From c40cda7e3c0227ef852de43b0429ac826e7b3363 Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Mon, 7 May 2012 14:30:42 -0400 Subject: [PATCH] Nope, loads of integration tests had to be changed. --- .../sting/utils/codecs/vcf/StandardVCFWriter.java | 1 + .../walkers/CNV/SymbolicAllelesIntegrationTest.java | 4 ++-- .../annotator/VariantAnnotatorIntegrationTest.java | 2 +- .../genotyper/UnifiedGenotyperIntegrationTest.java | 8 ++++---- .../ValidationSiteSelectorIntegrationTest.java | 10 +++++----- .../VariantRecalibrationWalkersIntegrationTest.java | 10 +++++----- .../variantutils/CombineVariantsIntegrationTest.java | 10 +++++----- .../variantutils/LeftAlignVariantsIntegrationTest.java | 2 +- .../variantutils/SelectVariantsIntegrationTest.java | 2 +- .../variantutils/VariantsToVCFIntegrationTest.java | 2 +- .../sting/utils/codecs/vcf/VCFIntegrationTest.java | 2 +- 11 files changed, 27 insertions(+), 26 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/StandardVCFWriter.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/StandardVCFWriter.java index 665a4ae0a..75b396bd9 100755 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/StandardVCFWriter.java +++ b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/StandardVCFWriter.java @@ -118,6 +118,7 @@ public class StandardVCFWriter extends IndexingVCFWriter { } if ( mHeader.hasGenotypingData() ) { + mWriter.write(VCFConstants.FIELD_SEPARATOR); mWriter.write("FORMAT"); for ( String sample : mHeader.getGenotypeSamples() ) { mWriter.write(VCFConstants.FIELD_SEPARATOR); diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/CNV/SymbolicAllelesIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/CNV/SymbolicAllelesIntegrationTest.java index 9e5fb2a70..e7169321c 100644 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/CNV/SymbolicAllelesIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/CNV/SymbolicAllelesIntegrationTest.java @@ -24,7 +24,7 @@ public class SymbolicAllelesIntegrationTest extends WalkerTest { WalkerTestSpec spec = new WalkerTestSpec( baseTestString(b36KGReference, "symbolic_alleles_1.vcf"), 1, - Arrays.asList("8c44f58039ec444bc376fa732d4856dd")); + Arrays.asList("444a20659f67592a8284e0b7849e4302")); executeTest("Test symbolic alleles", spec); } @@ -33,7 +33,7 @@ public class SymbolicAllelesIntegrationTest extends WalkerTest { WalkerTestSpec spec = new WalkerTestSpec( baseTestString(b36KGReference, "symbolic_alleles_2.vcf"), 1, - Arrays.asList("d2fc144d5996530b9161af3d22af41d9")); + Arrays.asList("93a24c019663a6011b4d6de12538df11")); executeTest("Test symbolic alleles mixed in with non-symbolic alleles", spec); } } diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java index 2f0ef1a0e..a3cd2d39f 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java @@ -152,7 +152,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { @Test public void testTabixAnnotations() { - final String MD5 = "13269d5a2e16f06fd755cc0fb9271acf"; + final String MD5 = "bb9a148716fc69d706c5be146c1afa00"; 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_HEADER", 1, diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java index 464dfb06e..d031d393c 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java @@ -172,7 +172,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { @Test public void testOutputParameter() { HashMap e = new HashMap(); - e.put( "-sites_only", "44f3b5b40e6ad44486cddfdb7e0bfcd8" ); + e.put( "-sites_only", "446ed9a72d210671ed48aa1f572b77e3" ); e.put( "--output_mode EMIT_ALL_CONFIDENT_SITES", "ecf92054c1e4bd9d6529b8002d385165" ); e.put( "--output_mode EMIT_ALL_SITES", "e10819a2a7960254e27ed2b958b45d56" ); @@ -376,7 +376,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { public void testMinIndelFraction0() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( assessMinIndelFraction + " -minIndelFrac 0.0", 1, - Arrays.asList("973178b97efd2daacc9e45c414275d59")); + Arrays.asList("1e4595c85159bd9b62eff575134b5dd9")); executeTest("test minIndelFraction 0.0", spec); } @@ -384,7 +384,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { public void testMinIndelFraction25() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( assessMinIndelFraction + " -minIndelFrac 0.25", 1, - Arrays.asList("220facd2eb0923515d1d8ab874055564")); + Arrays.asList("6d9dbb949626fdb0bca6a7904e9b0c1f")); executeTest("test minIndelFraction 0.25", spec); } @@ -392,7 +392,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { public void testMinIndelFraction100() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( assessMinIndelFraction + " -minIndelFrac 1", 1, - Arrays.asList("50fe9a4c5633f6395b45d9ec1e00d56a")); + Arrays.asList("a31a355bc2b8257b2a45494e97322694")); executeTest("test minIndelFraction 1.0", spec); } } diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/validation/ValidationSiteSelectorIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/validation/ValidationSiteSelectorIntegrationTest.java index d7c866a0a..1a4de3e87 100644 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/validation/ValidationSiteSelectorIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/validation/ValidationSiteSelectorIntegrationTest.java @@ -33,7 +33,7 @@ public class ValidationSiteSelectorIntegrationTest extends WalkerTest { WalkerTestSpec spec = new WalkerTestSpec( baseTestString(sampleNone + freqUnif + "--variant " + testfile), 1, - Arrays.asList("d49baeb8000a426c172ce1d81eb37963") + Arrays.asList("6a9e990a9252840904b5144213915b32") ); executeTest("testNoSampleSelectionFreqUniform--" + testfile, spec); @@ -45,7 +45,7 @@ public class ValidationSiteSelectorIntegrationTest extends WalkerTest { WalkerTestSpec spec = new WalkerTestSpec( baseTestString(sampleNone + freqAF + "--variant " + testfile), 1, - Arrays.asList("0fb0d015d462c34514fc7e96beea5f56") + Arrays.asList("eaa2385086cddff68cf4fdb81cbdbbb9") ); executeTest("testNoSampleSelectionFreqAF--" + testfile, spec); @@ -57,7 +57,7 @@ public class ValidationSiteSelectorIntegrationTest extends WalkerTest { WalkerTestSpec spec = new WalkerTestSpec( baseTestString(sampleGT + freqUnif + "--variant " + testfile), 1, - Arrays.asList("0672854299d42ea8af906976a3849ae6") + Arrays.asList("24077656f590d6905546f7e019c8dccb") ); executeTest("testPolyGTFreqUniform--" + testfile, spec); @@ -69,7 +69,7 @@ public class ValidationSiteSelectorIntegrationTest extends WalkerTest { WalkerTestSpec spec = new WalkerTestSpec( baseTestString(sampleGT + freqAF + "--variant " + testfile), 1, - Arrays.asList("5bdffda1a063d0bddd6b236854ec627d") + Arrays.asList("3c1180fd9b5e80e540b39c5a95fbe722") ); executeTest("testPolyGTFreqAF--" + testfile, spec); @@ -81,7 +81,7 @@ public class ValidationSiteSelectorIntegrationTest extends WalkerTest { WalkerTestSpec spec = new WalkerTestSpec( baseTestString(sampleGL + freqAF + "--variant " + testfile), 1, - Arrays.asList("35ef16aa41303606a4b94f7b88bd9aa8") + Arrays.asList("ad30c028864348204ebe80b9c8c503e8") ); executeTest("testPolyGLFreqAF--" + testfile, spec); diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java index 879a5bfa3..79a58c820 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java @@ -27,8 +27,8 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest { VRTest lowPass = new VRTest("phase1.projectConsensus.chr20.raw.snps.vcf", "0ddd1e0e483d2eaf56004615cea23ec7", // tranches - "f8e21a1987960b950db1f0d98be45352", // recal file - "f67d844b6252a55452cf4167b77530b1"); // cut VCF + "a45a78de049cfe767ce23d3423f80b01", // recal file + "1050c387d170639f8cec221e5dddd626"); // cut VCF @DataProvider(name = "VRTest") public Object[][] createData1() { @@ -74,8 +74,8 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest { VRTest indel = new VRTest("combined.phase1.chr20.raw.indels.sites.vcf", "da4458d05f6396f5c4ab96f274e5ccdc", // tranches - "cf380d9b0ae04c8918be8425f82035b4", // recal file - "b00e5e5a6807df8ed1682317948e8a6d"); // cut VCF + "918a5ecad5a2a8a46795144366683188", // recal file + "bf0e8ed5e250d52f0545074c61217d16"); // cut VCF @DataProvider(name = "VRIndelTest") public Object[][] createData2() { @@ -131,7 +131,7 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest { " -o %s" + " -tranchesFile " + validationDataLocation + "VQSR.mixedTest.tranches" + " -recalFile " + validationDataLocation + "VQSR.mixedTest.recal", - Arrays.asList("08060b7f5c9cf3bb1692b50c58fd5a4b")); + Arrays.asList("9039576b63728df7ee2c881817c0e9eb")); executeTest("testApplyRecalibrationSnpAndIndelTogether", spec); } } diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java index 0db6af10a..649a76941 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java @@ -96,8 +96,8 @@ public class CombineVariantsIntegrationTest extends WalkerTest { @Test public void uniqueSNPs() { combine2("pilot2.snps.vcf4.genotypes.vcf", "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf", "", "63fc20d6223e1387563a1164987d716c"); } - @Test public void omniHM3Union() { combineSites(" -filteredRecordsMergeType KEEP_IF_ANY_UNFILTERED", "917b5cb759afd27bce86a59d8355e85c"); } - @Test public void omniHM3Intersect() { combineSites(" -filteredRecordsMergeType KEEP_IF_ALL_UNFILTERED", "1b3a7f7ba51636173c33a56fefe7c0fe"); } + @Test public void omniHM3Union() { combineSites(" -filteredRecordsMergeType KEEP_IF_ANY_UNFILTERED", "5c60eb8d5d4b957a0cf52ca008f021ba"); } + @Test public void omniHM3Intersect() { combineSites(" -filteredRecordsMergeType KEEP_IF_ALL_UNFILTERED", "774b43e69cc7ec93090b4f6e9f4a1079"); } @Test public void threeWayWithRefs() { WalkerTestSpec spec = new WalkerTestSpec( @@ -129,15 +129,15 @@ public class CombineVariantsIntegrationTest extends WalkerTest { @Test public void complexTestFull() { combineComplexSites("", "dd805f6edfc3cf724512dfbbe8df5183"); } @Test public void complexTestMinimal() { combineComplexSites(" -minimalVCF", "14a205edb022f79abf1863588cfee56b"); } - @Test public void complexTestSitesOnly() { combineComplexSites(" -sites_only", "76fdd2acc8f80eb4f9372f542673a8e2"); } - @Test public void complexTestSitesOnlyMinimal() { combineComplexSites(" -sites_only -minimalVCF", "76fdd2acc8f80eb4f9372f542673a8e2"); } + @Test public void complexTestSitesOnly() { combineComplexSites(" -sites_only", "e118d04d1d47c02ad38c046561a9f616"); } + @Test public void complexTestSitesOnlyMinimal() { combineComplexSites(" -sites_only -minimalVCF", "e118d04d1d47c02ad38c046561a9f616"); } @Test public void combineDBSNPDuplicateSites() { WalkerTestSpec spec = new WalkerTestSpec( "-T CombineVariants -NO_HEADER -L 1:902000-903000 -o %s -R " + b37KGReference + " -V:v1 " + b37dbSNP132, 1, - Arrays.asList("ac59209efa4b21feda6493e397932f07")); + Arrays.asList("a838dc241cf357466cd4331fd298c73a")); executeTest("combineDBSNPDuplicateSites:", spec); } } \ No newline at end of file diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariantsIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariantsIntegrationTest.java index 2139a53e7..942bedc82 100644 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariantsIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariantsIntegrationTest.java @@ -40,7 +40,7 @@ public class LeftAlignVariantsIntegrationTest extends WalkerTest { WalkerTestSpec spec = new WalkerTestSpec( "-T LeftAlignVariants -o %s -R " + b37KGReference + " --variant:vcf " + validationDataLocation + "forLeftAlignVariantsTest.vcf -NO_HEADER", 1, - Arrays.asList("158b1d71b28c52e2789f164500b53732")); + Arrays.asList("8e0991576518823b339a4e2f83299d4f")); executeTest("test left alignment", spec); } } diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java index f969d8752..1308cb1e6 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java @@ -136,7 +136,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest { WalkerTestSpec spec = new WalkerTestSpec( "-T SelectVariants -R " + b36KGReference + " -select 'KG_FREQ < 0.5' --variant " + testFile + " -o %s -NO_HEADER", 1, - Arrays.asList("20b52c96f5c48258494d072752b53693") + Arrays.asList("ffa2524380d84a870d2e4a33d9f3d31a") ); executeTest("testMultipleRecordsAtOnePositionFirstIsFiltered--" + testFile, spec); diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCFIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCFIntegrationTest.java index 95fafac8d..b56d4ef87 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCFIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCFIntegrationTest.java @@ -19,7 +19,7 @@ public class VariantsToVCFIntegrationTest extends WalkerTest { @Test public void testVariantsToVCFUsingDbsnpInput() { List md5 = new ArrayList(); - md5.add("d64942fed2a5b7b407f9537dd2b4832e"); + md5.add("a26afcce2a89f905a49c3d09719586b2"); WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-R " + b36KGReference + diff --git a/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFIntegrationTest.java b/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFIntegrationTest.java index b7bbae68d..30e86af34 100644 --- a/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFIntegrationTest.java @@ -35,7 +35,7 @@ public class VCFIntegrationTest extends WalkerTest { String baseCommand = "-R " + b37KGReference + " -NO_HEADER -o %s "; String test1 = baseCommand + "-T SelectVariants -V " + testVCF; - WalkerTestSpec spec1 = new WalkerTestSpec(test1, 1, Arrays.asList("76075307afd26b4db6234795d9fb3c2f")); + WalkerTestSpec spec1 = new WalkerTestSpec(test1, 1, Arrays.asList("acee3b6bdb4b759992f54065c675a249")); executeTest("Test reading and writing breakpoint VCF", spec1); }