Update all the md5s for header reference path changes

protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantAnnotatorIntegrationTest.java

@@ -83,7 +83,7 @@ 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("b65bf866457f000926b76d0f9d40065e"));
+                Arrays.asList("73b8926ebc9bad0b694e14c6682e521b"));
         executeTest("test file has annotations, not asking for annotations, #1", spec);
     }
 
@@ -91,7 +91,7 @@ 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("8e830da0bf34f1dc91bbc2fa64b8a518"));
+                Arrays.asList("e4fe3944bb0e02c04ca611bada736f7e"));
         executeTest("test file has annotations, not asking for annotations, #2", spec);
     }
 
@@ -99,7 +99,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testHasAnnotsAsking1() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + STANDARD_ANNOTATIONS + "--variant " + privateTestDir + "vcfexample2.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("b63baada372925a76c3f279e16eb631d"));
+                Arrays.asList("67a6a9473fd4f0eea5d3951ed935ab16"));
         executeTest("test file has annotations, asking for annotations, #1", spec);
     }
 
@@ -107,7 +107,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testHasAnnotsAsking2() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + STANDARD_ANNOTATIONS + "--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("6f5856bc2d31f8aae4131717e5ab0b16"));
+                Arrays.asList("7daab54708e7c676d21ab7cfde4ee6f0"));
         executeTest("test file has annotations, asking for annotations, #2", spec);
     }
 
@@ -115,7 +115,7 @@ 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("58793dec36f8aec2cd8894898ece7c4e"));
+                Arrays.asList("9457b8a2a1f5324541859a7c1f078dd4"));
         executeTest("test file doesn't have annotations, not asking for annotations, #1", spec);
     }
 
@@ -125,7 +125,7 @@ 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("27745920cc780b04e8f5acba79f868ca"));
+                Arrays.asList("75155227165a6f1a2d1efc87f41a2c5e"));
         executeTest("test file doesn't have annotations, not asking for annotations, #2", spec);
     }
 
@@ -133,7 +133,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testNoAnnotsAsking1() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + STANDARD_ANNOTATIONS + "--variant " + privateTestDir + "vcfexample2empty.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("7ec5470f742f80cdfbfb203213bea8cc"));
+                Arrays.asList("9625b19e44bbcd6504c8f03017a1ad2f"));
         executeTest("test file doesn't have annotations, asking for annotations, #1", spec);
     }
 
@@ -141,7 +141,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testNoAnnotsAsking2() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + STANDARD_ANNOTATIONS + "--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("afc47e4f253d0999961f26920be8e834"));
+                Arrays.asList("9f580143dbd2c66265a46d8f42b6155d"));
 
         executeTest("test file doesn't have annotations, asking for annotations, #2", spec);
     }
@@ -150,7 +150,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testExcludeAnnotations() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + STANDARD_ANNOTATIONS + "-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("a8a87e2a67436e14ed32ce9d355a3440"));
+                Arrays.asList("88392f45a5d2644a05a73d1644694162"));
         executeTest("test exclude annotations", spec);
     }
 
@@ -160,7 +160,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
         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 "
                         + "-A StrandAlleleCountsBySample -log " + logFile.getAbsolutePath(), 1,
-                Arrays.asList("5c0fe344544a887acbb5cd83083d303b"));
+                Arrays.asList("d535675090abd8e2dbbf6286a300d447"));
         executeTest("test file has annotations, adding StrandAlleleCountsBySample annotation", spec);
 
         Assert.assertTrue(FileUtils.readFileToString(logFile).contains(AnnotationUtils.ANNOTATION_HC_WARN_MSG));
@@ -170,7 +170,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testAskingGCContent() throws IOException{
         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 -A GCContent", 1,
-                Arrays.asList("82238b65dbd085baaec68be2975a9bf8"));
+                Arrays.asList("fcc42d7e0351efa7c3db0a114cbc17ed"));
         final File outputVCF = executeTest("test file has annotations, adding GCContent annotation", spec).getFirst().get(0);
         final VCFCodec codec = new VCFCodec();
         final VCFHeader header = (VCFHeader) codec.readActualHeader(codec.makeSourceFromStream(new FileInputStream(outputVCF)));
@@ -183,7 +183,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testOverwritingHeader() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + STANDARD_ANNOTATIONS + "--variant " + privateTestDir + "vcfexample4.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,001,292", 1,
-                Arrays.asList("fc7958261af93681fde73c1fc6b578a0"));
+                Arrays.asList("c0a7492b8db7b591686c4a6ce46469f5"));
         executeTest("test overwriting header", spec);
     }
 
@@ -191,7 +191,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testNoReads() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + STANDARD_ANNOTATIONS + "--variant " + privateTestDir + "vcfexample3empty.vcf -L " + privateTestDir + "vcfexample3empty.vcf", 1,
-                Arrays.asList("2d535a48ec1c66aa9c707f6d498fc81d"));
+                Arrays.asList("0ae3821820745e11b8f99a44378f8108"));
         executeTest("not passing it any reads", spec);
     }
 
@@ -199,7 +199,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testDBTagWithDbsnp() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " --dbsnp " + b36dbSNP129 + STANDARD_ANNOTATIONS + "--variant " + privateTestDir + "vcfexample3empty.vcf -L " + privateTestDir + "vcfexample3empty.vcf", 1,
-                Arrays.asList("a2a2f9ce8e6f9c933ad46906719ce402"));
+                Arrays.asList("2502cc8b2f5a455a048637e29765af8f"));
         executeTest("getting DB tag with dbSNP", spec);
     }
 
@@ -207,7 +207,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testMultipleIdsWithDbsnp() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " --alwaysAppendDbsnpId --dbsnp " + b36dbSNP129 + STANDARD_ANNOTATIONS + "--variant " + privateTestDir + "vcfexample3withIDs.vcf -L " + privateTestDir + "vcfexample3withIDs.vcf", 1,
-                Arrays.asList("ed351765d63d92b1913784fa47b3d859"));
+                Arrays.asList("1a989a7cb8949028d4d05668e5ccc9f8"));
         executeTest("adding multiple IDs with dbSNP", spec);
     }
 
@@ -215,7 +215,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testDBTagWithHapMap() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " --comp:H3 " + privateTestDir + "fakeHM3.vcf" + STANDARD_ANNOTATIONS + "--variant " + privateTestDir + "vcfexample3empty.vcf -L " + privateTestDir + "vcfexample3empty.vcf", 1,
-                Arrays.asList("114d8300ec0fac613bb2e82f8951adc0"));
+                Arrays.asList("30ec9163c698580747f927a016065335"));
         executeTest("getting DB tag with HM3", spec);
     }
 
@@ -223,7 +223,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testDBTagWithTwoComps() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " --comp:H3 " + privateTestDir + "fakeHM3.vcf --comp:foo " + privateTestDir + "fakeHM3.vcf " + STANDARD_ANNOTATIONS + " --variant " + privateTestDir + "vcfexample3empty.vcf -L " + privateTestDir + "vcfexample3empty.vcf", 1,
-                Arrays.asList("af59185b6a03d4147d2755019dcc6bf9"));
+                Arrays.asList("31d8e3ad540094dd814d864f68c03af8"));
         executeTest("getting DB tag with 2 comps", spec);
     }
 
@@ -231,7 +231,7 @@ 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("b6321f3ce7a60d083be64d5ec9a54c1b"));
+                Arrays.asList("de394166962da00680bbed0f906101da"));
         executeTest("test file doesn't have QUALs", spec);
     }
 
@@ -239,7 +239,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testUsingExpression() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " --resource:foo " + privateTestDir + "targetAnnotations.vcf" + STANDARD_ANNOTATIONS + "--variant " + privateTestDir + "vcfexample3empty.vcf -E foo.AF -L " + privateTestDir + "vcfexample3empty.vcf", 1,
-                Arrays.asList("7bcbd8ad8388f371d1a990fde67d3273"));
+                Arrays.asList("75b87fc789fed987c6a5e206c56d7b43"));
         executeTest("using expression", spec);
     }
 
@@ -247,7 +247,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testUsingExpressionAlleleMisMatch() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " --resourceAlleleConcordance --resource:foo " + privateTestDir + "targetAnnotations.vcf" + STANDARD_ANNOTATIONS + "--variant " + privateTestDir + "vcfexample3empty-mod.vcf -E foo.AF -L " + privateTestDir + "vcfexample3empty-mod.vcf", 1,
-                Arrays.asList("76f716569e33d88914e479b70e08ac88"));
+                Arrays.asList("59fbb48d38aa901ad4833fc40687d1dc"));
         executeTest("using expression allele mismatch", spec);
     }
 
@@ -255,7 +255,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testUsingExpressionMultiAllele() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " --resource:foo " + privateTestDir + "targetAnnotations-multiAllele.vcf" + STANDARD_ANNOTATIONS + "--variant " + privateTestDir + "vcfexample3empty-multiAllele.vcf -E foo.AF -E foo.AC -L " + privateTestDir + "vcfexample3empty-multiAllele.vcf", 1,
-                Arrays.asList("0e3fc86349f5fd28159d00d22d278e84"));
+                Arrays.asList("7b6f802e15f763383981ea055abe5c70"));
         executeTest("using expression with multi-alleles", spec);
     }
 
@@ -264,7 +264,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
         /* The order of filters in the output seems platform-dependent. May need to change htsjdk to make the order consistent across platforms. [Sato] */
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " --resource:foo " + privateTestDir + "annotationResourceWithFilter.vcf" + STANDARD_ANNOTATIONS + "--variant " + privateTestDir + "vcfexample3empty-multiAllele.vcf -E foo.FILTER -L " + privateTestDir + "vcfexample3empty-multiAllele.vcf", 1,
-                Arrays.asList("6fe67e72232165a829fde7c3b12c2275"));
+                Arrays.asList("71d4322f73b232138f5dbca7e6943514"));
         executeTest("annotate a vcf with the FILTER field of another vcf", spec);
     }
 
@@ -272,13 +272,13 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testUsingExpressionWithID() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " --resource:foo " + privateTestDir + "targetAnnotations.vcf" + STANDARD_ANNOTATIONS + "--variant " + privateTestDir + "vcfexample3empty.vcf -E foo.ID -L " + privateTestDir + "vcfexample3empty.vcf", 1,
-                Arrays.asList("94b03ee63604ab8d61aacfd3297c5dca"));
+                Arrays.asList("4253b6e3741938cd3dcb51606b1cd2a6"));
         executeTest("using expression with ID", spec);
     }
 
     @Test
     public void testTabixAnnotationsAndParallelism() {
-        final String MD5 = "c5beea399dadbba66a7fc46036eeafe5";
+        final String MD5 = "8e1e7aaf73a52640c455ed5d52db266e";
         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,
@@ -313,7 +313,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
             "--snpEffFile  " + privateTestDir + "snpEff_unsupported_version_gatk_mode.vcf " +
             "-L 1:10001292-10012424",
             1,
-            Arrays.asList("5f952cfcd25653edcffd3916d52e94ec")
+            Arrays.asList("5c7bcbc36df5df0a5ec4a89288e7f47d")
         );
         executeTest("Testing SnpEff annotations (unsupported version, GATK mode)", spec);
     }
@@ -326,14 +326,14 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
             "--snpEffFile  " + privateTestDir + "snpEff_unsupported_version_no_gatk_mode.vcf " +
             "-L 1:10001292-10012424",
             1,
-            Arrays.asList("86fb28c2e3886eda194026b3b7d07c77")
+            Arrays.asList("10f506f317c6d621fdc9a49af41ae3b4")
         );
         executeTest("Testing SnpEff annotations (unsupported version, no GATK mode)", spec);
     }
 
     @Test(enabled = true)
     public void testTDTAnnotation() {
-        final String MD5 = "cf65fdfbcd822279e84326989b2f6378";
+        final String MD5 = "255d1b89001825328f4ba31873d7a804";
         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,
@@ -344,7 +344,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
 
     @Test(enabled = true)
     public void testChromosomeCountsPed() {
-        final String MD5 = "71045f20e4cd9f5fdaa367f6d7324e59";
+        final String MD5 = "0a18fe81dde8d0f94f9ac5e5f65d00d5";
         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,
@@ -354,7 +354,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
 
     @Test(enabled = true)
     public void testInbreedingCoeffPed() {
-        final String MD5 = "0cf7c115316950abc0213935b20a653a";
+        final String MD5 = "95408408863cc81c63ec3c53716bf9d2";
         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,
@@ -364,7 +364,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
 
     @Test(enabled = true)
     public void testAlleleTrimming() {
-        final String MD5 = "5db0cd72ad0ffc711afb95df58de31fa";
+        final String MD5 = "f4f77d372a4bc7ab0adb3e17de8d860d";
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T VariantAnnotator -R " + b37KGReference + " -A InbreedingCoeff --variant:vcf " + privateTestDir + "alleleTrim.vcf.gz" +
                         " -L 1:26608870-26608875 -no_cmdline_in_header --resource:exac " + privateTestDir +  "exacAlleleTrim.vcf.gz  -E exac.AC_Adj" +
@@ -423,7 +423,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
 
     @Test
     public void testStrandAlleleCountsBySample() {
-        final String MD5 = "994d1d3c53e3878e17d20e1327506d77";
+        final String MD5 = "323cefddc0abad26fe2a2b6c845f3d05";
         final WalkerTestSpec spec = new WalkerTestSpec(
                 "-T HaplotypeCaller --disableDithering " +
                 String.format("-R %s -I %s ", REF, CEUTRIO_BAM) +

protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/DiagnoseTargetsIntegrationTest.java

@@ -71,11 +71,11 @@ public class DiagnoseTargetsIntegrationTest extends WalkerTest {
 
     @Test(enabled = true)
     public void testSingleSample() {
-        DTTest("testSingleSample ", "-I " + singleSample + " -max 75", "19c56b853b20ac674b6de1332043586d");
+        DTTest("testSingleSample ", "-I " + singleSample + " -max 75", "4744f634145b7338888ae620334b6565");
     }
 
     @Test(enabled = true)
     public void testMultiSample() {
-        DTTest("testMultiSample ", "-I " + multiSample, "90770023666f3c1d6a3f35e5ecada4a8");
+        DTTest("testMultiSample ", "-I " + multiSample, "3de8beb346b41bc57b4b5d456c01d167");
     }
 }

protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/filters/VariantFiltrationIntegrationTest.java

@@ -68,7 +68,7 @@ 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("42a73683f2064a73d4b21a06c208205b"));
+                Arrays.asList("cc2398d5a69e4d3ead25e70e8c786dfa"));
         executeTest("test no action", spec);
     }
 
@@ -76,7 +76,7 @@ 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("5e5c03487b0b89169dafad327d8afd4a"));
+                Arrays.asList("92d9d04451f8fa510dd34db837a8314b"));
         executeTest("test clustered SNPs", spec);
     }
 
@@ -84,7 +84,7 @@ 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("a286b5919ff373f454d24374a115c696"));
+                Arrays.asList("e1e65e8d66e02715a73137a2cbb2d2d1"));
         executeTest("test mask all", spec1);
     }
 
@@ -92,7 +92,7 @@ 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("c05349a096f6c4919ed24b293f40ffa8"));
+                Arrays.asList("270e06d7e83e40e6a273668be890fe56"));
         executeTest("test mask some", spec2);
     }
 
@@ -100,7 +100,7 @@ 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("e45e4a287072cb6d4ec7596344fd0579"));
+                Arrays.asList("e4d1c66da07d1d0ccfe674ed2b013849"));
         executeTest("test mask extend", spec3);
     }
 
@@ -108,7 +108,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
     public void testMaskReversed() {
         WalkerTestSpec spec3 = new WalkerTestSpec(
                 baseTestString() + " -maskName outsideGoodSites -filterNotInMask --mask:BED " + privateTestDir + "goodMask.bed --variant " + privateTestDir + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("35428e4348a11abc260a1d40049bdefd"));
+                Arrays.asList("42e6dd3f30618753dc7411509c83c14f"));
         executeTest("test filter sites not in mask", spec3);
     }
 
@@ -124,7 +124,7 @@ 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("d7a9a49ed19bc0452595c293915a1480"));
+                Arrays.asList("f635fa722b962a6cdf429f84b0aa8b12"));
         executeTest("test filter #1", spec);
     }
 
@@ -132,7 +132,7 @@ 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("0c0fddb0eb6f9d3f74556332cd498079"));
+                Arrays.asList("0a7cdf3117b4e8bcfcc41fde34ef0a9e"));
         executeTest("test filter #2", spec);
     }
 
@@ -140,7 +140,7 @@ 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("45f90fd349d76b386fce4b9075d16b7e"));
+                Arrays.asList("7f798982ec0d90aa32484e35a89c7b4f"));
         executeTest("test filter with separate names #2", spec);
     }
 
@@ -148,7 +148,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
     public void testInvertFilter() {
         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 --invertFilterExpression", 1,
-                Arrays.asList("c88c845108a26bebfeb09c420671c06f"));
+                Arrays.asList("01dc0130f85ef609c6f4f6e7235ef644"));
         executeTest("test inversion of selection of filter with separate names #2", spec);
     }
 
@@ -156,7 +156,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
     public void testInvertJexlFilter() {
         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("f5e03e4584f9b1d82f9d430543f06bd6")); // Differs from testInvertFilter() because their VCF header FILTER description uses the -filter argument. Their filter statuses are identical.
+                Arrays.asList("23b6c0f2f682b744501ffdd1141d62ca")); // Differs from testInvertFilter() because their VCF header FILTER description uses the -filter argument. Their filter statuses are identical.
         executeTest("test inversion of selection of filter via JEXL with separate names #2", spec);
     }
 
@@ -164,7 +164,7 @@ 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("b6e8d70223826000ea1a6d6bc9c4fc65"));
+                Arrays.asList("fbb22221a531d68a6394042ebf247aa0"));
         executeTest("test genotype filter #1", spec1);
     }
 
@@ -172,7 +172,7 @@ 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("9cd315a433ab7d9da637156011328509"));
+                Arrays.asList("99eacba26598ab31501e09604ff88be2"));
         executeTest("test genotype filter #2", spec2);
     }
 
@@ -180,7 +180,7 @@ 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("32ed1e11fde63a57c1dfb7f83f5344f0"));
+                Arrays.asList("ff84050b969d1068eb9ef39058d0e007"));
         executeTest("test deletions", spec);
     }
 
@@ -189,7 +189,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
             "-T VariantFiltration -o %s --no_cmdline_in_header -R " + b37KGReference
                     + " --filterExpression 'FS > 60.0' --filterName SNP_FS -V " + privateTestDir + "unfilteredForFiltering.vcf", 1,
-                Arrays.asList("b9fa012770831c984101d23420ef0c38"));
+                Arrays.asList("3f828fd8768ec0e1708ae509fdb5e998"));
         executeTest("testUnfilteredBecomesFilteredAndPass", spec);
     }
 
@@ -198,7 +198,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T VariantFiltration -o %s --no_cmdline_in_header -R " + b37KGReference
                         + " --filterExpression 'DP < 8' --filterName lowDP -V " + privateTestDir + "filteringDepthInFormat.vcf", 1,
-                Arrays.asList("c3eff7d167e1bfca5726a6e475e6b3ec"));
+                Arrays.asList("397aa0a403d8c2aa47beb14788d81517"));
         executeTest("testFilteringDPfromINFO", spec);
     }
 
@@ -207,7 +207,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T VariantFiltration -o %s --no_cmdline_in_header -R " + b37KGReference
                         + " --genotypeFilterExpression 'DP < 8' --genotypeFilterName lowDP -V " + privateTestDir + "filteringDepthInFormat.vcf", 1,
-                Arrays.asList("b0016040127766a4163fcbd91afff3ea"));
+                Arrays.asList("8c82cc0ec68b2397512d7bf255c17730"));
         executeTest("testFilteringDPfromFORMAT", spec);
     }
 
@@ -220,7 +220,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T VariantFiltration -o %s --no_cmdline_in_header -R " + b37KGReference
                         + " --genotypeFilterExpression 'Z < 10' --genotypeFilterName lowZ -V " + privateTestDir + "filteringDepthInFormatWithMissing.vcf", 1,
-                Arrays.asList("47607708dee31b6033f14a3613c8acb8"));
+                Arrays.asList("fa1bf49c94a36fa79c99f741a9fad14e"));
         executeTest("testFilteringDPfromFORMATWithMissing", spec);
     }
 
@@ -230,7 +230,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T VariantFiltration -o %s --no_cmdline_in_header -R " + b37KGReference
                         + " --missingValuesInExpressionsShouldEvaluateAsFailing --genotypeFilterExpression 'Z < 10' --genotypeFilterName lowZ -V " + privateTestDir + "filteringDepthInFormatWithMissing.vcf", 1,
-                Arrays.asList("4f519e725203931841940707c50ab6a3"));
+                Arrays.asList("0bf39f791e1a4d9a935fca86407b1c0f"));
         executeTest("testFilteringDPfromFORMATAndFailMissing", spec);
     }
 
@@ -239,7 +239,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T VariantFiltration -o %s --no_cmdline_in_header -R " + b37KGReference
                         + " --genotypeFilterExpression 'DP < 8' --genotypeFilterName highDP -V " + privateTestDir + "filteringDepthInFormat.vcf --invertGenotypeFilterExpression", 1,
-                Arrays.asList("c6bc275c97a9e737748d16132ee76f48"));
+                Arrays.asList("cc8eab3f7cacc6d7effc9df9ba98210a"));
         executeTest("testInvertGenotypeFilterExpression", spec);
     }
 
@@ -248,7 +248,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T VariantFiltration -o %s --no_cmdline_in_header -R " + b37KGReference
                         + " --genotypeFilterExpression 'DP >= 8' --genotypeFilterName highDP -V " + privateTestDir + "filteringDepthInFormat.vcf", 1,
-                Arrays.asList("9321b5993d51a4da02f69e5467164587")); // Differs from testInvertFilter because FILTER description uses the -genotypeFilterExpression argument
+                Arrays.asList("bb22c3ca06bf22ca244504b2b3e27259")); // Differs from testInvertFilter because FILTER description uses the -genotypeFilterExpression argument
         executeTest("testInvertJexlGenotypeFilterExpression", spec);
     }
 
@@ -257,7 +257,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T VariantFiltration -o %s --no_cmdline_in_header -R " + b37KGReference
                         + " --genotypeFilterExpression 'DP < 8' --genotypeFilterName lowDP -V " + privateTestDir + "filteringDepthInFormat.vcf --setFilteredGtToNocall", 1,
-                Arrays.asList("00990d54017b7384ce9f979d796b9d16"));
+                Arrays.asList("7a9d29b6a002aa4fba11bcaf24401a70"));
         executeTest("testSetFilteredGtoNocall", spec);
     }
 
@@ -268,7 +268,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
                 "-T VariantFiltration -o %s --no_cmdline_in_header -R " + b37KGReference
                         + " -G_filter 'GQ < 20' -G_filterName lowDP -G_filter 'DP<10' -G_filterName lowGQ -V " + privateTestDir + "variantFiltrationInfoField.vcf --setFilteredGtToNocall",
                 1,
-                Arrays.asList("0f8ed3a62a53feca0c4b86671e4b53e4"));
+                Arrays.asList("fd39d39082d8a1535003a9d216905e73"));
         executeTest("testSetFilteredGtoNocallUpdateInfo", spec);
     }
 
@@ -279,7 +279,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T SelectVariants --setFilteredGtToNocall -R " + b37KGReference + " --variant " + testfile + " -o %s --no_cmdline_in_header",
                 1,
-                Arrays.asList("cb5ef9233503bebc81593e436a6de943")
+                Arrays.asList("fb3030518f7c4120989d37b2cca9abe6")
         );
 
         spec.disableShadowBCF();

protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/NanoSchedulerIntegrationTest.java

@@ -70,7 +70,7 @@ public class NanoSchedulerIntegrationTest extends WalkerTest {
 
         for ( final int nt : Arrays.asList(1, 2) )
             for ( final int nct : Arrays.asList(1, 2) ) {
-                tests.add(new Object[]{ "BOTH",  "e2fdd36a4eda18f748df944b428fa392", nt, nct });
+                tests.add(new Object[]{ "BOTH",  "5f0b3a9c45461f29bf963384752b8eb1", nt, nct });
             }
 
         return tests.toArray(new Object[][]{});

protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite1IntegrationTest.java

@@ -69,17 +69,17 @@ public class UnifiedGenotyperGeneralPloidySuite1IntegrationTest extends WalkerTe
 
     @Test(enabled = true)
     public void testSNP_ACS_Pools() {
-        executor.PC_LSV_Test_short("-A AlleleCountBySample -maxAltAlleles 1 -ploidy 6 -out_mode EMIT_ALL_CONFIDENT_SITES", "LSV_SNP_ACS", "SNP", "963e128314aceaab06c240850b836b10");
+        executor.PC_LSV_Test_short("-A AlleleCountBySample -maxAltAlleles 1 -ploidy 6 -out_mode EMIT_ALL_CONFIDENT_SITES", "LSV_SNP_ACS", "SNP", "33f9c8a6c32a7848a82cd9b4c943123d");
     }
 
     @Test(enabled = true)
     public void testBOTH_GGA_Pools() {
-        executor.PC_LSV_Test(String.format("-A AlleleCountBySample -maxAltAlleles 2 -ploidy 24 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles %s", LSV_ALLELES), "LSV_BOTH_GGA", "BOTH", "f3bf8b59a04db9fb52dcdea76664606d");
+        executor.PC_LSV_Test(String.format("-A AlleleCountBySample -maxAltAlleles 2 -ploidy 24 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles %s", LSV_ALLELES), "LSV_BOTH_GGA", "BOTH", "4c34d540516cd8407ecf31f00a7b6807");
     }
 
     @Test(enabled = true)
     public void testINDEL_GGA_Pools() {
-        executor.PC_LSV_Test(String.format("-A AlleleCountBySample -maxAltAlleles 1 -ploidy 24 -gt_mode GENOTYPE_GIVEN_ALLELES  -out_mode EMIT_ALL_SITES -alleles %s", LSV_ALLELES), "LSV_INDEL_GGA", "INDEL", "f8bae1491695d02ccb929205b4458759");
+        executor.PC_LSV_Test(String.format("-A AlleleCountBySample -maxAltAlleles 1 -ploidy 24 -gt_mode GENOTYPE_GIVEN_ALLELES  -out_mode EMIT_ALL_SITES -alleles %s", LSV_ALLELES), "LSV_INDEL_GGA", "INDEL", "154600bab3358d69bf94eb23e2cbf21d");
     }
 
     @Test(enabled = true)
@@ -88,6 +88,6 @@ public class UnifiedGenotyperGeneralPloidySuite1IntegrationTest extends WalkerTe
         //TODO the old MD5 is kept for the record.
         //TODO this should be revisit once we get into addressing inaccuracies by the independent allele approach.
 //        executor.PC_LSV_Test_NoRef("-A AlleleCountBySample -maxAltAlleles 2 -ploidy 1", "LSV_INDEL_DISC_NOREF_p1", "INDEL", "b5ff7530827f4b9039a58bdc8a3560d2");
-        executor.PC_LSV_Test_NoRef("-A AlleleCountBySample -maxAltAlleles 2 -ploidy 1", "LSV_INDEL_DISC_NOREF_p1", "INDEL", "f6b9e1ac0c51c9702525ee52bb2db18a");
+        executor.PC_LSV_Test_NoRef("-A AlleleCountBySample -maxAltAlleles 2 -ploidy 1", "LSV_INDEL_DISC_NOREF_p1", "INDEL", "5dcf0342449635b0ccd2457cf476cb1e");
     }
 }

protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite2IntegrationTest.java

@@ -63,16 +63,16 @@ public class UnifiedGenotyperGeneralPloidySuite2IntegrationTest extends WalkerTe
 
     @Test(enabled = true)
     public void testINDEL_maxAltAlleles2_ploidy3_Pools_noRef() {
-        executor.PC_LSV_Test_NoRef("-A AlleleCountBySample -maxAltAlleles 2 -ploidy 3","LSV_INDEL_DISC_NOREF_p3","INDEL","cdaa55c53005deb132f600fa5539c254");
+        executor.PC_LSV_Test_NoRef("-A AlleleCountBySample -maxAltAlleles 2 -ploidy 3","LSV_INDEL_DISC_NOREF_p3","INDEL","f8992deabd27e5b492f3a0edcbc93c40");
     }
 
     @Test(enabled = true)
     public void testMT_SNP_DISCOVERY_sp4() {
-        executor.PC_MT_Test(CEUTRIO_BAM, "-A AlleleCountBySample -maxAltAlleles 1 -ploidy 8", "MT_SNP_DISCOVERY_sp4","9757563c5e32f59cb47eb9b16f1016ac");
+        executor.PC_MT_Test(CEUTRIO_BAM, "-A AlleleCountBySample -maxAltAlleles 1 -ploidy 8", "MT_SNP_DISCOVERY_sp4","47f6c9d12801c73c8fff943f43db6ebc");
     }
 
     @Test(enabled = true)
     public void testMT_SNP_GGA_sp10() {
-        executor.PC_MT_Test(CEUTRIO_BAM, String.format("-A AlleleCountBySample -maxAltAlleles 1 -ploidy 20 -gt_mode GENOTYPE_GIVEN_ALLELES  -out_mode EMIT_ALL_SITES -alleles %s",NA12891_CALLS), "MT_SNP_GGA_sp10", "37f8ccc683dc525c25dddc4f8dad505c");
+        executor.PC_MT_Test(CEUTRIO_BAM, String.format("-A AlleleCountBySample -maxAltAlleles 1 -ploidy 20 -gt_mode GENOTYPE_GIVEN_ALLELES  -out_mode EMIT_ALL_SITES -alleles %s",NA12891_CALLS), "MT_SNP_GGA_sp10", "90ea74d14c9649702952bcad0153fc36");
     }
 }

protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperIndelCallingIntegrationTest.java

@@ -78,7 +78,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest {
                         " -o %s" +
                         " -L 1:10,000,000-10,500,000",
                 1,
-                Arrays.asList("96afa04944156c1ca5028e5506ba8b94"));
+                Arrays.asList("b40f9d9b7cf29318760a1c2915522e99"));
         executeTest(String.format("test indel caller in SLX"), spec);
     }
 
@@ -92,7 +92,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest {
                         " -minIndelCnt 1" +
                         " -L 1:10,000,000-10,100,000",
                 1,
-                Arrays.asList("897c6063236fcd7242c2ff5982585648"));
+                Arrays.asList("efdf45ab9ec9a55b063692dd58ab8e9b"));
 
         executeTest(String.format("test indel caller in SLX with low min allele count"), spec);
     }
@@ -105,7 +105,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest {
                         " -o %s" +
                         " -L 1:10,000,000-10,500,000",
                 1,
-                Arrays.asList("7e211573190003342af274e64a0612fb"));
+                Arrays.asList("a6c9cda80a5d4d4942dba78cdd979317"));
 
         executeTest(String.format("test indel calling, multiple technologies"), spec);
     }
@@ -115,7 +115,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 baseCommandIndels + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + privateTestDir + "indelAllelesForUG.vcf -I " + validationDataLocation +
                         "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,100,000", 1,
-                Arrays.asList("50622e495cad2a24fbc4a80f1281d4dc"));
+                Arrays.asList("0fcda99b3e68152540064ba53f2ae221"));
         executeTest("test MultiSample Pilot2 indels with alleles passed in", spec);
     }
 
@@ -125,7 +125,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest {
                 baseCommandIndels + " --output_mode EMIT_ALL_SITES --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles "
                         + privateTestDir + "indelAllelesForUG.vcf -I " + validationDataLocation +
                         "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,100,000", 1,
-                Arrays.asList("50622e495cad2a24fbc4a80f1281d4dc"));
+                Arrays.asList("0fcda99b3e68152540064ba53f2ae221"));
         executeTest("test MultiSample Pilot2 indels with alleles passed in and emitting all sites", spec);
     }
 
@@ -140,7 +140,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest 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 " + result.get(0).getAbsolutePath(), 1,
-                Arrays.asList("751334df2c7b14cc0e57df231825da57"));
+                Arrays.asList("9d98079079d88346b6558dabdd109b21"));
         executeTest("test MultiSample Pilot1 CEU indels using GENOTYPE_GIVEN_ALLELES", spec2);
     }
 
@@ -150,7 +150,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 baseCommandIndelsb37 + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles " + privateTestDir + vcf + " -I " + validationDataLocation +
                         "NA12878.HiSeq.WGS.bwa.cleaned.recal.hg19.20.bam -o %s -L " + validationDataLocation + vcf, 1,
-                Arrays.asList("41aa49e9c15198a006a1bc8e9638d6ec"));
+                Arrays.asList("0d04efc9c5ea0f6f7da954243f4450d6"));
         executeTest("test GENOTYPE_GIVEN_ALLELES with no evidence in reads", spec);
     }
 
@@ -162,7 +162,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest {
                         " -o %s" +
                         " -L 20:10,000,000-10,100,000",
                 1,
-                Arrays.asList("e883a8863bdd44c559c4440183c87078"));
+                Arrays.asList("bca5117bb7c5c2d2c8a2dd91bd13573b"));
 
         executeTest(String.format("test UG with base indel quality scores"), spec);
     }
@@ -181,7 +181,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest {
     public void testMinIndelFraction0() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 assessMinIndelFraction + " -minIndelFrac 0.0", 1,
-                Arrays.asList("0d1a5c865c382f1f0ca6f0f104478366"));
+                Arrays.asList("f26bb53b698144e469a73b9c8e777eab"));
         executeTest("test minIndelFraction 0.0", spec);
     }
 
@@ -189,7 +189,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest {
     public void testMinIndelFraction25() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 assessMinIndelFraction + " -minIndelFrac 0.25", 1,
-                Arrays.asList("aab86cec61adaeb3a5c6887e70211663"));
+                Arrays.asList("88d61c2af617e3fde2519b99e4d9548c"));
         executeTest("test minIndelFraction 0.25", spec);
     }
 
@@ -197,7 +197,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest {
     public void testMinIndelFraction100() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 assessMinIndelFraction + " -minIndelFrac 1", 1,
-                Arrays.asList("990b838ef13b8ccf257eb6cbcc7c7741"));
+                Arrays.asList("ccca66da09cbd54032cfae93ddad1513"));
         executeTest("test minIndelFraction 1.0", spec);
     }
 

protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperIntegrationTest.java

@@ -86,7 +86,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     public void testMinBaseQualityScore() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000 --min_base_quality_score 26", 1,
-                Arrays.asList("d0499af17dc66e77849e547bc5a182ff"));
+                Arrays.asList("db97b0b221288b5915e5b3b72c619edd"));
         executeTest("test min_base_quality_score 26", spec);
     }
 
@@ -94,7 +94,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     public void testSLOD() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-T UnifiedGenotyper --disableDithering -R " + b36KGReference + " --computeSLOD --no_cmdline_in_header -glm BOTH --dbsnp " + b36dbSNP129 + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000", 1,
-                Arrays.asList("31790ea2bd2fa7e5cec78e3ffbc98c81"));
+                Arrays.asList("3a57dbbc06ae8f8e97f5c1f2c1069db9"));
         executeTest("test SLOD", spec);
     }
 
@@ -102,7 +102,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     public void testNDA() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 baseCommand + " --annotateNDA -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000", 1,
-                Arrays.asList("5f69de274c0705cf1cb9387651df98bf"));
+                Arrays.asList("cb6b22ce72194bc4d94425ed79125252"));
         executeTest("test NDA", spec);
     }
 
@@ -110,7 +110,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     public void testCompTrack() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-T UnifiedGenotyper --disableDithering -R " + b36KGReference + " --no_cmdline_in_header -glm BOTH -comp:FOO " + b36dbSNP129 + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000", 1,
-                Arrays.asList("7645a06b917efb1ee799bf21bdf08bc4"));
+                Arrays.asList("fef47b4ab5522d725f4a63b594fc4a19"));
         executeTest("test using comp track", spec);
     }
 
@@ -124,17 +124,17 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
 
     @Test
     public void testOutputParameterSitesOnly() {
-        testOutputParameters("-sites_only", "4355f5b6fd8cd769a479677f1255bee5");
+        testOutputParameters("-sites_only", "5e7951f6b79da35b23759a9a1811ab7c");
     }
 
     @Test
     public void testOutputParameterAllConfident() {
-        testOutputParameters("--output_mode EMIT_ALL_CONFIDENT_SITES", "96567418000ec94abee98d70199a700a");
+        testOutputParameters("--output_mode EMIT_ALL_CONFIDENT_SITES", "7793846345ec89225e67f91b77e743fe");
     }
 
     @Test
     public void testOutputParameterAllSites() {
-        testOutputParameters("--output_mode EMIT_ALL_SITES", "5ccff12b34ace5e882e465047a286c5a");
+        testOutputParameters("--output_mode EMIT_ALL_SITES", "a01e1496a33ad4432aa61d7a2a0d537b");
     }
 
     private void testOutputParameters(final String args, final String md5) {
@@ -148,7 +148,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     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("c794c7681856c1ec3c3429dbd9e5dc75"));
+                Arrays.asList("add6c3cf336af60e8486fe7a126bd2d2"));
         executeTest("test confidence 1", spec1);
     }
 
@@ -156,7 +156,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     public void testNoPrior() {
         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 -inputPrior 0.33333 -inputPrior 0.33333", 1,
-                Arrays.asList("39d15f041a0c86058f46f23960bb129b"));
+                Arrays.asList("492399d4e0ecb3f7b7fdffe13824c2e5"));
         executeTest("test no prior 1", spec1);
 
     }
@@ -165,7 +165,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     public void testUserPrior() {
         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 -inputPrior 0.001 -inputPrior 0.495", 1,
-                Arrays.asList("00bff7a5dc584b5b6931a826eae6b013"));
+                Arrays.asList("197cf6731a872dae4741cfb61f2ab998"));
         executeTest("test user prior 1", spec1);
 
     }
@@ -174,7 +174,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     public void emitPLsAtAllSites() {
         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 --output_mode EMIT_ALL_SITES -allSitePLs", 1,
-                Arrays.asList("067d0a9d90c978c5563ea56a86fc682f"));
+                Arrays.asList("07907e90e5f2ca1846b2f6e8a03a05ed"));
         // GDA: TODO: BCF encoder/decoder doesn't seem to support non-standard values in genotype fields. IE even if there is a field defined in FORMAT and in the header the BCF2 encoder will still fail
         spec1.disableShadowBCF();
 
@@ -190,12 +190,12 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
 
     @Test
     public void testHeterozyosity1() {
-        testHeterozosity( 0.01, "0175a3d4dedea857f87149522d133d78" );
+        testHeterozosity( 0.01, "623dcc22c6a8486784801850fcac6b20" );
     }
 
     @Test
     public void testHeterozyosity2() {
-        testHeterozosity( 1.0 / 1850, "080a14940e4d3f5c14c533d019b99341" );
+        testHeterozosity( 1.0 / 1850, "e2bed193a372f88ab619cd0dfd58daf8" );
     }
 
     private void testHeterozosity(final double arg, final String md5) {
@@ -238,7 +238,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
 
         // Note that we need to turn off any randomization for this to work, so no downsampling and no annotations
 
-        String md5 = "75b4b097747f91b8b7ceea153d2b7e1c";
+        String md5 = "45eb2400f92a82dda2051d4fdfcd2326";
         final String myCommand = "-T UnifiedGenotyper --disableDithering -R " + b36KGReference + " --no_cmdline_in_header -glm BOTH -minIndelFrac 0.0 --dbsnp " + b36dbSNP129;
 
         WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
@@ -274,7 +274,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
                         " -o %s" +
                         " -L 1:10,000,000-10,100,000",
                 1,
-                Arrays.asList("482f6b310e59d05508811932ec21c801"));
+                Arrays.asList("7eaafbfa82378775869e74af6496a178"));
 
         executeTest(String.format("test multiple technologies"), spec);
     }
@@ -293,7 +293,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
                         " -L 1:10,000,000-10,100,000" +
                         " -baq CALCULATE_AS_NECESSARY",
                 1,
-                Arrays.asList("c99b7dbe881aa3274cb9876e495cf8f3"));
+                Arrays.asList("4d9270b73d69e12421e4722adfe96962"));
 
         executeTest(String.format("test calling with BAQ"), spec);
     }
@@ -310,7 +310,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
                 baseCommand + " -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -o %s -L 1:10,022,000-10,025,000 " +
                 "-A SnpEff",
                 1,
-                Arrays.asList("81ac0ffd22a0d0907848019944034359"));
+                Arrays.asList("210ac5718820e950eea0f06cec7d424f"));
 
         executeTest("testSnpEffAnnotationRequestedWithoutRodBinding", spec);
     }

protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperNormalCallingIntegrationTest.java

@@ -70,7 +70,7 @@ public class UnifiedGenotyperNormalCallingIntegrationTest extends WalkerTest{
     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("605f447127bf9c92f60bbaa9c6a6732e"));
+                Arrays.asList("693f83b637eb08fffb7681ab483dce3b"));
         executeTest("test MultiSample Pilot1", spec);
     }
 
@@ -78,7 +78,7 @@ public class UnifiedGenotyperNormalCallingIntegrationTest extends WalkerTest{
     public void testWithAllelesPassedIn1() {
         WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
                 baseCommand + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + privateTestDir + "allelesForUG.vcf -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,025,000", 1,
-                Arrays.asList("c35cadefda8a9f13c497f84193f9f841"));
+                Arrays.asList("33933081c341421963d8d101dd907e48"));
         executeTest("test MultiSample Pilot2 with alleles passed in", spec1);
     }
 
@@ -86,7 +86,7 @@ public class UnifiedGenotyperNormalCallingIntegrationTest extends WalkerTest{
     public void testWithAllelesPassedIn2() {
         WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
                 baseCommand + " --output_mode EMIT_ALL_SITES --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + privateTestDir + "allelesForUG.vcf -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,025,000", 1,
-                Arrays.asList("06b4ce476bf444305c8d76a765c5ddb6"));
+                Arrays.asList("2a8bbf4508993c1573f5a7c8a17033bb"));
         executeTest("test MultiSample Pilot2 with alleles passed in and emitting all sites", spec2);
     }
 
@@ -94,7 +94,7 @@ public class UnifiedGenotyperNormalCallingIntegrationTest extends WalkerTest{
     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("ac9905e26a2c51129d22b5c617679c6a"));
+                Arrays.asList("07d5cbb0bb47e854049802550b918ee7"));
         executeTest("test SingleSample Pilot2", spec);
     }
 
@@ -102,7 +102,7 @@ public class UnifiedGenotyperNormalCallingIntegrationTest extends WalkerTest{
     public void testMultipleSNPAlleles() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-T UnifiedGenotyper --contamination_fraction_to_filter 0.05 --disableDithering -R " + b37KGReference + " --no_cmdline_in_header -glm BOTH --dbsnp " + b37dbSNP129 + " -I " + privateTestDir + "multiallelic.snps.bam -o %s -L " + privateTestDir + "multiallelic.snps.intervals", 1,
-                Arrays.asList("3304a20af6745beeec07ef2c47d617d3"));
+                Arrays.asList("ff384cb588767f03ea6fa76c6095bacc"));
         executeTest("test Multiple SNP alleles", spec);
     }
 
@@ -110,7 +110,7 @@ public class UnifiedGenotyperNormalCallingIntegrationTest extends WalkerTest{
     public void testBadRead() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-T UnifiedGenotyper --contamination_fraction_to_filter 0.05 --disableDithering -R " + b37KGReference + " --no_cmdline_in_header -glm BOTH -I " + privateTestDir + "badRead.test.bam -o %s -L 1:22753424-22753464", 1,
-                Arrays.asList("1d5c55b2df63eb24832de3486c020453"));
+                Arrays.asList("4daa9bfe2c691ef29ff1e2d1a24ab7f9"));
         executeTest("test bad read", spec);
     }
 
@@ -118,7 +118,7 @@ public class UnifiedGenotyperNormalCallingIntegrationTest extends WalkerTest{
     public void testReverseTrim() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-T UnifiedGenotyper --contamination_fraction_to_filter 0.05 --disableDithering -R " + b37KGReference + " --no_cmdline_in_header -glm INDEL -I " + validationDataLocation + "CEUTrio.HiSeq.b37.chr20.10_11mb.bam -o %s -L 20:10289124 -L 20:10090289", 1,
-                Arrays.asList("87dbae957b1df41c1938906e23a88c5e"));
+                Arrays.asList("631fb3bc0f798f441745f9ce14188fdc"));
         executeTest("test reverse trim", spec);
     }
 
@@ -126,7 +126,7 @@ public class UnifiedGenotyperNormalCallingIntegrationTest extends WalkerTest{
     public void testMismatchedPLs() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-T UnifiedGenotyper --contamination_fraction_to_filter 0.05 --disableDithering -R " + b37KGReference + " --no_cmdline_in_header -glm INDEL -I " + privateTestDir + "mismatchedPLs.bam -o %s -L 1:24020341", 1,
-                Arrays.asList("5dc0ccd66105e0f12c72987d56c85235"));
+                Arrays.asList("c0e4fe0a1a9534d26223c0313316b8ef"));
         executeTest("test mismatched PLs", spec);
     }
 }

protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest.java

@@ -69,7 +69,7 @@ public class HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest extends Wa
 
     @Test
     public void testHaplotypeCallerMultiSampleComplex1() {
-        HCTestComplexVariants(privateTestDir + "AFR.complex.variants.bam", "", "93f89c04b4c74463f75da798cdcf5064");
+        HCTestComplexVariants(privateTestDir + "AFR.complex.variants.bam", "", "5a9893ec6e59ba1c0e00480a5d0e7dd1");
     }
 
     private void HCTestSymbolicVariants(String bam, String args, String md5) {
@@ -81,7 +81,7 @@ public class HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest extends Wa
     // TODO -- need a better symbolic allele test
     @Test
     public void testHaplotypeCallerSingleSampleSymbolic() {
-        HCTestSymbolicVariants(NA12878_CHR20_BAM, "", "e158212aba1d7d229563db11b08b7974");
+        HCTestSymbolicVariants(NA12878_CHR20_BAM, "", "dadf136ea2db7d2c4244fcc908042e27");
     }
 
     private void HCTestComplexGGA(String bam, String args, String md5) {
@@ -93,13 +93,13 @@ public class HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest extends Wa
     @Test
     public void testHaplotypeCallerMultiSampleGGAComplex() {
         HCTestComplexGGA(NA12878_CHR20_BAM, "-L 20:119673-119823 -L 20:121408-121538",
-                "558820f3b67f4434a41e0cb96b6469c7");
+                "fa080106b2982c0473f19161f8f9183d");
     }
 
     @Test
     public void testHaplotypeCallerMultiSampleGGAMultiAllelic() {
         HCTestComplexGGA(NA12878_CHR20_BAM, "-L 20:133041-133161 -L 20:300207-300337",
-                "d50cf0d1efd94227e930565a6d31de91");
+                "15ed9c20bfd1430b14ac68524bdb5698");
     }
 
     private void HCTestComplexConsensusMode(String bam, String args, String md5) {
@@ -111,7 +111,7 @@ public class HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest extends Wa
     @Test
     public void testHaplotypeCallerMultiSampleConsensusModeComplex() {
         HCTestComplexGGA(NA12878_CHR20_BAM, "-L 20:119673-119823 -L 20:121408-121538 -L 20:133041-133161 -L 20:300207-300337",
-                "390236e17de3465c8ba778041f1670ad");
+                "0dbb81db4736c4c0a5e57aae1074d9ca");
     }
 
 }

protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGVCFIntegrationTest.java

@@ -86,12 +86,12 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
         //TODO this might need to be addressed at some point.
         //TODO the following test is commented out for the record
         //tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "7f09c261950bf86e435edfa69ed2ec71"});
-        tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "c64e8f169b40dfcdac5bea71156753b5"});
+        tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "db25572025ab2481b40f100ec499db45"});
-        tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "2cc9f789100e138ffc0c383b12a1322a"});
+        tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "568ae19bd27bf81add12b8fd53a37b30"});
-        tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "44cc8f78e28d905efc30c218d821cc7c"});
+        tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "57ac809fc00eb87724eef6064193b2c9"});
-        tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "2e81881e92061ad4eb29025ffdc129c7"});
+        tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "2870f9cf471a737a5d6b23ba8e250e03"});
-        tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "39b2ad53ffdfcbaa4af3454c321daaa7"});
+        tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "516e51a94e968cbffdc37f6da470677c"});
-        tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals, "861fa31b135d200f765914126b422cf4"});
+        tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals, "e6c8108166c5c112e29bf8310e141dfe"});
 
         return tests.toArray(new Object[][]{});
     }
@@ -105,13 +105,13 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
         final String WExIntervals = "-L 20:10,000,000-10,100,000 -isr INTERSECTION -L " + hg19Chr20Intervals;
 
         // this functionality can be adapted to provide input data for whatever you might want in your data
-        tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "cd21856eec2f1c1920408f20fd08411b"});
+        tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "77c2e2075895ea7635949534d38b45c5"});
-        tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "d146c8dc4fc0605b3776ab5fec837d53"});
+        tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "5f8be6e9bdf2e8c06ed31b71804c8edc"});
-        tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "c317193f0d1c9a8168f2625c8bf1dd2b"});
+        tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "7a368e838fbb17ccfa529ba9210b02cd"});
-        tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "63ff771eed3e62340c8938b4963d0add"});
+        tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "a08926513178b6f82c37bea85e847437"});
-        tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "c6c19ff9dc229f6af6080a175267344c"});
+        tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "7debb053c4241c070625d7041da71196"});
 
-        final String NA12878bandedResolutionMD5 = "7240907ec3dc2ed49b55c9956546ba13";
+        final String NA12878bandedResolutionMD5 = "2eacf3a41f71d7a035223512886dc2c7";
         tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals, NA12878bandedResolutionMD5});
         tests.add(new Object[]{NA12878_WEx + " -I " + privateTestDir + "NA20313.highCoverageRegion.bam -sn NA12878",
                 ReferenceConfidenceMode.GVCF, WExIntervals, NA12878bandedResolutionMD5});
@@ -128,12 +128,12 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
         final String WExIntervals = "-L 20:10,000,000-10,100,000 -isr INTERSECTION -L " + hg19Chr20Intervals;
 
         // this functionality can be adapted to provide input data for whatever you might want in your data
-        tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "093f129861ea93526f6b80b4c8c70178"});
+        tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "c72403e4796942adfd272ecb28689df9"});
-        tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "6c727b804084a2324ecd1c98b72734b9"});
+        tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "3f446f0393a7d9eee75e107cafb1015b"});
-        tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "190cef14684c95ba290d7a5fa13fdc07"});
+        tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "6cb4b227cb733cbcb888094c4465cf6a"});
-        tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "6ad7855dbf6dda2060aa93a3ee010b3e"});
+        tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "e6efbcda94a9fda3d6a54e8ff7d22720"});
-        tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "21c87a3edafee3cb080169963e1e2623"});
+        tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "01e7e4e268cb2d7ce50bac5dc30c7b62"});
-        tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals, "e48bbcf453e63a6ea5eeda05f6865f94"});
+        tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals, "1d34a74bcec3513426f18e74f77a49e9"});
 
         return tests.toArray(new Object[][]{});
     }
@@ -146,12 +146,12 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
         final String WExIntervals = "-L 20:10,000,000-10,100,000 -isr INTERSECTION -L " + hg19Chr20Intervals;
 
         // this functionality can be adapted to provide input data for whatever you might want in your data
-        tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "468550db971e29b3696e5a14f3e31bfc"});
+        tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "47952bc713fb3c2d2beb8eca9ca4f2f2"});
-        tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "48521b89cecceb9846e4dfc0dd415874"});
+        tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "571931ace4b657d93ed295140963640b"});
-        tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "eaacbeaff99a37ffa07e1f11e7f1deb2"});
+        tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "403c700ad4374b337802056e79373538"});
-        tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "af0fe243e3b96e59097187cd16ba1597"});
+        tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "b699371662758d86d9d4b30f2b10f4c2"});
-        tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "868a097a8a108f5159dbbabbfdb2e38b"});
+        tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "7131959df133fafe2ac7884f7e09f687"});
-        tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals, "685025831ac783784d7838e568e35f46"});
+        tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals, "10c9a44f6933271dd64063607655abc2"});
 
         return tests.toArray(new Object[][]{});
     }
@@ -280,7 +280,7 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
     public void testWrongGVCFNonVariantRecordOrderBugFix() {
         final String commandLine = String.format("-T HaplotypeCaller --pcr_indel_model NONE -R %s -I %s -L %s -ERC GVCF --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d",
                 b37KGReference, WRONG_GVCF_RECORD_ORDER_BUGFIX_BAM, WRONG_GVCF_RECORD_ORDER_BUGFIX_INTERVALS, GATKVCFUtils.DEFAULT_GVCF_INDEX_TYPE, GATKVCFUtils.DEFAULT_GVCF_INDEX_PARAMETER);
-        final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("f70b7052dfeb065ee8c7d796f1a1f84a"));
+        final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("5d13d8f0db7106e0873eaf1fc40db3ef"));
         spec.disableShadowBCF();
         executeTest("testMissingGVCFIndexingStrategyException", spec);
     }
@@ -297,7 +297,7 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
     public void testNoCallGVCFMissingPLsBugFix() {
         final String commandLine = String.format("-T HaplotypeCaller --pcr_indel_model NONE -R %s -I %s -L %s -ERC GVCF --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d",
                 b37KGReference, NOCALL_GVCF_BUGFIX_BAM, NOCALL_GVCF_BUGFIX_INTERVALS, GATKVCFUtils.DEFAULT_GVCF_INDEX_TYPE, GATKVCFUtils.DEFAULT_GVCF_INDEX_PARAMETER);
-        final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("883fdc6c10fd7cbc1de375ed26ce5734"));
+        final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("c11f2be9a1dc4340b188b749c2b92929"));
         spec.disableShadowBCF();
         executeTest("testNoCallGVCFMissingPLsBugFix", spec);
     }
@@ -330,7 +330,7 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
     public void testAlleleSpecificAnnotations() {
         final String commandLine = String.format("-T HaplotypeCaller --pcr_indel_model NONE -R %s -I %s -L %s -ERC GVCF --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d -G Standard -G AS_Standard --disableDithering",
                 b37KGReference, privateTestDir + "NA12878.HiSeq.b37.chr20.10_11mb.bam", "20:10433000-10437000", GATKVCFUtils.DEFAULT_GVCF_INDEX_TYPE, GATKVCFUtils.DEFAULT_GVCF_INDEX_PARAMETER);
-        final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Collections.singletonList("7e74286e2c412855509ea5312ea0ec57"));
+        final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Collections.singletonList("d2031195a42cf857e4798090c15f9712"));
         spec.disableShadowBCF();
         executeTest(" testAlleleSpecificAnnotations", spec);
     }
@@ -339,7 +339,7 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
     public void testASMQMateRankSumAnnotation() {
         final String commandLine = String.format("-T HaplotypeCaller --pcr_indel_model NONE -R %s -I %s -L %s -ERC GVCF --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d -A AS_MQMateRankSumTest --disableDithering",
                 b37KGReference, privateTestDir + "NA12878.HiSeq.b37.chr20.10_11mb.bam", "20:10433000-10437000", GATKVCFUtils.DEFAULT_GVCF_INDEX_TYPE, GATKVCFUtils.DEFAULT_GVCF_INDEX_PARAMETER);
-        final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Collections.singletonList("e0b9135f68eb0b65cb36721dd3f40f00"));
+        final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Collections.singletonList("5ffa2b108046274aaf3180ea10bda8f5"));
         spec.disableShadowBCF();
         executeTest(" testASMQMateRankSumAnnotation", spec);
     }
@@ -348,7 +348,7 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
     public void testBetaTestingAnnotationGroup() {
         final String commandLine = String.format("-T HaplotypeCaller --pcr_indel_model NONE -R %s -I %s -L %s -ERC GVCF --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d -G BetaTesting --disableDithering",
                 b37KGReference, privateTestDir + "NA12878.HiSeq.b37.chr20.10_11mb.bam", "20:10433000-10437000", GATKVCFUtils.DEFAULT_GVCF_INDEX_TYPE, GATKVCFUtils.DEFAULT_GVCF_INDEX_PARAMETER);
-        final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Collections.singletonList("81f1fcddfec262a8aaedb9ea37d89873"));
+        final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Collections.singletonList("1231cc5e3a73cb0fb97c26011ce4881a"));
         spec.disableShadowBCF();
         executeTest(" testASMQMateRankSumAnnotation", spec);
     }
@@ -357,7 +357,7 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
     public void testASInsertSizeRankSum() {
         final String commandLine = String.format("-T HaplotypeCaller --pcr_indel_model NONE -R %s -I %s -L %s -ERC GVCF --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d -G Standard -G AS_Standard --disableDithering -A AS_InsertSizeRankSum",
                 b37KGReference, privateTestDir + "NA12878.HiSeq.b37.chr20.10_11mb.bam", "20:10433000-10437000", GATKVCFUtils.DEFAULT_GVCF_INDEX_TYPE, GATKVCFUtils.DEFAULT_GVCF_INDEX_PARAMETER);
-        final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Collections.singletonList("96934396683234559827a77c9bb38e21"));
+        final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Collections.singletonList("173347a78bafd67fffbef47144326c78"));
         spec.disableShadowBCF();
         executeTest(" testASInsertSizeRankSum", spec);
     }
@@ -366,7 +366,7 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
     public void testHaplotypeCallerMultiAllelicNonRef() {
         final String commandLine = String.format("-T HaplotypeCaller -R %s -I %s -L %s -ERC GVCF --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d -A StrandAlleleCountsBySample",
                 b37KGReference, privateTestDir + "multiallelic-nonref.bam", "2:47641259-47641859", GATKVCFUtils.DEFAULT_GVCF_INDEX_TYPE, GATKVCFUtils.DEFAULT_GVCF_INDEX_PARAMETER);
-        final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Collections.singletonList("7c707c66f77482e3f6b2b014b152bbf4"));
+        final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Collections.singletonList("279cd69241f26eed2227ee22b568f333"));
         spec.disableShadowBCF();
         executeTest(" testHaplotypeCallerMultiAllelicNonRef", spec);
     }
@@ -375,7 +375,7 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
     public void testHaplotypeCallerMaxNumPLValues() {
         final String commandLine = String.format("-T HaplotypeCaller -R %s -I %s -L %s -ERC GVCF --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d -ploidy 4 -maxNumPLValues 70",
                 b37KGReference, privateTestDir + "NA12878.HiSeq.b37.chr20.10_11mb.bam", validationDataLocation + "NA12878.HiSeq.b37.chr20.10_11mb.test.intervals", GATKVCFUtils.DEFAULT_GVCF_INDEX_TYPE, GATKVCFUtils.DEFAULT_GVCF_INDEX_PARAMETER);
-        final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Collections.singletonList("dd0bfade4f0a9f23a500fd23c3a24a29"));
+        final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Collections.singletonList("29d2edbbc3c5dda8a9b502fa4337cf30"));
         spec.disableShadowBCF();
         executeTest("testHaplotypeCallerMaxNumPLValues", spec);
     }
@@ -392,7 +392,7 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
         final String commandLine = String.format("-T HaplotypeCaller -R %s -I %s -L %s -ERC GVCF --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d -ploidy 4 -maxNumPLValues 30 -log %s",
                 b37KGReference, privateTestDir + "NA12878.HiSeq.b37.chr20.10_11mb.bam", validationDataLocation + "NA12878.HiSeq.b37.chr20.10_11mb.test.intervals",
                 GATKVCFUtils.DEFAULT_GVCF_INDEX_TYPE, GATKVCFUtils.DEFAULT_GVCF_INDEX_PARAMETER, logFileName);
-        final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("5ea45f32c09e9f7a4132f98d642f260b"));
+        final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("b2bf762651da36349319ece7628bb8aa"));
         spec.disableShadowBCF();
         executeTest("testHaplotypeCallerMaxNumPLValuesExceededWithWarnLogLevel", spec);
         // Make sure the "Maximum allowed number of PLs exceeded" messages are in the log
@@ -417,7 +417,7 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
         final String commandLine = String.format("-T HaplotypeCaller -R %s -I %s -L %s -ERC GVCF --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d -ploidy 4 -maxNumPLValues 30 -log %s",
                 b37KGReference, privateTestDir + "NA12878.HiSeq.b37.chr20.10_11mb.bam", validationDataLocation + "NA12878.HiSeq.b37.chr20.10_11mb.test.intervals",
                 GATKVCFUtils.DEFAULT_GVCF_INDEX_TYPE, GATKVCFUtils.DEFAULT_GVCF_INDEX_PARAMETER, logFileName);
-        final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("5ea45f32c09e9f7a4132f98d642f260b"));
+        final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("b2bf762651da36349319ece7628bb8aa"));
         spec.disableShadowBCF();
         executeTest("testHaplotypeCallerMaxNumPLValuesExceededWithDebugLogLevel", spec);
         // Make sure the "Maximum allowed number of PLs exceeded" messages are in the log
@@ -433,7 +433,7 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
     public void testHaplotypeCallerGVCFBlocks() {
         final String commandLine = String.format("-T HaplotypeCaller -R %s -I %s -L 1:1-1000000 -ERC GVCF --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d",
                 b37KGReference, privateTestDir + "gvcf_blocks_test.bam", GATKVCFUtils.DEFAULT_GVCF_INDEX_TYPE, GATKVCFUtils.DEFAULT_GVCF_INDEX_PARAMETER);
-        final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("0cdf4d6d0a45def15fb11ea30c78e470"));
+        final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("a9ac40d37f4ac398162ce131a258a661"));
         spec.disableShadowBCF();
         executeTest("testHaplotypeCallerGVCFBlocks", spec);
     }
@@ -461,7 +461,7 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
     public void testHaplotypeCallerGVCSpanDel() {
         final String commandLine = String.format("-T HaplotypeCaller -R %s -I %s -L 1:26357667 -ERC GVCF --no_cmdline_in_header -A AS_ReadPosRankSumTest -A ReadPosRankSumTest -variant_index_type %s -variant_index_parameter %d",
                 b37KGReference, privateTestDir + "NexPond-377866-1:26357600-26357700.bam", GATKVCFUtils.DEFAULT_GVCF_INDEX_TYPE, GATKVCFUtils.DEFAULT_GVCF_INDEX_PARAMETER);
-        final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("db29a87113b358805e18ac8c20f9145d"));
+        final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("e880bd94005a195e354c0ee811213a77"));
         spec.disableShadowBCF();
         executeTest("testHaplotypeCallerGVCSpanDel", spec);
     }

protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java

@@ -134,98 +134,98 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
     @Test
     public void testHaplotypeBAMOutFlags() throws IOException {
         final String md5BAMOut = "69aae17f8cd384666ec7c3c1f3d3eb57";
-        HCTestWithBAMOut(NA12878_BAM, " -L 20:10000000-10100000 ", "6588123afd06ff6acc9f10ea25250f54", md5BAMOut);
+        HCTestWithBAMOut(NA12878_BAM, " -L 20:10000000-10100000 ", "df622103b0a6917f2299b1acfd0ed0ac", md5BAMOut);
         validateForwardedProgramRecords(new ArrayList<>(Arrays.asList(new File(NA12878_BAM))), md5BAMOut);
     }
 
     @Test
     public void testHaplotypeCallerMultiSample() throws IOException {
-        HCTest(CEUTRIO_BAM, "", "ad472fbd63864caacf5bc018dcae9df9");
+        HCTest(CEUTRIO_BAM, "", "bdb96cb83b38e8f2109a0504772c2042");
     }
 
     @Test
     public void testHaplotypeCallerMultiSampleNoBadMateFilter() throws IOException {
-        HCTest(CEUTRIO_BAM, "-drf BadMate", "bb6b14675d62ff5b86430508ed688776");
+        HCTest(CEUTRIO_BAM, "-drf BadMate", "298f115ec3c04bbf16d5e3535d848651");
     }
 
     @Test
     public void testHaplotypeCallerSingleSample() throws IOException {
 
-        HCTest(NA12878_BAM, "", "9f17ce83e639a1bd9b3f2d9fa33b15b2");
+        HCTest(NA12878_BAM, "", "30e174f034010c262c42791217f00aeb");
     }
 
     @Test
     public void testHaplotypeCallerMultiSampleHaploid() throws IOException {
-        HCTest(CEUTRIO_BAM, "-ploidy 1", "7ee30877f0153257afdc691c638e7684");
+        HCTest(CEUTRIO_BAM, "-ploidy 1", "50a7241d55f5bb13da3719482c7a5947");
     }
 
     @Test
     public void testHaplotypeCallerSingleSampleHaploid() throws IOException {
-        HCTest(NA12878_BAM, "-ploidy 1", "9ca97bb743a369a1abb1e61168d63d69");
+        HCTest(NA12878_BAM, "-ploidy 1", "832d5ebde3b248150a45b9cbb5ddddab");
     }
 
     @Test
     public void testHaplotypeCallerSingleSampleTetraploid() throws IOException {
-        HCTest(NA12878_BAM, "-ploidy 4", "f993db900080aeb48c43982745e1084d");
+        HCTest(NA12878_BAM, "-ploidy 4", "4f0613e6c6d2a503ec6002b4ae4f342f");
     }
 
     @Test
     public void testHaplotypeCallerMinBaseQuality() throws IOException {
-        HCTest(NA12878_BAM, "-mbq 15", "9f17ce83e639a1bd9b3f2d9fa33b15b2");
+        HCTest(NA12878_BAM, "-mbq 15", "30e174f034010c262c42791217f00aeb");
     }
 
     @Test
     public void testHaplotypeCallerMinBaseQualityHaploid() throws IOException {
-        HCTest(NA12878_BAM, "-mbq 15 -ploidy 1", "9ca97bb743a369a1abb1e61168d63d69");
+        HCTest(NA12878_BAM, "-mbq 15 -ploidy 1", "832d5ebde3b248150a45b9cbb5ddddab");
     }
 
     @Test
     public void testHaplotypeCallerMinBaseQualityTetraploid() throws IOException {
-        HCTest(NA12878_BAM, "-mbq 15 -ploidy 4", "f993db900080aeb48c43982745e1084d");
+        HCTest(NA12878_BAM, "-mbq 15 -ploidy 4", "4f0613e6c6d2a503ec6002b4ae4f342f");
     }
 
     @Test
     public void testHaplotypeCallerGraphBasedSingleSample() throws IOException {
-        HCTest(NA12878_BAM, "-likelihoodEngine GraphBased", "420954190aef671edd02bd3c73e22642");
+        HCTest(NA12878_BAM, "-likelihoodEngine GraphBased", "b0f31e9c063c31a19731683b452eeaab");
     }
 
     @Test
     public void testHaplotypeCallerGraphBasedMultiSampleHaploid() throws IOException {
-        HCTest(CEUTRIO_BAM, "-likelihoodEngine GraphBased -ploidy 1", "01220e85ff6bc49e35a325a1df2519e5");
+        HCTest(CEUTRIO_BAM, "-likelihoodEngine GraphBased -ploidy 1", "b9239942268bf36af33fa2fbd025a697");
     }
 
     @Test
     public void testHaplotypeCallerGraphBasedMultiSample() throws IOException {
-        HCTest(CEUTRIO_BAM, "-likelihoodEngine GraphBased", "80c5b0f72a7962e1ba846ec20465001f");
+        HCTest(CEUTRIO_BAM, "-likelihoodEngine GraphBased", "38c15862ec906c9785c775106a2ab235");
     }
 
     @Test
     public void testHaplotypeCallerSingleSampleWithDbsnp() throws IOException {
-        HCTest(NA12878_BAM, "-D " + b37dbSNP132, "9e8513ed4065138bee8dd9363a9fd355");
+        HCTest(NA12878_BAM, "-D " + b37dbSNP132, "2e993547d6e9794c01d2d3f60bc562c3");
     }
 
     @Test
     public void testHaplotypeCallerMultiSampleGGA() throws IOException {
         HCTest(CEUTRIO_BAM, "--max_alternate_alleles 3 -gt_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "combined.phase1.chr20.raw.indels.sites.vcf" +
                 " -isr INTERSECTION -L " + GGA_INTERVALS_FILE,
-                "af3f54bee3347cafb34734dc7d3516a9");
+                "a53819d8ef397aad9a7b56fb989d24e2");
     }
 
     @Test
     public void testHaplotypeCallerMultiSampleGGAHaploid() throws IOException {
         HCTest(CEUTRIO_BAM, "--max_alternate_alleles 3 -gt_mode GENOTYPE_GIVEN_ALLELES -ploidy 1 -alleles " + validationDataLocation + "combined.phase1.chr20.raw.indels.sites.vcf -isr INTERSECTION -L 20:10080000-10100000",
-                "e60065998227f4ba8002165fb1729a71");
+                "5a568aa762adc17ddc192b3273b6085a");
     }
 
     @Test
     public void testHaplotypeCallerMultiSampleGGATetraploid() throws IOException {
         HCTest(CEUTRIO_BAM, "--max_alternate_alleles 3 -gt_mode GENOTYPE_GIVEN_ALLELES -ploidy 4 -alleles " + validationDataLocation + "combined.phase1.chr20.raw.indels.sites.vcf -isr INTERSECTION -L 20:10080000-10100000",
-                "d7c3aac002701bec6b6d0539c65207be");
+                "ae39f715b8a8fa05b6d13b4237af0971");
     }
 
     @Test
     public void testHaplotypeCallerInsertionOnEdgeOfContig() throws IOException {
-        HCTest(CEUTRIO_MT_TEST_BAM, "-L MT:1-10", "60e98012fbad5f429b3b2abc3a7aa454");
+        HCTest(CEUTRIO_MT_TEST_BAM, "-L MT:1-10", "6c83944eac2fa346e2677961e95fc4fd");
     }
 
     private void HCTestIndelQualityScores(String bam, String args, String md5) {
@@ -236,7 +236,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
 
     @Test
     public void testHaplotypeCallerSingleSampleIndelQualityScores() {
-        HCTestIndelQualityScores(NA12878_RECALIBRATED_BAM, "", "49b8fb444c6f88def2069b8b0efe47c7");
+        HCTestIndelQualityScores(NA12878_RECALIBRATED_BAM, "", "18f571c17aa53b66584b943f1d2b8c3a");
     }
 
     private void HCTestNearbySmallIntervals(String bam, String args, String md5) {
@@ -273,7 +273,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
 
     @Test
     public void testHaplotypeCallerNearbySmallIntervals() {
-        HCTestNearbySmallIntervals(NA12878_BAM, "", "591a58f16104fbb83ccf81c97cef931a");
+        HCTestNearbySmallIntervals(NA12878_BAM, "", "ce22f2b4956a1b02bce6bca3ae0214f8");
     }
 
     // This problem bam came from a user on the forum and it spotted a problem where the ReadClipper
@@ -283,14 +283,14 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
     @Test
     public void HCTestProblematicReadsModifiedInActiveRegions() {
         final String base = String.format("-T HaplotypeCaller --disableDithering --pcr_indel_model NONE -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("eb79b4c0bf9142c955f0a4501e9e6d8f"));
+        final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("5571e6c8f5cf4140438bc8cc8e67ea87"));
         executeTest("HCTestProblematicReadsModifiedInActiveRegions: ", spec);
     }
 
     @Test
     public void HCTestStructuralIndels() {
         final String base = String.format("-T HaplotypeCaller --disableDithering --pcr_indel_model NONE -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("8bddb7f343302ed20bc549df4b82825a"));
+        final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("09d588488dc13d99b1c4941278157a6c"));
         executeTest("HCTestStructuralIndels: ", spec);
     }
 
@@ -348,7 +348,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
     public void HCTestDBSNPAnnotationWGS() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-T HaplotypeCaller --disableDithering --pcr_indel_model NONE -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_PCRFREE + " -o %s -L 20:10,090,000-10,100,000 -D " + b37dbSNP132, 1,
-                Arrays.asList("fc71471b01f93bc531e3cf19cdf78b1f"));
+                Arrays.asList("9d087ba18448e4070c50637f0a60caaf"));
         executeTest("HC calling with dbSNP ID annotation on WGS intervals", spec);
     }
 
@@ -357,7 +357,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-T HaplotypeCaller --disableDithering --pcr_indel_model NONE -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_PCRFREE + " -o %s -L 20:10,100,000-11,000,000 -D " + b37dbSNP132
                         + " -L " + hg19Intervals + " -isr INTERSECTION", 1,
-                Arrays.asList("bf8bb5d13b01facdf90ec24bfbf82faa"));
+                Arrays.asList("d6b0354b01162822d0c9eeffd02a1c40"));
         executeTest("HC calling with dbSNP ID annotation on WEx intervals", spec);
     }
 
@@ -365,7 +365,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
     public void HCTestDBSNPAnnotationWGSGraphBased() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-T HaplotypeCaller -likelihoodEngine GraphBased --disableDithering --pcr_indel_model NONE -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_PCRFREE + " -o %s -L 20:10,090,000-10,100,000 -D " + b37dbSNP132, 1,
-                Arrays.asList("dbae51c7903e088b2e62cbada6ea2d50"));
+                Arrays.asList("9370d6d14261a68229d1ed0b720a2afd"));
         executeTest("HC calling with dbSNP ID annotation on WGS intervals", spec);
     }
 
@@ -374,7 +374,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-T HaplotypeCaller -likelihoodEngine GraphBased --disableDithering --pcr_indel_model NONE -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_PCRFREE + " -o %s -L 20:10,000,000-11,000,000 -D " + b37dbSNP132
                         + " -L " + hg19Intervals + " -isr INTERSECTION", 1,
-                Arrays.asList("2ffaf2e9ef293a6d5ce7c00be40edba7"));
+                Arrays.asList("cef6653e40e1acac44bbc0df908e4f7a"));
         executeTest("HC calling with dbSNP ID annotation on WEx intervals", spec);
     }
 
@@ -397,7 +397,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
     public void HCTestAggressivePcrIndelModelWGS() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-T HaplotypeCaller --disableDithering --pcr_indel_model AGGRESSIVE -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_BAM + " -o %s -L 20:10,270,000-10,300,000", 1,
-                Arrays.asList("7bd5bdfeb587a4c73f4c1cd8b850524f"));
+                Arrays.asList("77bbbdbadd4ae81dce6cf222ff1b4f91"));
         executeTest("HC calling with aggressive indel error modeling on WGS intervals", spec);
     }
 
@@ -405,7 +405,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
     public void HCTestConservativePcrIndelModelWGS() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-T HaplotypeCaller --disableDithering --pcr_indel_model CONSERVATIVE -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_BAM + " -o %s -L 20:10,270,000-10,300,000", 1,
-                Arrays.asList("5c1b487b0e7e1353a9a549a50c91d96f"));
+                Arrays.asList("502be63f1bc983c1a6c7255bd61c78c3"));
         executeTest("HC calling with conservative indel error modeling on WGS intervals", spec);
     }
 
@@ -466,7 +466,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
         // but please make sure that both outputs get the same variant,
         // alleles all with DBSNP ids
         // We test here that change in active region size does not have an effect in placement of indels.
-        final String md5 = "66caceac0a54cdfd847bfdf4226bb36a";
+        final String md5 = "5092360be669335a42935fb88b3cc612";
         final WalkerTestSpec shortSpec = new WalkerTestSpec(commandLineShortInterval + " -o %s",Arrays.asList(md5));
         executeTest("testDifferentIndelLocationsDueToSWExactDoubleComparisonsFix::shortInterval",shortSpec);
         final WalkerTestSpec longSpec = new WalkerTestSpec(commandLineLongInterval + " -o %s",Arrays.asList(md5));
@@ -519,18 +519,18 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
 
     @Test
     public void testHaplotypeCallerTandemRepeatAnnotator() throws IOException{
-        HCTest(NA12878_BAM, " -L 20:10001000-10010000 -A TandemRepeatAnnotator -XA MappingQualityZero -XA SpanningDeletions", "408c6940a090d31c11c171ed5e0e033c");
+        HCTest(NA12878_BAM, " -L 20:10001000-10010000 -A TandemRepeatAnnotator -XA MappingQualityZero -XA SpanningDeletions", "b3cab7c47d9f3dfb707ab4c6e38a5062");
     }
 
     @Test
     public void testBaseCounts() throws IOException{
-        HCTest(CEUTRIO_BAM, "-A BaseCountsBySample -A BaseCounts", "40def0e9c06031d6b624a22a093574c0");
+        HCTest(CEUTRIO_BAM, "-A BaseCountsBySample -A BaseCounts", "84700c805261791015592facdf85e6b2");
     }
 
     @Test
     public void testSetZeroGQsToNoCall() throws IOException{
         final File testBAM = new File(privateTestDir + "set.zero.GQs.no.call.bam");
-        final String md5 = "b90da12d97fce42f5127bcb6cad07b09";
+        final String md5 = "b37f65c2f0886ac7fdc825ac73aa1348";
         final String base = String.format("-T HaplotypeCaller  -R %s -I %s -L 8:17312375-17312975 ", REF, testBAM) +
                 " --no_cmdline_in_header -o %s";
         final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList(md5));
@@ -540,7 +540,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
     @Test
     public void testHaplotypeCallerReadPosRankSum() throws IOException {
         final File testBAM = new File(privateTestDir + "testReadPos.snippet.bam");
-        final String md5Variants = "03b3c464f22a3572f7d66890c18bdda4";
+        final String md5Variants = "e664b7a9da71cf81e14648ac7e698eea";
         final String md5BAMOut = "3ef35732e49980093ad445e3ac5731fa";
         final String base = String.format("-T HaplotypeCaller -R %s -I %s -L 1:3753063 -ip 100 ", REF, testBAM) +
                 " --no_cmdline_in_header -o %s -bamout %s";
@@ -552,7 +552,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
     @Test
     public void testHaplotypeCallerRemoveAltAlleleBasedOnHaptypeScores() {
         final File testBAM = new File(privateTestDir + "pretendTobeTetraPloidTetraAllelicSite.bam");
-        final String md5 = "289304f56833ea76b60cd08763b0f68b";
+        final String md5 = "bd3cb65a847d59b2d7298ab79d0a068a";
         final String base = String.format("-T HaplotypeCaller -R %s -I %s -L 20:11363580-11363600 -ploidy 4 -maxGT 15 ", REF, testBAM) +
                 " --no_cmdline_in_header -o %s";
         final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList(md5));
@@ -561,7 +561,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
 
     @Test
     public void testAlleleBalance() throws IOException{
-        HCTest(CEUTRIO_BAM, " -L 20:10001000-10010000 -A AlleleBalance -A AlleleBalanceBySample", "a210161843f4cb80143ff56e4e5c250f");
+        HCTest(CEUTRIO_BAM, " -L 20:10001000-10010000 -A AlleleBalance -A AlleleBalanceBySample", "91eb37aa94a24543fb18a0c25aceb625");
     }
 
     @Test()

protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerParallelIntegrationTest.java

@@ -67,7 +67,7 @@ public class HaplotypeCallerParallelIntegrationTest extends WalkerTest {
         List<Object[]> tests = new ArrayList<>();
 
         for ( final int nct : Arrays.asList(1, 2, 4) ) {
-            tests.add(new Object[]{nct, "da195c6c4c8e765acb35f08e37132108"});
+            tests.add(new Object[]{nct, "42737b2f5c3833773cc80fafc364f351"});
         }
 
         return tests.toArray(new Object[][]{});

protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/phasing/PhaseByTransmissionIntegrationTest.java

@@ -88,7 +88,7 @@ public class PhaseByTransmissionIntegrationTest extends WalkerTest {
                         "-o %s"
                 ),
                 2,
-                Arrays.asList("af979bcb353edda8dee2127605c71daf","7ed46f6aa4565b5012acde17119a1a31")
+                Arrays.asList("af979bcb353edda8dee2127605c71daf","d2072bbc439b83d2ea5d1690d130bd0c")
         );
         executeTest("testTrueNegativeMV", spec);
     }
@@ -107,7 +107,7 @@ public class PhaseByTransmissionIntegrationTest extends WalkerTest {
                         "-o %s"
                 ),
                 2,
-                Arrays.asList("1dc36ff8d1d5f5d2c1c1bf21517263bf","3260c4f7fda274aeb081744718cca829")
+                Arrays.asList("1dc36ff8d1d5f5d2c1c1bf21517263bf","5d64535c73ca18caf008e97fc26411a8")
         );
         executeTest("testTruePositiveMV", spec);
     }
@@ -126,7 +126,7 @@ public class PhaseByTransmissionIntegrationTest extends WalkerTest {
                         "-o %s"
                 ),
                 2,
-                Arrays.asList("ae60f2db6102ca1f4e93cd18d0634d7a","14158702ed830ae022db69cbce83b3ed")
+                Arrays.asList("ae60f2db6102ca1f4e93cd18d0634d7a","23c58cedfa9d2d756ec23d9c6964d466")
         );
         executeTest("testFalsePositiveMV", spec);
     }
@@ -145,7 +145,7 @@ public class PhaseByTransmissionIntegrationTest extends WalkerTest {
                         "-o %s"
                 ),
                 2,
-                Arrays.asList("590ee56e745984296f73e4277277eac7","a0940a778e2e3b5454f99a54b40820ce")
+                Arrays.asList("590ee56e745984296f73e4277277eac7","7c53e137e8d65e3b15d32d15fc9dc1d5")
         );
         executeTest("testSpecialCases", spec);
     }
@@ -167,7 +167,7 @@ public class PhaseByTransmissionIntegrationTest extends WalkerTest {
                         "-o %s"
                 ),
                 2,
-                Arrays.asList("78158d738917b8f0b7a736a1739b2cc5","3a45b5179dc32cb68f500ff78ef966a6")
+                Arrays.asList("78158d738917b8f0b7a736a1739b2cc5","a2e0feb499b39063d65994ff81188106")
         );
         executeTest("testPriorOption", spec);
     }
@@ -187,7 +187,7 @@ public class PhaseByTransmissionIntegrationTest extends WalkerTest {
                         "-o %s"
                 ),
                 1,
-                Arrays.asList("14158702ed830ae022db69cbce83b3ed")
+                Arrays.asList("23c58cedfa9d2d756ec23d9c6964d466")
         );
         executeTest("testMVFileOption", spec);
     }
@@ -208,7 +208,7 @@ public class PhaseByTransmissionIntegrationTest extends WalkerTest {
                         "-fatherAlleleFirst"
                 ),
                 2,
-                Arrays.asList("dc6afb769b55e6038677fa590b2b2e89","c534df2b637d07bed96e3cd644b31554")
+                Arrays.asList("dc6afb769b55e6038677fa590b2b2e89","585c783cc161408811309fb897183133")
         );
         executeTest("testFatherAlleleFirst", spec);
     }

protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/validation/ValidationSiteSelectorIntegrationTest.java

@@ -84,7 +84,7 @@ public class ValidationSiteSelectorIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString(sampleNone + freqUnif + "--variant " + testfile),
                 1,
-                Arrays.asList("d52bc5a7d99916ddda2d281694a733e2")
+                Arrays.asList("def3d92bb299c267cea8e991fb49ad48")
         );
 
         executeTest("testNoSampleSelectionFreqUniform--" + testfile, spec);
@@ -96,7 +96,7 @@ public class ValidationSiteSelectorIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString(sampleNone + freqAF + "--variant " + testfile),
                 1,
-                Arrays.asList("a509bacf1920bd080fc8a9026d187bf7")
+                Arrays.asList("5f6d0bed2cbe4bb3681975436cf7bf55")
         );
 
         executeTest("testNoSampleSelectionFreqAF--" + testfile, spec);
@@ -108,7 +108,7 @@ public class ValidationSiteSelectorIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString(sampleGT + freqUnif + "--variant " + testfile),
                 1,
-                Arrays.asList("dcb50e6c733b791bb79720a418d5683f")
+                Arrays.asList("ec639aa9ca38338854e5a180fa0962af")
         );
 
         executeTest("testPolyGTFreqUniform--" + testfile, spec);
@@ -120,7 +120,7 @@ public class ValidationSiteSelectorIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString(sampleGT + freqAF + "--variant " + testfile),
                 1,
-                Arrays.asList("c8a3892a8074d0ee5050119cc239fb76")
+                Arrays.asList("4af14ee923c451f2064f48acacd2609e")
         );
 
         executeTest("testPolyGTFreqAF--" + testfile, spec);
@@ -132,7 +132,7 @@ public class ValidationSiteSelectorIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString(sampleGL + freqAF + "--variant " + testfile),
                 1,
-                Arrays.asList("c8a3892a8074d0ee5050119cc239fb76")
+                Arrays.asList("4af14ee923c451f2064f48acacd2609e")
         );
 
         executeTest("testPolyGLFreqAF--" + testfile, spec);

protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java

@@ -97,14 +97,14 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
 
     VRTest lowPass = new VRTest(validationDataLocation + "phase1.projectConsensus.chr20.raw.snps.vcf",
             "3ccb3aa81aebee74d32641105a64ea32",  // tranches
-            "1a87e9cdc66c53891eab61ab39ff2434",  // recal file
+            "a502cee395a07443edec6c12a7c9d74a",  // recal file
-            "217ee1523b6ddaf31f0eb0464b89bab6"); // cut VCF
+            "66abfb6bce96bfd3c49d97d67d91c86d"); // cut VCF
 
     VRTest lowPassPlusExomes = new VRTest(validationDataLocation + "phase1.projectConsensus.chr20.raw.snps.vcf",
             validationDataLocation + "1kg_exomes_unfiltered.AFR.unfiltered.vcf",
             "be89401e09dd06817c43f152c789f854",  // tranches
-            "8ce11e7555cccb3f13ea34a9074aec00",  // recal file
+            "53b2697ed6403e7009c069a196104281",  // recal file
-            "c09c2425744e8d914d69a2585dba0e97"); // cut VCF
+            "c363dd8af19ec8bebc3afc69f780a41a"); // cut VCF
 
     @DataProvider(name = "VRTest")
     public Object[][] createData1() {
@@ -199,8 +199,8 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
 
     VRTest bcfTest = new VRTest(privateTestDir + "vqsr.bcf_test.snps.unfiltered.bcf",
             "3ad7f55fb3b072f373cbce0b32b66df4",  // tranches
-            "051a3b8c15988ee4cd86ae918bec896b",  // recal file
+            "39e09ea9a88d4a60d9d0737d62b23f8c",  // recal file
-            "93a6e7ab6cbd6ae24a5b2a6f0fd29d92"); // cut VCF
+            "262ab8776a3a5d1a1e1931279e6ba570"); // cut VCF
 
     @DataProvider(name = "VRBCFTest")
     public Object[][] createVRBCFTest() {
@@ -254,14 +254,14 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
     VRTest indelUnfiltered = new VRTest(
             validationDataLocation + "combined.phase1.chr20.raw.indels.unfiltered.sites.vcf", // all FILTERs as .
             "9a331328370889168a7aa3a625f73620",  // tranches
-            "d8f68f41c8fbdff84f909f4de4a67476",  // recal file
+            "01fc57bc179e1b8bed0a028082c6321a",  // recal file
-            "ca376c261dc041faa4dfa31e53fed1e2"); // cut VCF
+            "647b0952aa2c2b5f155ed05b621e602a"); // cut VCF
 
     VRTest indelFiltered = new VRTest(
             validationDataLocation + "combined.phase1.chr20.raw.indels.filtered.sites.vcf", // all FILTERs as PASS
             "9a331328370889168a7aa3a625f73620",  // tranches
-            "d8f68f41c8fbdff84f909f4de4a67476",  // recal file
+            "01fc57bc179e1b8bed0a028082c6321a",  // recal file
-            "c968a943ef24520de6ed15c830ab5ac4"); // cut VCF
+            "170f4ecee545b04ebf57031fa1c16e56"); // cut VCF
 
     @DataProvider(name = "VRIndelTest")
     public Object[][] createTestVariantRecalibratorIndel() {
@@ -319,7 +319,7 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
                         " -o %s" +
                         " -tranchesFile " + privateTestDir + "VQSR.mixedTest.tranches" +
                         " -recalFile " + privateTestDir + "VQSR.mixedTest.recal",
-                Arrays.asList("41d5c363bd311677ae1fcf98f4a18487"));
+                Arrays.asList("69134e2785a70b8fcd4a06ebd64dd412"));
         final List<File> outputFiles = executeTest("testApplyRecalibrationSnpAndIndelTogether", spec).getFirst();
         setPDFsForDeletion(outputFiles);
     }
@@ -362,7 +362,7 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
                 " -tranchesFile " + privateTestDir + "VQSR.AStest.snps.tranches" +
                 " -recalFile " + privateTestDir + "VQSR.AStest.snps.recal";
 
-        final WalkerTestSpec spec = new WalkerTestSpec(base, 1, Arrays.asList("dbcf0cb5c2a0eb2312e6ca7d4e3aeeda"));
+        final WalkerTestSpec spec = new WalkerTestSpec(base, 1, Arrays.asList("1efb75bbe9c272fdc91081843df97491"));
         final List<File> outputFiles = executeTest("testApplyRecalibrationAlleleSpecificSNPmode", spec).getFirst();
         setPDFsForDeletion(outputFiles);
     }
@@ -380,7 +380,7 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
                 " -tranchesFile " + privateTestDir + "VQSR.AStest.indels.tranches" +
                 " -recalFile " + privateTestDir + "VQSR.AStest.indels.recal";
 
-        final WalkerTestSpec spec = new WalkerTestSpec(base, 1, Arrays.asList("38d4b8e89dbf8acb6a36dfa1bb55c54c"));
+        final WalkerTestSpec spec = new WalkerTestSpec(base, 1, Arrays.asList("ece9049270d2062c5262fa7381933667"));
         final List<File> outputFiles = executeTest("testApplyRecalibrationAlleleSpecificINDELmode", spec).getFirst();
         setPDFsForDeletion(outputFiles);
     }

protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CalculateGenotypePosteriorsIntegrationTest.java

@@ -74,7 +74,7 @@ public class CalculateGenotypePosteriorsIntegrationTest extends WalkerTest {
                         " -L 20:10,000,000-10,001,432" +
                         " -V " + validationDataLocation + "1000G.phase3.broad.withGenotypes.chr20.1MB.vcf",
                 1,
-                Arrays.asList("43fa27382e654081af69ea05bd26e281"));
+                Arrays.asList("8f227698838bee7bea2f537be7348533"));
         executeTest("testUsingDiscoveredAF", spec);
     }
 
@@ -89,7 +89,7 @@ public class CalculateGenotypePosteriorsIntegrationTest extends WalkerTest {
                         " -L 20:10,000,000-10,001,432" +
                         " -V " + validationDataLocation + "1000G.phase3.broad.withGenotypes.chr20.1MB.vcf",
                 1,
-                Arrays.asList("d63893f530fb749505ec685a5c57ff69"));
+                Arrays.asList("bacd69e97eee216c9fa8f0a909d14ef7"));
         executeTest("testMissingPriors", spec);
     }
 
@@ -103,7 +103,7 @@ public class CalculateGenotypePosteriorsIntegrationTest extends WalkerTest {
                         " -V " + validationDataLocation + "NA12878.Jan2013.haplotypeCaller.subset.indels.vcf" +
                         " -supporting " + validationDataLocation + "1000G.phase3.broad.withGenotypes.chr20.1MB.vcf",
                 1,
-                Arrays.asList("a5d7bcad5a2a194441d00eb6574b8300"));
+                Arrays.asList("69e6b6b494bccdec126b00a0e67f3479"));
         executeTest("testInputINDELs", spec);
     }
 
@@ -117,7 +117,7 @@ public class CalculateGenotypePosteriorsIntegrationTest extends WalkerTest {
                         " -V " + CEUtrioTest +
                         " -supporting " + CEUtrioPopPriorsTest,
                 1,
-                Arrays.asList("98bf63fd2ae3fa1cc42e66fa6b4f50f5"));
+                Arrays.asList("a2b123d282f029b95ed2ce2959a17f24"));
         executeTest("testFamilyPriors", spec);
     }
 
@@ -131,7 +131,7 @@ public class CalculateGenotypePosteriorsIntegrationTest extends WalkerTest {
                         " -V " + getThreeMemberNonTrioTest +
                         " -skipPop",
                 1,
-                Arrays.asList("e71420099fcfc824f1cf92ff2010b69e"));
+                Arrays.asList("dc52a9b5a09d15c8cfb004ffee5f42d0"));
         executeTest("testFamilyPriors", spec);
     }
 

protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineGVCFsIntegrationTest.java

@@ -102,7 +102,7 @@ public class CombineGVCFsIntegrationTest extends WalkerTest {
                         " -V:sample3 " + privateTestDir + "tetraploid-gvcf-3.vcf" +
                         " -L " + privateTestDir + "tetraploid-gvcfs.intervals",
                 1,
-                Arrays.asList("787aca81ad51cd40267f92f3309fa47e"));
+                Arrays.asList("8472fcd43a41e7501b4709f0f1f5f432"));
         executeTest("combineSingleSamplePipelineGVCF", spec);
     }
 
@@ -114,7 +114,7 @@ public class CombineGVCFsIntegrationTest extends WalkerTest {
                         " -V:sample3 " + privateTestDir + "diploid-gvcf-3.vcf" +
                         " -L " + privateTestDir + "tetraploid-gvcfs.intervals",
                 1,
-                Arrays.asList("d52f018643ffed072f43dfd4d33ca082"));
+                Arrays.asList("f88b2b4d285276130cf088e7a03ca6a7"));
         executeTest("combineSingleSamplePipelineGVCF", spec);
     }
 
@@ -192,7 +192,7 @@ public class CombineGVCFsIntegrationTest extends WalkerTest {
     @Test
     public void testMD5s() throws Exception {
         final String cmd = baseTestString(" -L 1:69485-69791");
-        final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("021ec495e70044039d092ebd5ef4b82a"));
+        final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("e1a888e8116cf59d53ad919634a18e6c"));
         spec.disableShadowBCF();
         executeTest("testMD5s", spec);
     }
@@ -200,7 +200,7 @@ public class CombineGVCFsIntegrationTest extends WalkerTest {
     @Test
     public void testBasepairResolutionOutput() throws Exception {
         final String cmd = baseTestString(" -L 1:69485-69791 --convertToBasePairResolution");
-        final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("d5bc938a26cd197d9b1c80cb8dfefbba"));
+        final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("e7e86722a49ad9730743c4952cdbedc7"));
         spec.disableShadowBCF();
         executeTest("testBasepairResolutionOutput", spec);
     }
@@ -208,7 +208,7 @@ public class CombineGVCFsIntegrationTest extends WalkerTest {
     @Test
     public void testBreakBlocks() throws Exception {
         final String cmd = baseTestString(" -L 1:69485-69791 --breakBandsAtMultiplesOf 5");
-        final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("31c2f26e6b172a957a3f504734df5eff"));
+        final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("bd279625ccfb3adcd39d97f07f3a236e"));
         spec.disableShadowBCF();
         executeTest("testBreakBlocks", spec);
     }
@@ -219,7 +219,7 @@ public class CombineGVCFsIntegrationTest extends WalkerTest {
                 "-T CombineGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference +
                         " -V " + privateTestDir + "spanningDel.1.g.vcf -V " + privateTestDir + "spanningDel.2.g.vcf",
                 1,
-                Arrays.asList("097160606e65547722a1726e031529ec"));
+                Arrays.asList("b22238e1ff584a157335429309fbfc5b"));
         spec.disableShadowBCF();
         executeTest("testSpanningDeletions", spec);
     }
@@ -230,7 +230,7 @@ public class CombineGVCFsIntegrationTest extends WalkerTest {
                 "-T CombineGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference +
                         " -V " + privateTestDir + "spanningDel.many.g.vcf",
                 1,
-                Arrays.asList("f517c2d361defeaac245916c835811d5"));
+                Arrays.asList("b828ba5b69422ce32e234ea24d2df4c7"));
         spec.disableShadowBCF();
         executeTest("testMultipleSpanningDeletionsForOneSample", spec);
     }
@@ -241,7 +241,7 @@ public class CombineGVCFsIntegrationTest extends WalkerTest {
                 "-T CombineGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference +
                         " -V " + privateTestDir + "spanningDel.many.haploid.g.vcf",
                 1,
-                Arrays.asList("0a8d217b2833070dcaa3bbc1e7602b1c"));
+                Arrays.asList("e707335ebd61bbe20775f76ad9b8c20d"));
         spec.disableShadowBCF();
         executeTest("testMultipleSpanningDeletionsForOneSampleHaploid", spec);
     }
@@ -252,7 +252,7 @@ public class CombineGVCFsIntegrationTest extends WalkerTest {
                 "-T CombineGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference +
                         " -V " + privateTestDir + "spanningDel.many.tetraploid.g.vcf",
                 1,
-                Arrays.asList("3fd437ad1f9e18303fec517653a30b6d"));
+                Arrays.asList("d4c22bd32d136414bfd7a6ebc5152026"));
         spec.disableShadowBCF();
         executeTest("testMultipleSpanningDeletionsForOneSampleTetraploid", spec);
     }
@@ -261,7 +261,7 @@ public class CombineGVCFsIntegrationTest extends WalkerTest {
     public void testWrongReferenceBaseBugFix() throws Exception {
         final String cmd = "-T CombineGVCFs -R " + b37KGReference + " -V " + (privateTestDir + "combine-gvcf-wrong-ref-input1.vcf"
                 + " -V " + (privateTestDir + "combine-gvcf-wrong-ref-input2.vcf") + " -o %s --no_cmdline_in_header");
-        final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("129879954e5b453d30326f100cbc2e83"));
+        final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("5fec22c9c8a0063f43c86ac86bb12e27"));
         spec.disableShadowBCF();
         executeTest("testWrongReferenceBaseBugFix",spec);
 
@@ -270,7 +270,7 @@ public class CombineGVCFsIntegrationTest extends WalkerTest {
     @Test
     public void testBasepairResolutionInput() throws Exception {
         final String cmd = "-T CombineGVCFs -R " + b37KGReference + " -o %s --no_cmdline_in_header -V " + privateTestDir + "gvcf.basepairResolution.vcf";
-        final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("d5b4abe639081e6bf9c8970ca8405dbe"));
+        final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("a839f81014758d1bdc900d59d35dd5bc"));
         spec.disableShadowBCF();
         executeTest("testBasepairResolutionInput", spec);
     }
@@ -279,7 +279,7 @@ public class CombineGVCFsIntegrationTest extends WalkerTest {
     public void testAlleleSpecificAnnotations() throws Exception {
         final String cmd = "-T CombineGVCFs -R " + b37KGReference + " -o %s --no_cmdline_in_header -G Standard -G AS_Standard -V "
                 + privateTestDir + "NA12878.AS.chr20snippet.g.vcf -V " + privateTestDir + "NA12892.AS.chr20snippet.g.vcf";
-        final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("f053aaa50427ea3fa9a43240e56eefc1"));
+        final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("26606fbfc3e9e5a8813307227d898b9a"));
         spec.disableShadowBCF();
         executeTest("testAlleleSpecificAnnotations", spec);
     }
@@ -300,7 +300,7 @@ public class CombineGVCFsIntegrationTest extends WalkerTest {
     public void testASMateRankSumAnnotation() throws Exception {
         final String cmd = "-T CombineGVCFs -R " + b37KGReference + " -o %s --no_cmdline_in_header -G Standard -G AS_Standard -A AS_MQMateRankSumTest -V "
                 + privateTestDir + "NA12878.AS.MateRankSum.chr20snippet.g.vcf -V " + privateTestDir + "NA12892.AS.MateRankSum.chr20snippet.g.vcf";
-        final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("951b59bf05eb4401da6a1bc8b2cdc261"));
+        final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("9fd72e0f1f0f08a5aff6875225eec567"));
         spec.disableShadowBCF();
         executeTest("testASMateRankSumAnnotation", spec);
     }
@@ -309,7 +309,7 @@ public class CombineGVCFsIntegrationTest extends WalkerTest {
     public void testASInsertSizeRankSumAnnotation() throws Exception {
         final String cmd = "-T CombineGVCFs -R " + b37KGReference + " -o %s --no_cmdline_in_header -G Standard -G AS_Standard -A AS_InsertSizeRankSum -V "
                 + privateTestDir + "NA12878.AS.InsertSizeRankSum.chr20snippet.g.vcf -V " + privateTestDir + "NA12892.AS.InsertSizeRankSum.chr20snippet.g.vcf";
-        final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("9df5f327028768e4c5d20e5742d6d0ad"));
+        final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("b8e10684010702d11ee71538b1f201ac"));
         spec.disableShadowBCF();
         executeTest("testASInsertSizeRankSumAnnotation", spec);
     }

protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineVariantsIntegrationTest.java

@@ -132,30 +132,30 @@ public class CombineVariantsIntegrationTest extends WalkerTest {
          cvExecuteTest("combine PLs 1:" + new File(file1).getName() + " 2:" + new File(file2).getName(), spec, true);
     }
 
-    @Test public void test1SNP() { test1InOut("pilot2.snps.vcf4.genotypes.vcf", "e3dbdfa14aefb2f6bd1213287d34a2e5", " -U LENIENT_VCF_PROCESSING"); }
+    @Test public void test1SNP() { test1InOut("pilot2.snps.vcf4.genotypes.vcf", "554a6cfd4e57d8131281d7c3441ececc", " -U LENIENT_VCF_PROCESSING"); }
-    @Test public void test2SNP() { test1InOut("pilot2.snps.vcf4.genotypes.vcf", "d727fab83b4265859c4a902f6e66ac3d", " -setKey foo -U LENIENT_VCF_PROCESSING"); }
+    @Test public void test2SNP() { test1InOut("pilot2.snps.vcf4.genotypes.vcf", "dc550d1a673f7115601ac8390b039bbc", " -setKey foo -U LENIENT_VCF_PROCESSING"); }
-    @Test public void test3SNP() { test1InOut("pilot2.snps.vcf4.genotypes.vcf", "42fc3d2c68415a61ff15e594a63d9349", " -setKey null -U LENIENT_VCF_PROCESSING"); }
+    @Test public void test3SNP() { test1InOut("pilot2.snps.vcf4.genotypes.vcf", "2f59d80c01ab21d5a8bfa1edae2f330b", " -setKey null -U LENIENT_VCF_PROCESSING"); }
-    @Test public void testOfficialCEUPilotCalls() { test1InOut("CEU.trio.2010_03.genotypes.vcf.gz", "a3994d6145bb3813950939238db4c592"); } // official project VCF files in tabix format
+    @Test public void testOfficialCEUPilotCalls() { test1InOut("CEU.trio.2010_03.genotypes.vcf.gz", "9c094f4f3f7be94561278128328ec02c"); } // official project VCF files in tabix format
 
-    @Test public void test1Indel1() { test1InOut("CEU.dindel.vcf4.trio.2010_06.indel.genotypes.vcf", "e7fd959312e2aff0b4231963ee690aec"); }
+    @Test public void test1Indel1() { test1InOut("CEU.dindel.vcf4.trio.2010_06.indel.genotypes.vcf", "cf66b8bc832cb2b21cd452a0b90db50d"); }
-    @Test public void test1Indel2() { test1InOut("CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "23439a1f0108b57a14e18efe9482cc88"); }
+    @Test public void test1Indel2() { test1InOut("CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "62b6624da8af9cdf2f8e7c2d93dc7b30"); }
 
-    @Test public void combineWithPLs() { combinePLs("combine.3.vcf", "combine.4.vcf", "27aa46cdb022be3959e7240a0d7ac794"); }
+    @Test public void combineWithPLs() { combinePLs("combine.3.vcf", "combine.4.vcf", "d418c467e04b4d2f784887b3cb4f8796"); }
 
-    @Test public void combineTrioCalls() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "YRI.trio.2010_03.genotypes.vcf.gz", "", "9bdda937754e1407183406808f560723"); } // official project VCF files in tabix format
+    @Test public void combineTrioCalls() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "YRI.trio.2010_03.genotypes.vcf.gz", "", "0cb105be750ddd6e461e5c65cecf0114"); } // 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", "6344953a82a422115bd647ec1d696b94"); } // 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", "3a3b16abf4170918ed763349041a0af3"); } // 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", "", "9a62e340fe17c8659786f56cc992975a"); }
+    @Test public void combine2Indels() { combine2("CEU.dindel.vcf4.trio.2010_06.indel.genotypes.vcf", "CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "", "ba9909557cb6882b79441b85ca11ba12"); }
 
-    @Test public void combineSNPsAndIndels() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "", "f9d1d7e6246f0ce9e493357d5b320323"); }
+    @Test public void combineSNPsAndIndels() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "", "a353e2adbc1356f6db2b1be655abef2a"); }
 
     @Test public void uniqueSNPs() {
         // parallelism must be disabled because the input VCF is malformed (DB=0) and parallelism actually fixes this which breaks the md5s
         //both of these files have the YRI trio and merging of duplicate samples without priority must be specified with UNSORTED merge type
-        combine2("pilot2.snps.vcf4.genotypes.vcf", "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf", " -genotypeMergeOptions UNSORTED", "698f591bdc8dca1c9a3473ebc447c787", true);
+        combine2("pilot2.snps.vcf4.genotypes.vcf", "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf", " -genotypeMergeOptions UNSORTED", "4812bb9a6ae7842f08361d01c206e359", true);
     }
 
-    @Test public void omniHM3Union() { combineSites(" -filteredRecordsMergeType KEEP_IF_ANY_UNFILTERED", "7750b77316b8f02df5c9a60cc64c156d"); }
+    @Test public void omniHM3Union() { combineSites(" -filteredRecordsMergeType KEEP_IF_ANY_UNFILTERED", "53653c3cab8d064c376f2f8aef5630ef"); }
-    @Test public void omniHM3Intersect() { combineSites(" -filteredRecordsMergeType KEEP_IF_ALL_UNFILTERED", "3af8a310fca5a4ace3172528d0bc1d38"); }
+    @Test public void omniHM3Intersect() { combineSites(" -filteredRecordsMergeType KEEP_IF_ALL_UNFILTERED", "52d30251d397ca990703296d0c348f02"); }
 
     @Test public void threeWayWithRefs() {
         WalkerTestSpec spec = new WalkerTestSpec(
@@ -169,7 +169,7 @@ public class CombineVariantsIntegrationTest extends WalkerTest {
                         " -priority NA19240_BGI,NA19240_ILLUMINA,NA19240_WUGSC,denovoInfo" +
                         " -genotypeMergeOptions UNIQUIFY -L 1"),
                 1,
-                Arrays.asList("085258a3c507e30860ec87b6b65f5f11"));
+                Arrays.asList("98299ecb58963d069ebbc5b0da33cda7"));
         cvExecuteTest("threeWayWithRefs", spec, true);
     }
 
@@ -186,17 +186,17 @@ public class CombineVariantsIntegrationTest extends WalkerTest {
         cvExecuteTest("combineComplexSites 1:" + new File(file1).getName() + " 2:" + new File(file2).getName() + " args = " + args, spec, true);
     }
 
-    @Test public void complexTestFull() { combineComplexSites("", "80c3b7ba39c8a3f3511fc1ea61ecd4da"); }
+    @Test public void complexTestFull() { combineComplexSites("", "166fe9233adb30c13a1638215e79e86d"); }
-    @Test public void complexTestMinimal() { combineComplexSites(" -minimalVCF", "e7da95bbcf3890a4debbfa07cbd646e5"); }
+    @Test public void complexTestMinimal() { combineComplexSites(" -minimalVCF", "17f43aab1aeb9609c3834e8257f04422"); }
-    @Test public void complexTestSitesOnly() { combineComplexSites(" -sites_only", "d7ee8da6ceee4dd1212122c2e9cab2a6"); }
+    @Test public void complexTestSitesOnly() { combineComplexSites(" -sites_only", "89ff19389c40b8c0bff710be2b969d98"); }
-    @Test public void complexTestSitesOnlyMinimal() { combineComplexSites(" -sites_only -minimalVCF", "d7ee8da6ceee4dd1212122c2e9cab2a6"); }
+    @Test public void complexTestSitesOnlyMinimal() { combineComplexSites(" -sites_only -minimalVCF", "89ff19389c40b8c0bff710be2b969d98"); }
 
     @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("b0d4b86702b44fc4faa527c34adf6239"));
+                 Arrays.asList("719c2e7726b1ba4aa22f5d2b87206300"));
          cvExecuteTest("combineDBSNPDuplicateSites:", spec, true);
     }
 
@@ -207,7 +207,7 @@ public class CombineVariantsIntegrationTest extends WalkerTest {
                         + " -R " + b37KGReference
                         + " -V " + privateTestDir + "combineVariantsLeavesRecordsUnfiltered.vcf",
                 1,
-                Arrays.asList("0f221847e76521250de1abcba535e49c"));
+                Arrays.asList("57c65954cf6a2316e1270a40f4b016b4"));
         cvExecuteTest("combineLeavesUnfilteredRecordsUnfiltered: ", spec, false);
     }
 
@@ -261,7 +261,7 @@ public class CombineVariantsIntegrationTest extends WalkerTest {
                         + " -V " + privateTestDir + "same.variant.mixed.vcf"
                         + " -multipleAllelesMergeType MIX_TYPES",
                 1,
-                Arrays.asList("629bb763e9af8edbec0a77cc91eea617"));
+                Arrays.asList("a21c03e0398af88daefe259c6746707f"));
         executeTest("combineDifferentTypes: ", spec);
     }
 }

protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeGVCFsIntegrationTest.java

@@ -83,7 +83,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
         final WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString(" -V " + privateTestDir + "testUpdatePGT.vcf", b37KGReference),
                 1,
-                Collections.singletonList("326ec5afa27ade4d0c562aa227997d88"));
+                Collections.singletonList("2ae06d89572175a124e9e09565b5012e"));
         executeTest("testUpdatePGT", spec);
     }
 
@@ -93,7 +93,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
         final WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString(" -V " + privateTestDir + "testUpdatePGT.vcf -A StrandAlleleCountsBySample -log " + logFileName, b37KGReference),
                 1,
-                Collections.singletonList("b995bf820c3edff5b721338ea9cf44aa"));
+                Collections.singletonList("e1765034661d6c2d91588d558ba629b9"));
         executeTest("testUpdatePGTStrandAlleleCountsBySample", spec);
 
         final File file = new File(logFileName);
@@ -108,7 +108,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
                         " -V:sample3 " + privateTestDir + "combine.single.sample.pipeline.3.vcf" +
                         " -L 20:10,000,000-11,000,000", b37KGReference),
                 1,
-                Collections.singletonList("7b2a135e694f9d1190e041e6fd420123"));
+                Collections.singletonList("33ddc7bea3acf3108a8566daefcdfd61"));
         executeTest("combineSingleSamplePipelineGVCF", spec);
     }
 
@@ -120,7 +120,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
                         " -V:sample3 " + privateTestDir + "tetraploid-gvcf-3.vcf" +
                         " -L " + privateTestDir + "tetraploid-gvcfs.intervals", b37KGReference),
                 1,
-                Collections.singletonList("d6ef5e411ac5829a12d825a0fefac883"));
+                Collections.singletonList("2702b5293ad8b7e4c7e5949b44a1d603"));
         executeTest("testTetraploidRun", spec);
     }
 
@@ -132,7 +132,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
                         " -V:sample3 " + privateTestDir + "diploid-gvcf-3.vcf" +
                         " -L " + privateTestDir + "tetraploid-gvcfs.intervals", b37KGReference),
                 1,
-                Collections.singletonList("b497f16cd9eb99e353d9430fe7f34635"));
+                Collections.singletonList("543652ce573eb5aa032b636fde124565"));
         executeTest("testMixedPloidyRun", spec);
     }
 
@@ -145,7 +145,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
                         " -L " + privateTestDir + "tetraploid-gvcfs.intervals" +
                         " -maxNumPLValues 3", b37KGReference),
                 1,
-                Collections.singletonList("8c8ebe2069977ba13024a95827c6c50d"));
+                Collections.singletonList("b784056ef1a8424e7038b473c1fd164e"));
         executeTest("testMixedPloidyMaxNumPLValuesRun", spec);
     }
 
@@ -157,7 +157,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
                         " -V:sample3 " + privateTestDir + "combine.single.sample.pipeline.3.vcf" +
                         " --includeNonVariantSites -L 20:10,030,000-10,033,000 -L 20:10,386,000-10,386,500", b37KGReference),
                 1,
-                Collections.singletonList("a9ecd152ec4b5b541887a0aed016f40d"));
+                Collections.singletonList("0d62b80fd164cc15dca5bd17604bf6cc"));
         spec.disableShadowBCF();
         executeTest("combineSingleSamplePipelineGVCF_includeNonVariants", spec);
     }
@@ -171,7 +171,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
                         " -V:sample3 " + privateTestDir + "combine.single.sample.pipeline.3.vcf" +
                         " -L 20:10,000,000-20,000,000", b37KGReference),
                 1,
-                Collections.singletonList("8a37077d9a52b9d556cdd19403e27635"));
+                Collections.singletonList("23576dfb470f2439bfb665e6e27cb303"));
         executeTest("combineSingleSamplePipelineGVCFHierarchical", spec);
     }
 
@@ -183,7 +183,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
                         " -V:sample3 " + privateTestDir + "combine.single.sample.pipeline.3.vcf" +
                         " -L 20:10,000,000-11,000,000 --dbsnp " + b37dbSNP132, b37KGReference),
                 1,
-                Collections.singletonList("181fcb5d240b9bd92e3c793ca5aa7954"));
+                Collections.singletonList("9deb58f3db3a003601d00ea7b9940ee7"));
         executeTest("combineSingleSamplePipelineGVCF_addDbsnp", spec);
     }
 
@@ -194,7 +194,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
                 " -V " + privateTestDir + "NA12892.BPres.g.vcf" +
                 " -L 20:10433000-10436909", b37KGReference),
                 1,
-                Collections.singletonList("f342872f485e6978501facc78c354078"));
+                Collections.singletonList("fe97f63d7677eb9ba843266a918792a8"));
         executeTest("combineBPresGVCFs", spec);
     }
 
@@ -204,7 +204,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
                 "-T GenotypeGVCFs --no_cmdline_in_header -L 1:69485-69791 -o %s -R " + b37KGReference +
                 " -V " + privateTestDir + "gvcfExample1.vcf",
                 1,
-                Collections.singletonList("df88bbf2eea39a06f2bcc47d9379e5fa"));
+                Collections.singletonList("901dae2ec1ac2f99a35a19f7c2bcf37e"));
         executeTest("testJustOneSample", spec);
     }
 
@@ -215,7 +215,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
                         " -V " + privateTestDir + "gvcfExample1.vcf" +
                         " -V " + privateTestDir + "gvcfExample2.vcf",
                 1,
-                Collections.singletonList("933c3ec48870c54f7f74b259272d6645"));
+                Collections.singletonList("7544d9e000f5ddeabe8b2234b7b51759"));
         executeTest("testSamplesWithDifferentLs", spec);
     }
 
@@ -242,7 +242,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
         final WalkerTestSpec spec = new WalkerTestSpec(
                 baseBPResolutionString("-nda"),
                 1,
-                Collections.singletonList("b92742a67c5b1718fb5674393b2008fd"));
+                Collections.singletonList("c724a3067add87cf7686109165ae72cb"));
         executeTest("testNDA", spec);
     }
 
@@ -251,7 +251,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
         final WalkerTestSpec spec = new WalkerTestSpec(
                 baseBPResolutionString("-allSites"),
                 1,
-                Collections.singletonList("77ae407c276aa7070fa22b110160c684"));
+                Collections.singletonList("89425fd1857f6bafb110629fc2e9cfb4"));
         spec.disableShadowBCF();
         executeTest("testAllSitesNonBiallelic", spec);
     }
@@ -261,7 +261,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
         final WalkerTestSpec spec = new WalkerTestSpec(
                 baseBPResolutionString("-maxAltAlleles 1"),
                 1,
-                Collections.singletonList("312f01d41dff851f449d9b4ecf0e78d2"));
+                Collections.singletonList("5f7dd4dec4f75dbfa0248f2d0f579fa8"));
         executeTest("testMaxAltAlleles", spec);
     }
 
@@ -270,7 +270,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
         final WalkerTestSpec spec = new WalkerTestSpec(
                 baseBPResolutionString("-stand_call_conf 300"),
                 1,
-                Collections.singletonList("89582b2a32e3f04d3daa565a0c185003"));
+                Collections.singletonList("b2fcb9c55d955ed85c209a34f1f6c825"));
         executeTest("testStandardConf", spec);
     }
 
@@ -293,7 +293,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
         final WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString(" -V " + gVCF.getAbsolutePath(), b37KGReference),
                 1,
-                Collections.singletonList("f613d0bc0d45aafe53227bc0d13712f1"));
+                Collections.singletonList("fb847b9f5723b29af04fb5798f38b58a"));
         spec.disableShadowBCF();  //TODO: Remove when BaseTest.assertAttributesEquals() works with SAC
         executeTest("testStrandAlleleCountsBySample", spec);
     }
@@ -310,7 +310,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
                         " -V:combined2 " + privateTestDir + "combine.single.sample.pipeline.combined.vcf" +
                         " --uniquifySamples", b37KGReference),
                 1,
-                Collections.singletonList("0c99b1b20fb035a5dada036bd4cf39e5"));
+                Collections.singletonList("5d7d0aa1256054e6bb70ce9fa909bf0e"));
         executeTest("testUniquifiedSamples", spec);
 
     }
@@ -482,7 +482,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
     }
 
 
-    private static final String simpleSpanningDeletionsMD5 = "53f2b8991e49a47efc44b8e02ebb8d91";
+    private static final String simpleSpanningDeletionsMD5 = "d9383e3d74e92a69c983bab873dacf4e";
 
     @Test
     public void testSpanningDeletionsMD5() {
@@ -512,7 +512,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
                 "-T GenotypeGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference +
                         " -V " + privateTestDir + "spanningDel.1.g.vcf -V " + privateTestDir + "spanningDel.2.g.vcf -V " + privateTestDir + "spanningDel.3.g.vcf",
                 1,
-                Collections.singletonList("907dfaa4d31c22705eadd5890ae23929"));
+                Collections.singletonList("2322e2584425559864af77ac7c53da56"));
         spec.disableShadowBCF();
         executeTest("testMultipleSpanningDeletionsMD5", spec);
     }
@@ -523,7 +523,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
                 "-T GenotypeGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference +
                         " -V " + privateTestDir + "spanningDel.delOnly.g.vcf",
                 1,
-                Collections.singletonList("b923e5c6d5dbce62034178bd5234b932"));
+                Collections.singletonList("22e584f080222520e0376dcb236645b1"));
         spec.disableShadowBCF();
         executeTest("testSpanningDeletionDoesNotGetGenotypedWithNoOtherAlleles", spec);
     }
@@ -534,7 +534,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
                 "-T GenotypeGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference +
                         " -V " + privateTestDir + "spanningDel.depr.delOnly.g.vcf",
                 1,
-                Collections.singletonList("01ae75dfe5c0c2350fcef0f4cdca36b2"));
+                Collections.singletonList("75b7d0f5f6dfb73943c429f434f0dbe3"));
         spec.disableShadowBCF();
         executeTest("testSpanningDeletionDoesNotGetGenotypedWithNoOtherAlleles", spec);
     }
@@ -557,7 +557,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
                 "-T GenotypeGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference +
                         " -V " + privateTestDir + "ad-bug-input.vcf",
                 1,
-                Collections.singletonList("4d6cbd8d666a43fc136d73de2b217719"));
+                Collections.singletonList("f61ee09133636ec93adbbe6de2a5462a"));
         spec.disableShadowBCF();
         executeTest("testBadADPropagationHaploidBugTest", spec);
     }
@@ -568,7 +568,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
                 "-T GenotypeGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference +
                         " -V " + privateTestDir + "261_S01_raw_variants_gvcf.vcf",
                 1,
-                Collections.singletonList("ea96440b537dd1b2b25ea565dfaa71fc"));
+                Collections.singletonList("90c4c58469c072fec95341221d56f650"));
         spec.disableShadowBCF();
         executeTest("testSAC", spec);
     }
@@ -579,7 +579,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
                 "-T GenotypeGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference +
                         " -V " + privateTestDir + "tetraploid-multisample-sac.g.vcf",
                 1,
-                Collections.singletonList("c21c847ef794c11e249985a16893b2fa"));
+                Collections.singletonList("5d78514e1bdac1f857074ed2fe54a2b7"));
         spec.disableShadowBCF();
         executeTest("testSACMultisampleTetraploid", spec);
     }
@@ -599,7 +599,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
     public void testAlleleSpecificAnnotations() {
         final String cmd = "-T GenotypeGVCFs -R " + b37KGReference + " -o %s --no_cmdline_in_header -G Standard -G AS_Standard --disableDithering -V "
                 + privateTestDir + "NA12878.AS.chr20snippet.g.vcf -V " + privateTestDir + "NA12892.AS.chr20snippet.g.vcf";
-        final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Collections.singletonList("f8ea6b63ea0bf7b0fdc266845762b927"));
+        final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Collections.singletonList("6e24254a6903b7280f1d2f8e0b62ff65"));
         spec.disableShadowBCF();
         executeTest("testAlleleSpecificAnnotations", spec);
     }
@@ -619,7 +619,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
     public void testASMateRankSumAnnotation() {
         final String cmd = "-T GenotypeGVCFs -R " + b37KGReference + " -o %s --no_cmdline_in_header -G Standard -G AS_Standard -A AS_MQMateRankSumTest --disableDithering -V "
                 + privateTestDir + "NA12878.AS.MateRankSum.chr20snippet.g.vcf -V " + privateTestDir + "NA12892.AS.MateRankSum.chr20snippet.g.vcf";
-        final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Collections.singletonList("a3fc424534c31b43bdaaa4de3803f73b"));
+        final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Collections.singletonList("03e1188bf5bdd196b392b3c56d33112f"));
         spec.disableShadowBCF();
         executeTest("testASMateRankSumAnnotation", spec);
     }
@@ -628,7 +628,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
     public void testASInsertSizeRankSumAnnotation() {
         final String cmd = "-T GenotypeGVCFs -R " + b37KGReference + " -o %s --no_cmdline_in_header -G Standard -G AS_Standard -A AS_InsertSizeRankSum --disableDithering -V "
                 + privateTestDir + "NA12878.AS.InsertSizeRankSum.chr20snippet.g.vcf -V " + privateTestDir + "NA12892.AS.InsertSizeRankSum.chr20snippet.g.vcf";
-        final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Collections.singletonList("55e14518c955de9158d98e55da75b643"));
+        final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Collections.singletonList("1ca5f4c67340a3087159f29cc31772b8"));
         spec.disableShadowBCF();
         executeTest("testASInsertSizeRankSumAnnotation", spec);
     }
@@ -641,7 +641,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
     public void testAlleleSpecificAnnotations_oneSample() {
         final String cmd = "-T GenotypeGVCFs -R " + b37KGReference + " -o %s --no_cmdline_in_header -G Standard -G AS_Standard --disableDithering -V "
                 + privateTestDir + "NA12878.AS.chr20snippet.g.vcf";
-        final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Collections.singletonList("78c3ed48b17faebf77f4cc9f225b9045"));
+        final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Collections.singletonList("d2d59eac6879bfc54ce32f46e9ac9dad"));
         spec.disableShadowBCF();
         executeTest("testAlleleSpecificAnnotations_oneSample", spec);
     }
@@ -651,7 +651,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
     public void testAlleleSpecificAnnotations_moreSamples() {
         final String cmd = "-T GenotypeGVCFs -R " + b37KGReference + " -o %s --no_cmdline_in_header -G Standard -G AS_Standard -A AS_InsertSizeRankSum -A AS_MQMateRankSumTest --disableDithering -V "
                 + privateTestDir + "multiSamples.g.vcf";
-        final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Collections.singletonList("5b007393f598cde9f18b03d4ac5cab25"));
+        final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Collections.singletonList("8cc75a852b59145721163300e1be8392"));
         spec.disableShadowBCF();
         executeTest("testAlleleSpecificAnnotations_moreSamples", spec);
     }
@@ -660,7 +660,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
     public void testMonomorphicVCwithAlt() {
         final String cmd = "-T GenotypeGVCFs -R " + b37KGReference + " -G AS_Standard -o %s --no_cmdline_in_header --disableDithering -V "
                 + privateTestDir + "monomorphicGVCwithAlt.vcf";
-        final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Collections.singletonList("43953b3e75a4d470b65773b1b5bea066"));
+        final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Collections.singletonList("6452f7fe5123b07cb1e30d6f80e9bb53"));
         spec.disableShadowBCF();
         executeTest("testAlleleSpecificAnnotations", spec);
     }
@@ -669,7 +669,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
     public void testFractionInformativeReads() {
         final String cmd = "-T GenotypeGVCFs -R " + b37KGReference + " -G AS_Standard -o %s --no_cmdline_in_header -A FractionInformativeReads --disableDithering -V "
                 + privateTestDir + "NA12878.AS.chr20snippet.g.vcf -V " + privateTestDir + "NA12891.AS.chr20snippet.g.vcf";
-        final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Collections.singletonList("e5db4edf2d2b2abdb0b07a57d658785b"));
+        final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Collections.singletonList("9245c5abfba583dc6532fd82c6815da2"));
         spec.disableShadowBCF();
         executeTest("testAlleleSpecificAnnotations", spec);
     }
@@ -679,7 +679,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
     public void testGenotypingSpanningDeletionWithAllSites() {
         final WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString(" -V " + privateTestDir + "spanningDel.genotyping.g.vcf -allSites", b37KGReference),
-                Collections.singletonList("04cfe93e92444cbde80e13ca8b8c3913"));
+                Collections.singletonList("5e9cca337c4304d995a288ee54946372"));
         spec.disableShadowBCF();
         executeTest("testGenotypingSpanningDeletionWithAllSites", spec);
     }
@@ -688,7 +688,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
     public void testGenotypingSpanningDeletionAcrossLines() {
         final WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString(" -V " + privateTestDir + "input-1_2256566.vcf", b37KGReference),
-                Collections.singletonList("152c8e07e35c592868f43626f27365de"));
+                Collections.singletonList("71443d092f80a2eda95bce73125ad4d0"));
         spec.disableShadowBCF();
         executeTest("testGenotypingSpanningDeletionAcrossLines", spec);
     }
@@ -707,7 +707,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
         final WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString(" -V " + privateTestDir + "NA18503.22.vcf -V " + privateTestDir + "NA18504.22.vcf -V " +
                         privateTestDir + "NA18505.22.vcf -allSites", b37KGReference),
-                Collections.singletonList("6d253024246e1024b9b6e8f885f53799"));
+                Collections.singletonList("fb23ea41f934fcb4c28a89e44e7988a0"));
         spec.disableShadowBCF();
         executeTest("testHomRefHighMQ", spec);
     }
@@ -717,7 +717,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
         final WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString(" -V " + privateTestDir + "gvcfExample1.vcf -V " + privateTestDir + "gvcfExample2.vcf " +
                         "-L 1:69485-69791 -inputPrior 0.2 -inputPrior 0.2 -inputPrior 0.2 -inputPrior 0.2", b37KGReference),
-                Collections.singletonList("860d133262160bbc75ce5849e5fa491f"));
+                Collections.singletonList("cc126c27bedb41b5e6328b46aef699d9"));
         spec.disableShadowBCF();
         executeTest("testInputPrior", spec);
     }

protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/LeftAlignAndTrimVariantsIntegrationTest.java

@@ -71,7 +71,7 @@ public class LeftAlignAndTrimVariantsIntegrationTest extends WalkerTest {
          WalkerTestSpec spec = new WalkerTestSpec(
                  "-T LeftAlignAndTrimVariants -o %s -R " + b37KGReference + " --variant:vcf " + privateTestDir + "forLeftAlignVariantsTest.vcf --no_cmdline_in_header",
                  1,
-                 Arrays.asList("5d82f53b036d9a0fca170e5be68d5ab2"));
+                 Arrays.asList("f01f0eb9a0ee7f1f7dd5089a40071956"));
          executeTest("test left alignment", spec);
     }
 
@@ -88,7 +88,7 @@ public class LeftAlignAndTrimVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T LeftAlignAndTrimVariants -o %s -R " + b37KGReference + " --variant:vcf " + privateTestDir + "longAlleles.vcf --no_cmdline_in_header -log " + logFileName,
                 1,
-                Arrays.asList("136f88a5bd07a022a3404089359cb8ee"));
+                Arrays.asList("138f4284278a652dd860a30333b95987"));
         executeTest("test left alignment with long alleles with an error", spec);
 
         // Make sure the "reference allele too long" message is in the log
@@ -112,7 +112,7 @@ public class LeftAlignAndTrimVariantsIntegrationTest extends WalkerTest {
                 "-T LeftAlignAndTrimVariants -o %s -R " + b37KGReference + " --variant:vcf " + privateTestDir +
                         "longAlleles.vcf --no_cmdline_in_header --reference_window_stop 208 -log " + logFileName,
                 1,
-                Arrays.asList("c4ca5520ee499da171053059e3717b2f"));
+                Arrays.asList("1a2c2d8f12483c69a596ec7844363af6"));
         executeTest("test left alignment with long alleles fix", spec);
 
         // Make sure the "reference allele too long" message is in the log
@@ -127,7 +127,7 @@ public class LeftAlignAndTrimVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T LeftAlignAndTrimVariants -o %s -R " + b37KGReference + " --variant:vcf " + privateTestDir + "forLeftAlignVariantsTest.vcf --dontTrimAlleles --no_cmdline_in_header",
                 1,
-                Arrays.asList("dd238fe14b4a495a489907c1e021221e"));
+                Arrays.asList("cc20380fb6f8571b455814f001d08b1f"));
         executeTest("test left alignment, don't trim", spec);
     }
 
@@ -136,7 +136,7 @@ public class LeftAlignAndTrimVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T LeftAlignAndTrimVariants -o %s -R " + b37KGReference + " --variant:vcf " + privateTestDir + "forHardLeftAlignVariantsTest.vcf --no_cmdline_in_header -split",
                 1,
-                Arrays.asList("58c09033814d41fab5da4c152eab7fa2"));
+                Arrays.asList("981a51ccc0eb4bd5ce5bee4a35573107"));
         executeTest("test left alignment with hard multiple alleles", spec);
     }
 
@@ -145,7 +145,7 @@ public class LeftAlignAndTrimVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T LeftAlignAndTrimVariants -o %s -R " + b37KGReference + " --variant:vcf " + privateTestDir + "forHardLeftAlignVariantsTest.vcf --dontTrimAlleles --no_cmdline_in_header -split",
                 1,
-                Arrays.asList("6d22a6b78d24ee2329b91f27a91751cf"));
+                Arrays.asList("01bc359d01c8625ba25f644bbb3ad192"));
         executeTest("test left alignment with hard multiple alleles, don't trim", spec);
     }
 
@@ -154,7 +154,7 @@ public class LeftAlignAndTrimVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T LeftAlignAndTrimVariants -o %s -R " + b37KGReference + " --variant:vcf " + privateTestDir + "multiallele-gt.vcf --no_cmdline_in_header -split",
                 1,
-                Arrays.asList("0acb354a2c28e250ef2853c1e0a0fafb"));
+                Arrays.asList("80b4a994a569ecfbd628121b85e64339"));
         executeTest("test left alignment of multiple alleles with genoptypes", spec);
     }
 
@@ -163,7 +163,7 @@ public class LeftAlignAndTrimVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T LeftAlignAndTrimVariants -o %s -R " + b37KGReference + " --variant:vcf " + privateTestDir + "multiallele-gt-het-noref.vcf --no_cmdline_in_header -split",
                 1,
-                Arrays.asList("a335913de938082061d6bbb863626ee2"));
+                Arrays.asList("9ffe7aa7e0c51885d04dc5c0ad8d6462"));
         executeTest("test left alignment of multiple alleles with genoptypes, including het-noref", spec);
     }
 
@@ -172,7 +172,7 @@ public class LeftAlignAndTrimVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T LeftAlignAndTrimVariants -o %s -R " + b37KGReference + " --variant:vcf " + privateTestDir + "multiallele-gt.vcf --no_cmdline_in_header -split -keepOriginalAC",
                 1,
-                Arrays.asList("67657ee509665fd0d7a2c9024981ba92"));
+                Arrays.asList("6774b43d9446278e716d7198717a5f85"));
         executeTest("test left alignment of multiple alleles with genoptypes, keep original AC", spec);
     }
 

protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/RegenotypeVariantsIntegrationTest.java

@@ -66,7 +66,7 @@ public class RegenotypeVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T RegenotypeVariants -R " + b36KGReference + " --variant " + testFile + " -o %s --no_cmdline_in_header",
                 1,
-                Arrays.asList("88118ebd39d6576aa1171082d8f37cd8")
+                Arrays.asList("dec333f2808d769622b15860a0964355")
         );
 
         executeTest("testRegenotype--" + testFile, spec);

protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariantsIntegrationTest.java

@@ -65,10 +65,10 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
         return "-T SelectVariants -R " + b36KGReference + " -L 1 -o %s --no_cmdline_in_header" + args;
     }
 
-    private static final String SAMPLE_EXCLUSION_MD5 = "2e52f21e7dcc67151a51630807a4eef2";
+    private static final String SAMPLE_EXCLUSION_MD5 = "df3b373d2ae302d075c07332a4b9438c";
-    private static final String INVERT_SELECTION_MD5 = "26d192b868746ab14133f145ae812e7c";
+    private static final String INVERT_SELECTION_MD5 = "7f6288a198e618ad540fa9a8c7c1a031";
-    private static final String MAX_FILTERED_GT_SELECTION_MD5 = "66d92fac72b339195b393c9915643a14";
+    private static final String MAX_FILTERED_GT_SELECTION_MD5 = "5804066a1af1639d9c8bc4744928d80a";
-    private static final String MIN_FILTERED_GT_SELECTION_MD5 = "965c0cf7daa03a1731b371bb20b582d4";
+    private static final String MIN_FILTERED_GT_SELECTION_MD5 = "9b8003cb3d6457be2d0cc5b9b4f5ffe8";
     private static final String NO_CALL_FILTERING_KEEP_ONE = "6e2401190c5ada6a3bed2640c068f43b";
     private static final String NO_CALL_FILTERING_KEEP_TWO =  "6bced1ab6a3d58f1fd905b7f601987a3";
 
@@ -107,7 +107,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString(" -sn A -sn B -sn C --variant " + testfile),
                 1,
-                Arrays.asList("792962a5cc830e86dfc89caffbda1707")
+                Arrays.asList("496e17163d2608b86661518e333eadc4")
         );
 
         executeTest("testRepeatedLineSelection--" + testfile, spec);
@@ -137,7 +137,7 @@ 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("8090c349d12549b437a80e29c285fdd5")
+                Arrays.asList("46451eaf6b7d02a5462c0a2463db2402")
         );
         spec.disableShadowBCF();
         executeTest("testComplexSelection--" + testfile, spec);
@@ -151,7 +151,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString(" --ALLOW_NONOVERLAPPING_COMMAND_LINE_SAMPLES -sn A -se '[CDH]' -sn Z -sn T -sf " + samplesFile + " -env -ef -select 'DP < 250' --variant " + testfile),
                 1,
-                Arrays.asList("8090c349d12549b437a80e29c285fdd5")
+                Arrays.asList("46451eaf6b7d02a5462c0a2463db2402")
         );
         spec.disableShadowBCF();
         executeTest("testComplexSelectionWithNonExistingSamples--" + testfile, spec);
@@ -164,7 +164,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString(" -env -ef -select 'foo!=0||DP>0' --variant " + testfile),
                 1,
-                Arrays.asList("e7ec1f2c8077d07b54721e68b603d42c")    // should yield empty vcf because the foo!=0 will yield complete expression false
+                Arrays.asList("c98b30546c994aecd05c91dfbd64e665")    // should yield empty vcf because the foo!=0 will yield complete expression false
         );
         spec.disableShadowBCF();
         executeTest("testNonExistingSelection--" + testfile, spec);
@@ -181,7 +181,7 @@ 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("30aabc865634bf887cad0c02cdcde042")
+                Arrays.asList("6837e14be8c53d4b065e9b087b1ea851")
         );
         spec.disableShadowBCF();
 
@@ -199,7 +199,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T SelectVariants -R " + b36KGReference + " -L 1:1-1000000 -o %s --no_cmdline_in_header -xl_sf " + samplesFile + " --variant " + testfile,
                 1,
-                Arrays.asList("1afba8d53094bdef63db1e39d52be5aa")
+                Arrays.asList("5e7114974aff723c7a04cde5c2e3f90c")
         );
         spec.disableShadowBCF();
 
@@ -284,7 +284,7 @@ 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("41dda9f4b9ec9f9b0f3593b2cbd82cd5")
+                Arrays.asList("2837de9b1fdde19a4692e7c648a26423")
         );
 
         executeTest("testVariantTypeSelection--" + testFile, spec);
@@ -300,7 +300,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T SelectVariants -R " + b36KGReference + " -selectType INDEL --variant " + testFile + " -o %s --no_cmdline_in_header --maxIndelSize 2",
                 1,
-                Arrays.asList("41dda9f4b9ec9f9b0f3593b2cbd82cd5")
+                Arrays.asList("2837de9b1fdde19a4692e7c648a26423")
         );
 
         executeTest("testMaxIndelLengthSelection--" + testFile, spec);
@@ -316,7 +316,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T SelectVariants -R " + b36KGReference + " -selectType INDEL --variant " + testFile + " -o %s --no_cmdline_in_header --minIndelSize 2",
                 1,
-                Arrays.asList("ad0965edb1dbd30060afd21ba9f11bf7")
+                Arrays.asList("0425c469e9f83aa33bc6d77586f97046")
         );
 
         executeTest("testMinIndelLengthSelection--" + testFile, spec);
@@ -329,7 +329,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T SelectVariants -R " + b36KGReference + " -sn NA12892 --variant:dbsnp " + testFile + " -o %s --no_cmdline_in_header",
                 1,
-                Arrays.asList("86d97e682b2dccff75d079f3b5d17f4b")
+                Arrays.asList("384d267b4cbf22b380b5c78c2fd1ceb8")
         );
 
         executeTest("testUsingDbsnpName--" + testFile, spec);
@@ -342,7 +342,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T SelectVariants -R " + b36KGReference + " -sn NA12892 --variant " + testFile + " -o %s --no_cmdline_in_header",
                 1,
-                Arrays.asList("86d97e682b2dccff75d079f3b5d17f4b")
+                Arrays.asList("384d267b4cbf22b380b5c78c2fd1ceb8")
         );
 
         executeTest("testRemoveMLE--" + testFile, spec);
@@ -355,7 +355,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T SelectVariants --keepOriginalAC -R " + b36KGReference + " -sn NA12892 --variant " + testFile + " -o %s --no_cmdline_in_header",
                 1,
-                Arrays.asList("6f26cf5a7fd20682e1de193e5bb5f61f")
+                Arrays.asList("e37dbd8dd97ec6d7763ddefd4e0fb3f6")
         );
 
         executeTest("testKeepOriginalAC--" + testFile, spec);
@@ -368,7 +368,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T SelectVariants --keepOriginalAC -env -trimAlternates -R " + b36KGReference + " -sn NA12892 --variant " + testFile + " -o %s --no_cmdline_in_header",
                 1,
-                Arrays.asList("e0ac2b37387048bf51ac2914bdd2e178")
+                Arrays.asList("02a57132d7a7a1d1e8a969c233b4881e")
         );
 
         executeTest("testKeepOriginalACAndENV--" + testFile, spec);
@@ -381,7 +381,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T SelectVariants --keepOriginalDP -R " + b37KGReference + " -sn NA12892 --variant " + testFile + " -o %s --no_cmdline_in_header",
                 1,
-                Arrays.asList("9ad02f0df308eecb0634b3cd386956e9")
+                Arrays.asList("1dd3944a62db62fc163c3518fa828daf")
         );
 
         executeTest("testKeepOriginalDP--" + testFile, spec);
@@ -394,7 +394,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T SelectVariants -R " + b36KGReference + " -select 'KG_FREQ < 0.5' --variant " + testFile + " -o %s --no_cmdline_in_header",
                 1,
-                Arrays.asList("bfbfefbd4a84b093ee0b63eab8cc1be9")
+                Arrays.asList("1b468e69d8df060c4dba006f00b8ea33")
         );
 
         executeTest("testMultipleRecordsAtOnePosition--" + testFile, spec);
@@ -407,7 +407,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T SelectVariants -R " + b37KGReference + " --variant " + testFile + " -o %s --no_cmdline_in_header",
                 1,
-                Arrays.asList("1fc77d7f47e75a24222a358c69de7f3d")
+                Arrays.asList("c21f7f6b5bd22a321de21539bc34c0aa")
         );
 
         executeTest("testNoGTs--" + testFile, spec);
@@ -420,7 +420,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T SelectVariants -R " + b37KGReference + " -o %s --no_cmdline_in_header -sf " + samplesFile + " --excludeNonVariants -trimAlternates --variant " + testfile,
                 1,
-                Arrays.asList("c963ca96d543ecccab8055295d2a4dab")
+                Arrays.asList("496a6a3ea6097f62c6ac4a6e8503ed5d")
         );
         executeTest("test select from multi allelic with excludeNonVariants --" + testfile, spec);
     }
@@ -432,7 +432,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
                 "-T SelectVariants -R " + b37KGReference + " -o %s --no_cmdline_in_header " +
                         "-sn SAMPLE-CC -sn SAMPLE-CT -sn SAMPLE-CA --excludeNonVariants --variant " + testfile,
                 1,
-                Arrays.asList("7f5484a74ab648608228eafea96f8ad3")
+                Arrays.asList("cd2e8a223140fa88a7bc049a990d571b")
         );
         executeTest("test multi allelic annotation ordering --" + testfile, spec);
     }
@@ -483,19 +483,19 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
         final String testFile = privateTestDir + "forHardLeftAlignVariantsTest.vcf";
         final String cmd = "-T SelectVariants -R " + b37KGReference + " -sn NA12878 -env -trimAlternates "
                 + "-V " + testFile + " -o %s --no_cmdline_in_header";
-        WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("21d83006b012eeea84c6612976348d3c"));
+        WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("c4157e8f5b11bade08a67791d4bb7e40"));
         executeTest("testAlleleTrimming", spec);
     }
 
     @DataProvider(name="unusedAlleleTrimmingProvider")
     public Object[][] unusedAlleleTrimmingProvider() {
         return new Object[][] {
-                { privateTestDir+"forHardLeftAlignVariantsTest.vcf", "-trimAlternates", "21d83006b012eeea84c6612976348d3c"},
+                { privateTestDir+"forHardLeftAlignVariantsTest.vcf", "-trimAlternates", "c4157e8f5b11bade08a67791d4bb7e40"},
-                { privateTestDir+"forHardLeftAlignVariantsTest.vcf", "", "8fc0c8a7de6bb579e1534b936f844090"},
+                { privateTestDir+"forHardLeftAlignVariantsTest.vcf", "", "a835454cbd132f2d56defb55ba13b2dd"},
-                { privateTestDir+"multi-allelic-ordering.vcf", "-sn SAMPLE-CC -sn SAMPLE-CT", "595392b623b0869f1d87e46edf3de122"},
+                { privateTestDir+"multi-allelic-ordering.vcf", "-sn SAMPLE-CC -sn SAMPLE-CT", "b19e508640a89f176f7ea347babfcc66"},
-                { privateTestDir+"multi-allelic-ordering.vcf", "-sn SAMPLE-CC -sn SAMPLE-CT -env", "bba873b8eeeb4c01199140c37deb6f6b"},
+                { privateTestDir+"multi-allelic-ordering.vcf", "-sn SAMPLE-CC -sn SAMPLE-CT -env", "15d982a280754804fa384ccc0f3a2ccf"},
-                { privateTestDir+"multi-allelic-ordering.vcf", "-sn SAMPLE-CC -sn SAMPLE-CT -trimAlternates", "93858f706dac876a8581f6b89bb85cc5"},
+                { privateTestDir+"multi-allelic-ordering.vcf", "-sn SAMPLE-CC -sn SAMPLE-CT -trimAlternates", "cbad00c0722a94c382f75b428f2a8e6c"},
-                { privateTestDir+"multi-allelic-ordering.vcf", "-sn SAMPLE-CC -sn SAMPLE-CT -env -trimAlternates", "5d831401367eb8b0ab49ffa34e0dd278"}
+                { privateTestDir+"multi-allelic-ordering.vcf", "-sn SAMPLE-CC -sn SAMPLE-CT -env -trimAlternates", "a9f448502a27e777b3112cf98e1d325f"}
         };
     }
 
@@ -618,7 +618,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString(" -IDs " + idFile + " --variant " + testFile),
                 1,
-                Arrays.asList("da1117cba380345c622a6d8e52c2270b")
+                Arrays.asList("29bc6716310aea154431716b8bc101c2")
         );
         spec.disableShadowBCF();
         executeTest("testKeepSelectionID--" + testFile, spec);
@@ -637,7 +637,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString(" -xlIDs " + idFile + " --variant " + testFile + " --forceValidOutput"),
                 1,
-                Arrays.asList("613826acb415f05bf288536701a87855")
+                Arrays.asList("7d13000098708491fc27a16ae0034cb5")
         );
         spec.disableShadowBCF();
         executeTest("testExcludeSelectionID--" + testFile, spec);
@@ -653,7 +653,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T SelectVariants -R " + b36KGReference + " -xlSelectType SNP --variant " + testFile + " -o %s --no_cmdline_in_header",
                 1,
-                Arrays.asList("ad0965edb1dbd30060afd21ba9f11bf7")
+                Arrays.asList("0425c469e9f83aa33bc6d77586f97046")
         );
 
         executeTest("testExcludeSelectionType--" + testFile, spec);
@@ -667,7 +667,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T SelectVariants -R "+b37KGReference + " -mv -mvq 0 --variant  " + testFile + " -ped " + pedFile + " -o %s  --no_cmdline_in_header",
                 1,
-                Arrays.asList("c68779547b28dfef39792598df8a93e9"));
+                Arrays.asList("f5b2178bf59f20911a809a50f92c8c35"));
 
         executeTest("testMendelianViolationSelection--" + testFile, spec);
     }
@@ -680,7 +680,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T SelectVariants -R "+b37KGReference + " -mv -mvq 0 -invMv --variant  " + testFile + " -ped " + pedFile + " -o %s --no_cmdline_in_header",
                 1,
-                Arrays.asList("0ac6fda76228080bdb39c0e698440718"));
+                Arrays.asList("01ee9eb113e8d6b5961b4eb8f1ca5d1e"));
 
         executeTest("testInvertMendelianViolationSelection--" + testFile, spec);
     }
@@ -744,7 +744,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T SelectVariants --setFilteredGtToNocall -R " + b37KGReference + " --variant " + testfile + " -o %s --no_cmdline_in_header",
                 1,
-                Arrays.asList("cb5ef9233503bebc81593e436a6de943")
+                Arrays.asList("fb3030518f7c4120989d37b2cca9abe6")
         );
 
         spec.disableShadowBCF();
@@ -759,7 +759,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
                 "-T SelectVariants --setFilteredGtToNocall --removeUnusedAlternates --excludeNonVariants -R " + b37KGReference + " --variant " +
                         testfile + " -o %s --no_cmdline_in_header",
                 1,
-                Arrays.asList("f5b2592361d8ab0d47e5047e63f78e4c"));
+                Arrays.asList("d43ff4701e3f42095059867e1a18857e"));
         executeTest("testSetFilteredGtoNocallUpdateInfo", spec);
     }
 
@@ -770,7 +770,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T SelectVariants -R " + b37KGReference + " --variant " + testfile + " -o %s --no_cmdline_in_header -trimAlternates",
                 1,
-                Arrays.asList("d3bb7ea37a7c9dce8b34bf2020961619"));
+                Arrays.asList("beaa34a786d96796925093486558b103"));
         spec.disableShadowBCF();
         executeTest("testSACSimpleDiploid", spec);
     }
@@ -782,7 +782,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T SelectVariants -R " + b37KGReference + " --variant " + testfile + " -o %s --no_cmdline_in_header -sn NA12891 -trimAlternates",
                 1,
-                Arrays.asList("67a92b4d4174ff41f6f88ddf5ab6e422"));
+                Arrays.asList("c8203bea524cdb66717abbbc50a234b5"));
         spec.disableShadowBCF();
         executeTest("testSACDiploid", spec);
     }
@@ -794,7 +794,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T SelectVariants -R " + b37KGReference + " --variant " + testfile + " -o %s --no_cmdline_in_header -sn NA12891 -trimAlternates",
                 1,
-                Arrays.asList("7880f8a1dfae1804998b6a994574e734"));
+                Arrays.asList("f48a3c789898e24fbec6db9c6e8d800a"));
         spec.disableShadowBCF();
         executeTest("testSACNonDiploid", spec);
     }
@@ -858,7 +858,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T SelectVariants -R " + b37KGReference + " --variant " + testfile + " -o %s --no_cmdline_in_header -sn HG00610 -select 'DP > 7'",
                 1,
-                Arrays.asList("bc6caa81836f4c94a1216babd0c1ac72"));
+                Arrays.asList("cdb7ca5a57a4afd49ad4513aa8487873"));
         spec.disableShadowBCF();
 
         executeTest("testHaploid", spec);
@@ -871,7 +871,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T SelectVariants -R " + b37KGReference + " --variant " + testfile + " -o %s --no_cmdline_in_header -sn NA18486 -select 'DP > 19'",
                 1,
-                Arrays.asList("4fcfa5e0ba5d39ca9f0593aa0c0f7a63"));
+                Arrays.asList("36f7508b0e1ebf02977235f901c1025e"));
         spec.disableShadowBCF();
 
         executeTest("testTetraploid", spec);
@@ -884,7 +884,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T SelectVariants -R " + b37KGReference + " --variant " + testfile + " -o %s --no_cmdline_in_header -sn NA12878 -select 'DP > 48' -trimAlternates",
                 1,
-                Arrays.asList("709782f7a07cd500d41370e6a275fcdf"));
+                Arrays.asList("51c002569e91726008feb316032b55c4"));
         spec.disableShadowBCF();
 
         executeTest("testTetraDiploid", spec);

protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariantsParallelIntegrationTest.java

@@ -90,17 +90,17 @@ public class SelectVariantsParallelIntegrationTest extends WalkerTest {
                 String testfile = validationDataLocation + "test.filtered.maf_annotated.vcf";
                 String samplesFile = validationDataLocation + "SelectVariants.samples.txt";
                 String args = " -sn A -se '[CDH]' -sf " + samplesFile + " -env -ef -select 'DP < 250' --variant " + testfile;
-                new ParallelSelectTestProvider(b36KGReference, args, "8090c349d12549b437a80e29c285fdd5", nt);
+                new ParallelSelectTestProvider(b36KGReference, args, "46451eaf6b7d02a5462c0a2463db2402", nt);
             }
             { // new tests on b37 using testdir VCF
                 final String testfile = privateTestDir + "NA12878.hg19.example1.vcf";
                 final String args = "-select 'DP > 30' -V " + testfile;
-                new ParallelSelectTestProvider(b37KGReference, args, "51645037428729c3a9fa0e25fc2104ad", nt);
+                new ParallelSelectTestProvider(b37KGReference, args, "25eab4762a6381b6f456d2d5c0616419", nt);
             }
             { // AD and PL decoding race condition
                 final String testfile = privateTestDir + "race_condition.vcf";
                 final String args = "-env -trimAlternates -sn SAMPLE -L 1:1-10,000,000 -V " + testfile;
-                new ParallelSelectTestProvider(b37KGReference, args, "f289f22aacf1a5638a9fb6b32c5cf6fb", nt);
+                new ParallelSelectTestProvider(b37KGReference, args, "9983e6a41472e8956dd32f967bf87f05", nt);
             }
         }
 

protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VCFStreamingIntegrationTest.java

@@ -87,7 +87,7 @@ public class VCFStreamingIntegrationTest extends WalkerTest {
                     " --no_cmdline_in_header " +
                     " -o %s",
             1,
-            Arrays.asList("94057d7a98c1af0a7490540ea1d9b247")
+            Arrays.asList("e2aa529552bf924848d956b3b5ee70ca")
         );
 
         executeTest("testSimpleVCFStreaming", spec);

protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/ValidateVariantsIntegrationTest.java

@@ -354,7 +354,7 @@ public class ValidateVariantsIntegrationTest extends WalkerTest {
         String baseIntervals = " 1:1-100 -L 5:1-200 ";
         String intervalString = " -L " + baseIntervals;
         final WalkerTestSpec hc = new WalkerTestSpec("-T HaplotypeCaller " + intervalString + " -I " + privateTestDir + "NA12878.4.snippet.bam " +
-                " -R /humgen/1kg/reference/human_g1k_v37_decoy.fasta -ERC GVCF -o " + output, Collections.singletonList(EMPTY_MD5));
+                " -R /humgen/gsa-hpprojects/GATK/bundle/current/b37/human_g1k_v37_decoy.fasta -ERC GVCF -o " + output, Collections.singletonList(EMPTY_MD5));
         executeTest("running hc", hc);
 
         WalkerTestSpec spec = new WalkerTestSpec(

protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantFiltrationParallelIntegrationTest.java

@@ -89,17 +89,17 @@ public class VariantFiltrationParallelIntegrationTest extends WalkerTest {
                 String testfile = privateTestDir + "vcfexample2.vcf" ;
                 String args = " -filter 'AlleleBalance < 70.0 && FisherStrand == 1.4' -filterName bar --variant -V " + testfile +
                         " -L 1:10,020,000-10,021,000";
-                new ParallelVariantFiltrationTestProvider(b36KGReference, args, "0c0fddb0eb6f9d3f74556332cd498079", nt);
+                new ParallelVariantFiltrationTestProvider(b36KGReference, args, "0a7cdf3117b4e8bcfcc41fde34ef0a9e", nt);
             }
             {
                 final String testfile = privateTestDir + "filteringDepthInFormat.vcf";
                 final String args = " --genotypeFilterExpression 'DP < 8' --genotypeFilterName highDP --invertGenotypeFilterExpression -V " + testfile;
-                new ParallelVariantFiltrationTestProvider(b37KGReference, args, "c6bc275c97a9e737748d16132ee76f48", nt);
+                new ParallelVariantFiltrationTestProvider(b37KGReference, args, "cc8eab3f7cacc6d7effc9df9ba98210a", nt);
             }
             {
                 final String testfile = privateTestDir + "filteringDepthInFormat.vcf";
                 final String args = "  --genotypeFilterExpression 'DP < 8' --genotypeFilterName lowDP -V " + testfile;
-                new ParallelVariantFiltrationTestProvider(b37KGReference, args, "b0016040127766a4163fcbd91afff3ea", nt);
+                new ParallelVariantFiltrationTestProvider(b37KGReference, args, "8c82cc0ec68b2397512d7bf255c17730", nt);
             }
         }
 

protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToAllelicPrimitivesIntegrationTest.java

@@ -66,7 +66,7 @@ public class VariantsToAllelicPrimitivesIntegrationTest extends WalkerTest {
          WalkerTestSpec spec = new WalkerTestSpec(
                  "-T VariantsToAllelicPrimitives -o %s -R " + b37KGReference + " -V " + privateTestDir + "vcfWithMNPs.vcf --no_cmdline_in_header",
                  1,
-                 Arrays.asList("db9929eef707d7dff0aef576f49e4a0d"));
+                 Arrays.asList("d6d817cf5331794bb2dcc31180c2892b"));
          executeTest("test MNPs To SNPs", spec);
     }
 }

protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToVCFIntegrationTest.java

@@ -70,7 +70,7 @@ public class VariantsToVCFIntegrationTest extends WalkerTest {
     @Test
     public void testGenotypesToVCFUsingHapMapInput() {
         List<String> md5 = new ArrayList<String>();
-        md5.add("970157c9e15c53a6e50faaad41227487");
+        md5.add("0c10e87bd40fb6030f7e43462e89e711");
 
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-R " + b36KGReference +
@@ -87,7 +87,7 @@ public class VariantsToVCFIntegrationTest extends WalkerTest {
     @Test
     public void testGenotypesToVCFUsingVCFInput() {
         List<String> md5 = new ArrayList<String>();
-        md5.add("975830cb2bff58c7df426bbf09a08244");
+        md5.add("2cb826f35aea5bec736205820a2bc394");
 
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-R " + b36KGReference +

public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/EngineFeaturesIntegrationTest.java

@@ -757,8 +757,8 @@ public class EngineFeaturesIntegrationTest extends WalkerTest {
     @DataProvider(name = "vcfFeaturesData")
     public Object[][] getVCFFeaturesData() {
         return new Object[][]{
-                {"--sites_only", "99c07e55fc44694087af6a7d4795e1be"},
+                {"--sites_only", "a40ea77cf2654ae8db97e8192231d13b"},
-                {"--bcf", "b300dd7a1300c55640d9f2e42520d086"}
+                {"--bcf", "9b01f83627bb6ae8aa295ffd4fab586f"}
         };
     }
 
@@ -774,8 +774,8 @@ public class EngineFeaturesIntegrationTest extends WalkerTest {
     @DataProvider(name = "vcfFormatHandlingData")
     public Object[][] getVCFFormatHandlingData() {
         return new Object[][]{
-                {true, "7517264dd6eb0c1ac5ca8dfd103c94fb"},
+                {true, "3d772e5b48ae5e2be51cf376eb69759b"},
-                {false, "4c69e6ae1d506ba3c029de3229de407b"}
+                {false, "b0070622dfa6e86e37e534377e31a64c"}
         };
     }
 

public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/CNV/SymbolicAllelesIntegrationTest.java

@@ -48,7 +48,7 @@ public class SymbolicAllelesIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString(b36KGReference, "symbolic_alleles_1.vcf"),
                 1,
-                Arrays.asList("a1de53ac340f4ca02367c40680628251"));
+                Arrays.asList("5de035b91a1d65ce43a1a5d3997e70f1"));
         executeTest("Test symbolic alleles", spec);
     }
 
@@ -57,7 +57,7 @@ public class SymbolicAllelesIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString(b36KGReference, "symbolic_alleles_2.vcf"),
                 1,
-                Arrays.asList("3f97ed3243fad7f953f4859af92d227f"));
+                Arrays.asList("c6b5a044750e50a5553bc8df86cb796e"));
         executeTest("Test symbolic alleles mixed in with non-symbolic alleles", spec);
     }
 }

public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VCFIntegrationTest.java

@@ -55,7 +55,7 @@ public class VCFIntegrationTest extends WalkerTest {
     @Test(enabled = true)
     public void testReadingAndWritingWitHNoChanges() {
 
-        String md5ofInputVCF = "a492a97a8d18ace8eeef02a6fe5f179b";
+        String md5ofInputVCF = "8c20749122424fe9590203bb72b352f8";
         String testVCF = privateTestDir + "vcf4.1.example.vcf";
 
         String baseCommand = "-R " + b37KGReference + " --no_cmdline_in_header -o %s ";
@@ -76,7 +76,7 @@ public class VCFIntegrationTest extends WalkerTest {
         String baseCommand = "-R " + b37KGReference + " --no_cmdline_in_header -o %s ";
 
         String test1 = baseCommand + "-T SelectVariants -V " + testVCF;
-        WalkerTestSpec spec1 = new WalkerTestSpec(test1, 1, Arrays.asList("b8b18a9a015cba1f3a44af532bf45338"));
+        WalkerTestSpec spec1 = new WalkerTestSpec(test1, 1, Arrays.asList("a9784cc33bf7be0c4f9bdc0a76f087b1"));
         executeTest("Test reading and writing breakpoint VCF", spec1);
     }
 
@@ -87,7 +87,7 @@ public class VCFIntegrationTest extends WalkerTest {
         String baseCommand = "-R " + b37KGReference + " --no_cmdline_in_header -o %s ";
 
         String test1 = baseCommand + "-T SelectVariants -V " + testVCF;
-        WalkerTestSpec spec1 = new WalkerTestSpec(test1, 1, Arrays.asList("89daaa81f64e96cf4d9aa0abf9be0b76"));
+        WalkerTestSpec spec1 = new WalkerTestSpec(test1, 1, Arrays.asList("98406032e610166b146f81d0dc647dbd"));
         executeTest("Test reading VCF with lower-case bases", spec1);
     }
 
@@ -98,7 +98,7 @@ public class VCFIntegrationTest extends WalkerTest {
         String baseCommand = "-R " + b37KGReference + " --no_cmdline_in_header -o %s ";
 
         String test1 = baseCommand + "-T SelectVariants -V " + testVCF;
-        WalkerTestSpec spec1 = new WalkerTestSpec(test1, 1, Arrays.asList("5d91e685c760f7e869cb06596d741116"));
+        WalkerTestSpec spec1 = new WalkerTestSpec(test1, 1, Arrays.asList("86994335e476b0dba026057c73920ec1"));
         executeTest("Test reading and writing 1000G Phase I SVs", spec1);
     }
 
@@ -109,7 +109,7 @@ public class VCFIntegrationTest extends WalkerTest {
         String baseCommand = "-R " + b37KGReference + " --no_cmdline_in_header -o %s ";
 
         String test1 = baseCommand + "-T SelectVariants -V " + testVCF;
-        WalkerTestSpec spec1 = new WalkerTestSpec(test1, 1, Arrays.asList("8e35e142fea8891f72e577e7b1526756"));
+        WalkerTestSpec spec1 = new WalkerTestSpec(test1, 1, Arrays.asList("d23c39222ca1f6992bec01cd32091c3f"));
         executeTest("Test reading and writing samtools vcf", spec1);
     }
 
@@ -118,7 +118,7 @@ public class VCFIntegrationTest extends WalkerTest {
         String testVCF = privateTestDir + "ex2.vcf";
         String baseCommand = "-R " + b36KGReference + " --no_cmdline_in_header -o %s ";
         String test1 = baseCommand + "-T SelectVariants -V " + testVCF;
-        WalkerTestSpec spec1 = new WalkerTestSpec(test1, 1, Arrays.asList("5245b967ac66b29c8e836bfa5b5b4643"));
+        WalkerTestSpec spec1 = new WalkerTestSpec(test1, 1, Arrays.asList("2d9a50fab59aed30526c187f2ef7fec8"));
         executeTest("Test writing samtools WEx BCF example", spec1);
     }
 
@@ -127,7 +127,7 @@ public class VCFIntegrationTest extends WalkerTest {
         String testVCF = privateTestDir + "ex2.bcf";
         String baseCommand = "-R " + b36KGReference + " --no_cmdline_in_header -o %s ";
         String test1 = baseCommand + "-T SelectVariants -V " + testVCF;
-        WalkerTestSpec spec1 = new WalkerTestSpec(test1, 1, Arrays.asList("0ca1a078d4801886ef4abac327df7104"));
+        WalkerTestSpec spec1 = new WalkerTestSpec(test1, 1, Arrays.asList("56d9daa70e38ecff6531df2538e5374c"));
         executeTest("Test reading samtools WEx BCF example", spec1);
     }
 
@@ -144,7 +144,7 @@ public class VCFIntegrationTest extends WalkerTest {
 
     @Test
     public void testPassingOnVCFWithoutHeadersWithLenientProcessing() {
-        runVCFWithoutHeaders("-U LENIENT_VCF_PROCESSING", "a8f4be8ad9820286ea13a28a675133f1", null, true);
+        runVCFWithoutHeaders("-U LENIENT_VCF_PROCESSING", "9904322d524db1ce5f38ff418c9f01fb", null, true);
     }
 
     private void runVCFWithoutHeaders(final String moreArgs, final String expectedMD5, final Class expectedException, final boolean disableBCF) {
@@ -360,7 +360,7 @@ public class VCFIntegrationTest extends WalkerTest {
                 " -o %s ";
         final String name = "testBlockCompressedInput: " + testSpec.toString();
 
-        final WalkerTestSpec spec = new WalkerTestSpec(commandLine, 1, Arrays.asList("1cc0ab636f33b9105d54bdaf2b80ad28"));
+        final WalkerTestSpec spec = new WalkerTestSpec(commandLine, 1, Arrays.asList("dc3092c94e84076fdfa22af356b60c11"));
 
         executeTest(name, spec);
     }

public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/BaseTest.java

@@ -95,8 +95,8 @@ public abstract class BaseTest {
 
     public static final String hg18Reference = "/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta";
     public static final String hg19Reference = "/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta";
-    public static final String b36KGReference = "/humgen/1kg/reference/human_b36_both.fasta";
+    public static final String b36KGReference = "/humgen/gsa-hpprojects/GATK/bundle/current/b36/human_b36_both.fasta";
-    public static final String b37KGReference = "/humgen/1kg/reference/human_g1k_v37.fasta";
+    public static final String b37KGReference = "/humgen/gsa-hpprojects/GATK/bundle/current/b37/human_g1k_v37.fasta";
     public static final String b38Reference = "/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta";
     public static final String b37KGReferenceWithDecoy = "/humgen/gsa-hpprojects/GATK/bundle/current/b37/human_g1k_v37_decoy.fasta";
     public static final String hg19ReferenceWithChrPrefixInChromosomeNames = "/humgen/gsa-hpprojects/GATK/bundle/current/hg19/ucsc.hg19.fasta";