asList("d9291845ce5a8576898d293a829a05b7")
         );
         executeTest("Testing SnpEff annotations", spec);
     }
@@ -187,7 +187,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
 
     @Test
     public void testTDTAnnotation() {
-        final String MD5 = "81f85f0ce8cc36df7c717c478e100ba1";
+        final String MD5 = "427dfdc665359b67eff210f909ebf8a2";
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T VariantAnnotator -R " + b37KGReference + " -A TransmissionDisequilibriumTest --variant:vcf " + privateTestDir + "ug.random50000.subset300bp.chr1.family.vcf" +
                         " -L " + privateTestDir + "ug.random50000.subset300bp.chr1.family.vcf --no_cmdline_in_header -ped " + privateTestDir + "ug.random50000.family.ped -o %s", 1,
@@ -198,7 +198,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
 
     @Test
     public void testChromosomeCountsPed() {
-        final String MD5 = "9830fe2247651377e68ad0b0894e9a4e";
+        final String MD5 = "6b5cbedf4a8b3385edf128d81c8a46f2";
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T VariantAnnotator -R " + b37KGReference + " -A ChromosomeCounts --variant:vcf " + privateTestDir + "ug.random50000.subset300bp.chr1.family.vcf" +
                         " -L " + privateTestDir + "ug.random50000.subset300bp.chr1.family.vcf --no_cmdline_in_header -ped " + privateTestDir + "ug.random50000.family.ped -o %s", 1,
@@ -208,7 +208,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
 
     @Test
     public void testInbreedingCoeffPed() {
-        final String MD5 = "e94d589b5691e3ecfd9cc9475a384890";
+        final String MD5 = "159a771c1deaeffb786097e106943893";
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T VariantAnnotator -R " + b37KGReference + " -A InbreedingCoeff --variant:vcf " + privateTestDir + "ug.random50000.subset300bp.chr1.family.vcf" +
                         " -L " + privateTestDir + "ug.random50000.subset300bp.chr1.family.vcf --no_cmdline_in_header -ped " + privateTestDir + "ug.random50000.family.ped -o %s", 1,

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

@@ -41,7 +41,7 @@ public class BeagleIntegrationTest extends WalkerTest {
                         "--beagleR2:BEAGLE " + beagleValidationDataLocation + "inttestbgl.r2 " +
                         "--beagleProbs:BEAGLE " + beagleValidationDataLocation + "inttestbgl.gprobs " +
                         "--beaglePhased:BEAGLE " + beagleValidationDataLocation + "inttestbgl.phased " +
-                        "-o %s --no_cmdline_in_header -U LENIENT_VCF_PROCESSING", 1, Arrays.asList("cba514105039f7a56f7ecdd241fbdcca"));
+                        "-o %s --no_cmdline_in_header -U LENIENT_VCF_PROCESSING", 1, Arrays.asList("c5522304abf0633041c7772dd7dafcea"));
         spec.disableShadowBCF();
         executeTest("test BeagleOutputToVCF", spec);
     }
@@ -75,7 +75,7 @@ public class BeagleIntegrationTest extends WalkerTest {
                 "--beagleR2:beagle /humgen/gsa-hpprojects/GATK/data/Validation_Data/EUR_beagle_in_test.r2 "+
                 "--beagleProbs:beagle /humgen/gsa-hpprojects/GATK/data/Validation_Data/EUR_beagle_in_test.gprobs.bgl "+
                 "--beaglePhased:beagle /humgen/gsa-hpprojects/GATK/data/Validation_Data/EUR_beagle_in_test.phased.bgl "+
-                "-L 20:1-70000 -o %s --no_cmdline_in_header -U LENIENT_VCF_PROCESSING",1,Arrays.asList("d95a97068a97c9059811b2574b73ea60"));
+                "-L 20:1-70000 -o %s --no_cmdline_in_header -U LENIENT_VCF_PROCESSING",1,Arrays.asList("fbbbebfda35bab3f6f62eea2f0be1c01"));
         spec.disableShadowBCF();
         executeTest("testBeagleChangesSitesToRef",spec);
     }

public/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() + " --variant " + privateTestDir + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("fbf88e25df30181ca5422a374c7b36fa"));
+                Arrays.asList("a890cd298298e22bc04a2e5a20b71170"));
         executeTest("test no action", spec);
     }
 
@@ -24,7 +24,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
     public void testClusteredSnps() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -window 10 --variant " + privateTestDir + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("bb69f49e9ef0054f0ccd6d38f5ffa46a"));
+                Arrays.asList("f46b2fe2dbe6a423b5cfb10d74a4966d"));
         executeTest("test clustered SNPs", spec);
     }
 
@@ -32,7 +32,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
     public void testMask1() {
         WalkerTestSpec spec1 = new WalkerTestSpec(
                 baseTestString() + " -maskName foo --mask " + privateTestDir + "vcfexample2.vcf --variant " + privateTestDir + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("7e3225a32fcd6066901247992b2c5ca8"));
+                Arrays.asList("86dbbf62a0623b2dc5e8969c26d8cb28"));
         executeTest("test mask all", spec1);
     }
 
@@ -40,7 +40,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
     public void testMask2() {
         WalkerTestSpec spec2 = new WalkerTestSpec(
                 baseTestString() + " -maskName foo --mask:VCF " + privateTestDir + "vcfMask.vcf --variant " + privateTestDir + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("3485fe95e3f0864c3575baf05cef4bcc"));
+                Arrays.asList("2fb33fccda1eafeea7a2f8f9219baa39"));
         executeTest("test mask some", spec2);
     }
 
@@ -48,7 +48,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
     public void testMask3() {
         WalkerTestSpec spec3 = new WalkerTestSpec(
                 baseTestString() + " -maskName foo -maskExtend 10 --mask:VCF " + privateTestDir + "vcfMask.vcf --variant " + privateTestDir + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("367ab9c028a68e4eda2055e3bb8b486c"));
+                Arrays.asList("4351e00bd9d821e37cded5a86100c973"));
         executeTest("test mask extend", spec3);
     }
 
@@ -56,7 +56,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
     public void testFilter1() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -filter 'DoC < 20 || FisherStrand > 20.0' -filterName foo --variant " + privateTestDir + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("5a10d969e50a58d8dfbf1da54bf293df"));
+                Arrays.asList("2f056b50a41c8e6ba7645ff4c777966d"));
         executeTest("test filter #1", spec);
     }
 
@@ -64,7 +64,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
     public void testFilter2() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -filter 'AlleleBalance < 70.0 && FisherStrand == 1.4' -filterName bar --variant " + privateTestDir + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("886dbbca2350083819ff67224f6efbd6"));
+                Arrays.asList("b2a8c1a5d99505be79c03120e9d75f2f"));
         executeTest("test filter #2", spec);
     }
 
@@ -72,7 +72,7 @@ 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' --variant " + privateTestDir + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("ee78c2e7128a8f9549233493c7cf6949"));
+                Arrays.asList("e350d9789bbdf334c1677506590d0798"));
         executeTest("test filter with separate names #2", spec);
     }
 
@@ -80,7 +80,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
     public void testGenotypeFilters1() {
         WalkerTestSpec spec1 = new WalkerTestSpec(
                 baseTestString() + " -G_filter 'GQ == 0.60' -G_filterName foo --variant " + privateTestDir + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("285dd348c47c8c1e85d2886f9b33559e"));
+                Arrays.asList("060e9e7b6faf8b2f7b3291594eb6b39c"));
         executeTest("test genotype filter #1", spec1);
     }
 
@@ -88,7 +88,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
     public void testGenotypeFilters2() {
         WalkerTestSpec spec2 = new WalkerTestSpec(
                 baseTestString() + " -G_filter 'isHomVar == 1' -G_filterName foo --variant " + privateTestDir + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("a9c835a13eb72aa22d5e271894d8ac33"));
+                Arrays.asList("00f90028a8c0d56772c47f039816b585"));
         executeTest("test genotype filter #2", spec2);
     }
 
@@ -96,7 +96,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
     public void testDeletions() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " --filterExpression 'QUAL < 100' --filterName foo --variant:VCF " + privateTestDir + "twoDeletions.vcf", 1,
-                Arrays.asList("a1c02a5a90f1262e9eb3d2cad1fd08f2"));
+                Arrays.asList("8077eb3bab5ff98f12085eb04176fdc9"));
         executeTest("test deletions", spec);
     }
 }

public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmissionIntegrationTest.java

@@ -29,7 +29,7 @@ public class PhaseByTransmissionIntegrationTest extends WalkerTest {
                         "-o %s"
                 ),
                 2,
-                Arrays.asList("cd112ec37a9e28d366aff29a85fdcaa0","313cc749c7ee97713e4551de39e01ac5")
+                Arrays.asList("cd112ec37a9e28d366aff29a85fdcaa0","f8721f4f5d3bae2848ae15c3f120709b")
         );
         executeTest("testTrueNegativeMV", spec);
     }
@@ -48,7 +48,7 @@ public class PhaseByTransmissionIntegrationTest extends WalkerTest {
                         "-o %s"
                 ),
                 2,
-                Arrays.asList("27ccd6feb51de7e7dcdf35f4697fa4eb","dd90dad9fd11e1b16e6660c3ca0553e7")
+                Arrays.asList("27ccd6feb51de7e7dcdf35f4697fa4eb","547fdfef393f3045a96d245ef6af8acb")
         );
         executeTest("testTruePositiveMV", spec);
     }
@@ -67,7 +67,7 @@ public class PhaseByTransmissionIntegrationTest extends WalkerTest {
                         "-o %s"
                 ),
                 2,
-                Arrays.asList("719d681bb0a52a40bc854bba107c5c94","b35a86d2cad17f0db7b5e84ddc0e5545")
+                Arrays.asList("719d681bb0a52a40bc854bba107c5c94","9529e2bf214d72e792d93fbea22a3b91")
         );
         executeTest("testFalsePositiveMV", spec);
     }
@@ -86,7 +86,7 @@ public class PhaseByTransmissionIntegrationTest extends WalkerTest {
                         "-o %s"
                 ),
                 2,
-                Arrays.asList("7f4a277aee2c7398fcfa84d6c98d5fb3","c53b5fd377bef48e9c6035a94db398db")
+                Arrays.asList("7f4a277aee2c7398fcfa84d6c98d5fb3","8c157d79dd00063d2932f0d2b96f53d8")
         );
         executeTest("testSpecialCases", spec);
     }
@@ -108,7 +108,7 @@ public class PhaseByTransmissionIntegrationTest extends WalkerTest {
                         "-o %s"
                 ),
                 2,
-                Arrays.asList("44e09d2f9e4d8a9488226d03a97fe999","6f596470740e1a57679bbb38c0126364")
+                Arrays.asList("44e09d2f9e4d8a9488226d03a97fe999","343e418850ae4a687ebef2acd55fcb07")
         );
         executeTest("testPriorOption", spec);
     }
@@ -128,7 +128,7 @@ public class PhaseByTransmissionIntegrationTest extends WalkerTest {
                         "-o %s"
                 ),
                 1,
-                Arrays.asList("b35a86d2cad17f0db7b5e84ddc0e5545")
+                Arrays.asList("9529e2bf214d72e792d93fbea22a3b91")
         );
         executeTest("testMVFileOption", spec);
     }
@@ -149,7 +149,7 @@ public class PhaseByTransmissionIntegrationTest extends WalkerTest {
                         "-fatherAlleleFirst"
                 ),
                 2,
-                Arrays.asList("60ced3d078792a150a03640b62926857","6d550784382aa910f78b533d889c91c0")
+                Arrays.asList("60ced3d078792a150a03640b62926857","52ffa82428e63ade22ea37b72ae58492")
         );
         executeTest("testFatherAlleleFirst", spec);
     }

public/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("442c819569417c1b7d6be9f41ce05394"));
+                Arrays.asList("1c9a7fe4db41864cd85d16e5cf88986c"));
         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("2a51ee7d3c024f2410dcee40c5412993"));
+                Arrays.asList("a3ca151145379e0d4bae64a91165ea0b"));
         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("85bc9b03e24159f746dbd0cb988f9ec8"));
+                Arrays.asList("f685803333123a102ce1851d984cbd10"));
         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("96bb413a83c777ebbe622438e4565e8f"));
+                Arrays.asList("aaa7c25d118383639f273128d241e140"));
         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("7d2402f055d243e2208db9ea47973e13"));
+                Arrays.asList("418e29400762972e77bae4f73e16befe"));
         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("72682b3f27c33580d2d4515653ba6de7"));
+                Arrays.asList("4c8f6190ecc86766baba3aba08542991"));
         executeTest("MAX 10 het sites [TEST SIX]; require PQ >= 10; cacheWindow = 20000; has inconsistent sites", spec);
     }
 

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

@@ -27,7 +27,7 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
     VRTest lowPass = new VRTest("phase1.projectConsensus.chr20.raw.snps.vcf",
             "0ddd1e0e483d2eaf56004615cea23ec7",  // tranches
             "b9709e4180e56abc691b208bd3e8626c",  // recal file
-            "c58ff4140e8914f0b656ed625c7f73b9"); // cut VCF
+            "4c73ff0c8c5ae0055bfacf33329a2406"); // cut VCF
 
     @DataProvider(name = "VRTest")
     public Object[][] createData1() {
@@ -119,6 +119,7 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
                         " -tranchesFile " + getMd5DB().getMD5FilePath(params.tranchesMD5, null) +
                         " -recalFile " + getMd5DB().getMD5FilePath(params.recalMD5, null),
                 Arrays.asList(params.cutVCFMD5));
+        spec.disableShadowBCF(); // TODO -- enable when we support symbolic alleles
         executeTest("testApplyRecalibrationIndel-"+params.inVCF, spec);
     }
 

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

@@ -142,17 +142,17 @@ public class CombineVariantsIntegrationTest extends WalkerTest {
         cvExecuteTest("combineComplexSites 1:" + new File(file1).getName() + " 2:" + new File(file2).getName() + " args = " + args, spec);
     }
 
-    @Test public void complexTestFull() { combineComplexSites("", "8b19b54516b59de40992f0c4b328258a"); }
-    @Test public void complexTestMinimal() { combineComplexSites(" -minimalVCF", "a38dd097adc37420fe36ef8be14cfded"); }
-    @Test public void complexTestSitesOnly() { combineComplexSites(" -sites_only", "a3957dac9a617f50ce2668607e3baef0"); }
-    @Test public void complexTestSitesOnlyMinimal() { combineComplexSites(" -sites_only -minimalVCF", "a3957dac9a617f50ce2668607e3baef0"); }
+    @Test public void complexTestFull() { combineComplexSites("", "151a4970367dd3e73ba3e7f3c2f874f6"); }
+    @Test public void complexTestMinimal() { combineComplexSites(" -minimalVCF", "c0625e092b878b3d3eb1703c48e216b7"); }
+    @Test public void complexTestSitesOnly() { combineComplexSites(" -sites_only", "6978329d6a1033ac16f83b49072c679b"); }
+    @Test public void complexTestSitesOnlyMinimal() { combineComplexSites(" -sites_only -minimalVCF", "6978329d6a1033ac16f83b49072c679b"); }
 
     @Test
     public void combineDBSNPDuplicateSites() {
          WalkerTestSpec spec = new WalkerTestSpec(
                  "-T CombineVariants --no_cmdline_in_header -L 1:902000-903000 -o %s -R " + b37KGReference + " -V:v1 " + b37dbSNP132,
                  1,
-                 Arrays.asList("3d2a5a43db86e3f6217ed2a63251285b"));
+                 Arrays.asList("aa926eae333208dc1f41fe69dc95d7a6"));
          cvExecuteTest("combineDBSNPDuplicateSites:", spec);
     }
 }

public/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 + " --variant " + privateTestDir + "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("a139480c004859452d4095fe4859b42e"));
+                 Arrays.asList("7d5f91fcf419211ae9eca6c66dcec0e6"));
          executeTest("test b36 to hg19", spec);
     }
 
@@ -49,7 +49,7 @@ public class LiftoverVariantsIntegrationTest extends WalkerTest {
          WalkerTestSpec spec = new WalkerTestSpec(
                  "-T LiftoverVariants -o %s -R " + b36KGReference + " --variant " + privateTestDir + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.500.noheader.unsortedSamples.vcf -chain " + validationDataLocation + "b36ToHg19.broad.over.chain -dict /seq/references/Homo_sapiens_assembly19/v0/Homo_sapiens_assembly19.dict",
                  1,
-                 Arrays.asList("91344768f1e98c979364ec0d5d3aa9d6"));
+                 Arrays.asList("29dab3555e7f1ee6a60e267b00215a11"));
          executeTest("test b36 to hg19, unsorted samples", spec);
     }
 
@@ -58,7 +58,7 @@ public class LiftoverVariantsIntegrationTest extends WalkerTest {
          WalkerTestSpec spec = new WalkerTestSpec(
                  "-T LiftoverVariants -o %s -R " + hg18Reference + " --variant:vcf " + privateTestDir + "liftover_test.vcf -chain " + validationDataLocation + "hg18ToHg19.broad.over.chain -dict /seq/references/Homo_sapiens_assembly19/v0/Homo_sapiens_assembly19.dict",
                  1,
-                 Arrays.asList("e0b813ff873185ab51995a151f80ec98"));
+                 Arrays.asList("7e7bad0e1890753a01303c09a38ceb8d"));
          executeTest("test hg18 to hg19, unsorted", spec);
     }
 }

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

@@ -34,7 +34,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString(" -sn A -sn B -sn C --variant " + testfile),
                 1,
-                Arrays.asList("337bb7fc23153cf67acc42a466834775")
+                Arrays.asList("3d98a024bf3aecbd282843e0af89d0e6")
         );
 
         executeTest("testRepeatedLineSelection--" + testfile, spec);
@@ -64,7 +64,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString(" -sn A -se '[CDH]' -sf " + samplesFile + " -env -ef -select 'DP < 250' --variant " + testfile),
                 1,
-                Arrays.asList("ad0514b723ee1479d861291622bd4311")
+                Arrays.asList("433eccaf1ac6e6be500ef0984a5d8d8b")
         );
         spec.disableShadowBCF();
         executeTest("testComplexSelection--" + testfile, spec);
@@ -78,7 +78,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T SelectVariants -R " + b36KGReference + " -L 1:1-1000000 -o %s --no_cmdline_in_header -xl_sn A -xl_sf " + samplesFile + " --variant " + testfile,
                 1,
-                Arrays.asList("bc0e00d0629b2bc6799e7e9db0dc775c")
+                Arrays.asList("1f5c72951a35667c4bdf1be153787e27")
         );
         spec.disableShadowBCF();
 
@@ -109,7 +109,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T SelectVariants -R " + b36KGReference + " -restrictAllelesTo MULTIALLELIC -selectType MIXED --variant " + testFile + " -o %s --no_cmdline_in_header",
                 1,
-                Arrays.asList("a111642779b05de33ad04073d6022c21")
+                Arrays.asList("ca2b70e3171420b08b0a2659bfe2a794")
         );
 
         executeTest("testVariantTypeSelection--" + testFile, spec);
@@ -176,7 +176,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
         spec = new WalkerTestSpec(
                 baseTestString(" -sn A -se '[CDH]' -sf " + samplesFile + " -env -ef -select 'DP < 250' --variant " + testfile + " -nt 2"),
                 1,
-                Arrays.asList("ad0514b723ee1479d861291622bd4311")
+                Arrays.asList("433eccaf1ac6e6be500ef0984a5d8d8b")
         );
         spec.disableShadowBCF();
         executeTest("testParallelization (2 threads)--" + testfile, spec);
@@ -190,7 +190,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
         spec = new WalkerTestSpec(
                 baseTestString(" -sn A -se '[CDH]' -sf " + samplesFile + " -env -ef -select 'DP < 250' --variant " + testfile + " -nt 4"),
                 1,
-                Arrays.asList("ad0514b723ee1479d861291622bd4311")
+                Arrays.asList("433eccaf1ac6e6be500ef0984a5d8d8b")
         );
         spec.disableShadowBCF();
 
@@ -204,7 +204,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T SelectVariants -R " + b37KGReference + " -o %s --no_cmdline_in_header -sf " + samplesFile + " --excludeNonVariants --variant " + testfile,
                 1,
-                Arrays.asList("9acd6effcc78bfb832bed5edfd6a1b5b")
+                Arrays.asList("3ab35d5e81a29fb5db3e2add11c7e823")
         );
         executeTest("test select from multi allelic with excludeNonVariants --" + testfile, spec);
     }
@@ -223,7 +223,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
         final String testFile = privateTestDir + "missingHeaderLine.vcf";
         final String cmd = "-T SelectVariants -R " + b36KGReference + " -sn NA12892 --variant:dbsnp "
                 + testFile + " -o %s --no_cmdline_in_header"
-                + (expectedException == null ? " -lenientVCFProcessing" : "");
+                + (expectedException == null ? " -U LENIENT_VCF_PROCESSING" : "");
         WalkerTestSpec spec =
                 expectedException != null
                         ? new WalkerTestSpec(cmd, 1, expectedException)

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

@@ -89,7 +89,7 @@ public class VariantsToVCFIntegrationTest extends WalkerTest {
     @Test
     public void testGenotypesToVCFUsingVCFInput() {
         List<String> md5 = new ArrayList<String>();
-        md5.add("95898aad8c9f9515c0e668e2fb65a024");
+        md5.add("21084d32ce7ac5df3cee1730bfaaf71c");
 
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-R " + b36KGReference +