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 216406b63..78167e7e9 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 @@ -30,7 +30,7 @@ public class UnifiedGenotyperIntegrationTest 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("ac3737b4212f634a03c640c83f670955")); + Arrays.asList("d3191b2f10139c969501990ffdf29082")); executeTest("test MultiSample Pilot1", spec); } @@ -54,7 +54,7 @@ public class UnifiedGenotyperIntegrationTest 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("c5b53231f4f6d9524bc4ec8115f44f5c")); + Arrays.asList("7c7288170c6aadae555a44e79ca5bf19")); executeTest("test SingleSample Pilot2", spec); } @@ -62,7 +62,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { public void testMultipleSNPAlleles() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-T UnifiedGenotyper -R " + b37KGReference + " -nosl -NO_HEADER -glm BOTH --dbsnp " + b37dbSNP129 + " -I " + validationDataLocation + "multiallelic.snps.bam -o %s -L " + validationDataLocation + "multiallelic.snps.intervals", 1, - Arrays.asList("6f70dfbaf3bb70c702f9e9dbacd67c17")); + Arrays.asList("c956f0ea0e5f002288a09f4bc4af1319")); executeTest("test Multiple SNP alleles", spec); } @@ -72,7 +72,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { // // -------------------------------------------------------------------------------------------------------------- - private final static String COMPRESSED_OUTPUT_MD5 = "a08df9aea2b3df09cf90ff8e6e3be3ea"; + private final static String COMPRESSED_OUTPUT_MD5 = "2158eb918abb95225ea5372fcd9c9236"; @Test public void testCompressedOutput() { @@ -93,7 +93,7 @@ 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 = "6358934c1c26345013a38261b8c45aa4"; + String md5 = "834e85f6af4ad4a143b913dfc7defb08"; WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec( baseCommand + " -dt NONE -G none -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,075,000", 1, @@ -147,7 +147,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { HashMap e = new HashMap(); e.put( "-sites_only", "44f3b5b40e6ad44486cddfdb7e0bfcd8" ); e.put( "--output_mode EMIT_ALL_CONFIDENT_SITES", "ecf92054c1e4bd9d6529b8002d385165" ); - e.put( "--output_mode EMIT_ALL_SITES", "119c9fcefbc69e0fc10b1dc52f6438e3" ); + e.put( "--output_mode EMIT_ALL_SITES", "e10819a2a7960254e27ed2b958b45d56" ); for ( Map.Entry entry : e.entrySet() ) { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( @@ -181,8 +181,8 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { @Test public void testHeterozyosity() { HashMap e = new HashMap(); - e.put( 0.01, "926b58038dd4989bf7eda697a847eea9" ); - e.put( 1.0 / 1850, "93f44105b43b65730a3b821e27b0fa16" ); + e.put( 0.01, "d5879f1c277035060434d79a441b31ca" ); + e.put( 1.0 / 1850, "13f80245bab2321b92d27eebd5c2fc33" ); for ( Map.Entry entry : e.entrySet() ) { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( @@ -206,7 +206,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { " -o %s" + " -L 1:10,000,000-10,100,000", 1, - Arrays.asList("a1b75a7e12b160b0be823228c958573f")); + Arrays.asList("8c134a6e0abcc70d2ed3216d5f8e0100")); executeTest(String.format("test multiple technologies"), spec); } @@ -225,7 +225,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { " -L 1:10,000,000-10,100,000" + " -baq CALCULATE_AS_NECESSARY", 1, - Arrays.asList("3bda1279cd6dcb47885f3e19466f11b9")); + Arrays.asList("34baad3177712f6cd0b476f4c578e08f")); executeTest(String.format("test calling with BAQ"), spec); } @@ -244,7 +244,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { " -o %s" + " -L 1:10,000,000-10,500,000", 1, - Arrays.asList("d9fc3ba94a0d46029778c7b457e7292a")); + Arrays.asList("4bf4f819a39a73707cae60fe30478742")); executeTest(String.format("test indel caller in SLX"), spec); } @@ -259,7 +259,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { " -minIndelCnt 1" + " -L 1:10,000,000-10,100,000", 1, - Arrays.asList("b2e30ae3e5ffa6108f9f6178b1d2e679")); + Arrays.asList("ae08fbd6b0618cf3ac1be763ed7b41ca")); executeTest(String.format("test indel caller in SLX with low min allele count"), spec); } @@ -272,7 +272,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { " -o %s" + " -L 1:10,000,000-10,500,000", 1, - Arrays.asList("2cd182a84613fa91a6020466d2d327e2")); + Arrays.asList("120600f2bfa3a47bd93b50f768f98d5b")); executeTest(String.format("test indel calling, multiple technologies"), spec); } @@ -282,7 +282,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( baseCommandIndels + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "indelAllelesForUG.vcf -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,100,000", 1, - Arrays.asList("9cd08dc412a007933381e9c76c073899")); + Arrays.asList("2e75d2766235eab23091a67ea2947d13")); executeTest("test MultiSample Pilot2 indels with alleles passed in", spec); } @@ -292,7 +292,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { baseCommandIndels + " --output_mode EMIT_ALL_SITES --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "indelAllelesForUG.vcf -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,100,000", 1, - Arrays.asList("5ef1f007d3ef77c1b8f31e5e036eff53")); + Arrays.asList("5057bd7d07111e8b1085064782eb6c80")); executeTest("test MultiSample Pilot2 indels with alleles passed in and emitting all sites", spec); } @@ -300,13 +300,13 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { public void testMultiSampleIndels() { WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec( baseCommandIndels + " -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -o %s -L 1:10450700-10551000", 1, - Arrays.asList("fbc48d7d9e622c9af7922f91bc858151")); + Arrays.asList("c0f9ca3ceab90ebd38cc0eec9441d71f")); List result = executeTest("test MultiSample Pilot1 CEU indels", spec1).getFirst(); 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 1:10450700-10551000", 1, - Arrays.asList("94c52ef70e44709ccd947d32e9c27da9")); + Arrays.asList("0240f34e71f137518be233c9890a5349")); executeTest("test MultiSample Pilot1 CEU indels using GENOTYPE_GIVEN_ALLELES", spec2); } @@ -349,7 +349,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { public void testMinIndelFraction0() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( assessMinIndelFraction + " -minIndelFrac 0.0", 1, - Arrays.asList("f08ff07ad49d388198c1887baad05977")); + Arrays.asList("53758e66e3a3188bd9c78d2329d41962")); executeTest("test minIndelFraction 0.0", spec); } @@ -357,7 +357,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { public void testMinIndelFraction25() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( assessMinIndelFraction + " -minIndelFrac 0.25", 1, - Arrays.asList("a0945fd21369aaf68c7f1d96dbb930d1")); + Arrays.asList("3aa39b1f6f3b1eb051765f9c21f6f461")); executeTest("test minIndelFraction 0.25", spec); }