From 902eb0c61e6b6ba00d5ed82c25d114d494324a69 Mon Sep 17 00:00:00 2001 From: Ryan Poplin Date: Thu, 11 Aug 2011 13:55:03 -0400 Subject: [PATCH] Adding dbsnp annotation back into the UG integration tests --- .../UnifiedGenotyperIntegrationTest.java | 51 +++++++++---------- 1 file changed, 25 insertions(+), 26 deletions(-) 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 d11fb7e29..da0c8f81f 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 @@ -16,8 +16,8 @@ import java.util.Map; public class UnifiedGenotyperIntegrationTest extends WalkerTest { - private final static String baseCommand = "-T UnifiedGenotyper -R " + b36KGReference + " -NO_HEADER -glm BOTH"; - private final static String baseCommandIndels = "-T UnifiedGenotyper -R " + b36KGReference + " -NO_HEADER -glm INDEL"; + private final static String baseCommand = "-T UnifiedGenotyper -R " + b36KGReference + " -NO_HEADER -glm BOTH --dbsnp " + b36dbSNP129; + private final static String baseCommandIndels = "-T UnifiedGenotyper -R " + b36KGReference + " -NO_HEADER -glm INDEL --dbsnp " + b36dbSNP129; // -------------------------------------------------------------------------------------------------------------- // @@ -28,7 +28,7 @@ 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("16b0c7b47745abcd1ddaa2e261719530")); + Arrays.asList("149e6ad9b3fd23551254a691286a96b3")); executeTest("test MultiSample Pilot1", spec); } @@ -54,12 +54,12 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { public void testWithAllelesPassedIn() { WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec( baseCommand + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "allelesForUG.vcf -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,025,000", 1, - Arrays.asList("811ddc0bd8322b14f14f58df8c627aa9")); + Arrays.asList("8de2602679ffc92388da0b6cb4325ef6")); executeTest("test MultiSample Pilot2 with alleles passed in", spec1); WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec( baseCommand + " --output_mode EMIT_ALL_SITES --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "allelesForUG.vcf -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,025,000", 1, - Arrays.asList("5cf08dd7ac3d218082f7be3915ce0b15")); + Arrays.asList("ec43daadfb15b00b41aeb0017a45df0b")); executeTest("test MultiSample Pilot2 with alleles passed in and emitting all sites", spec2); } @@ -67,7 +67,7 @@ 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("75156264696563c2f47620fef9424f7c")); + Arrays.asList("82d469145c174486ccc494884852cc58")); executeTest("test SingleSample Pilot2", spec); } @@ -77,7 +77,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { // // -------------------------------------------------------------------------------------------------------------- - private final static String COMPRESSED_OUTPUT_MD5 = "7255e03430549cb97d8fcae34cbffb02"; + private final static String COMPRESSED_OUTPUT_MD5 = "a5a9f38c645d6004d4640765a8b77ce4"; @Test public void testCompressedOutput() { @@ -107,7 +107,7 @@ 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 = "7912109e83fda21dae90ef8d5dd0140d"; + String md5 = "0a45761c0e557d9c2080eb9e7f4f6c41"; 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, @@ -138,10 +138,9 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { @Test public void testCallingParameters() { HashMap e = new HashMap(); - e.put( "--min_base_quality_score 26", "6d3aa9f783ca63f37c952f83eeda593c" ); - e.put( "--min_mapping_quality_score 26", "51bfdf777123bf49de5d92ffde5c74e7" ); - e.put( "--p_nonref_model GRID_SEARCH", "333328ab2c8da2875fade599e80a271f" ); - e.put( "--computeSLOD", "226caa28a4fa9fe34f3beb8a23f3d53d" ); + e.put( "--min_base_quality_score 26", "531966aee1cd5dced61c96c4fedb59a9" ); + e.put( "--min_mapping_quality_score 26", "c71ca370947739cb7d87b59452be7a07" ); + e.put( "--computeSLOD", "1a5648f26c18ced27df4be031b44e72d" ); for ( Map.Entry entry : e.entrySet() ) { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( @@ -154,9 +153,9 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { @Test public void testOutputParameter() { HashMap e = new HashMap(); - e.put( "-sites_only", "5f659dee408710d3709ed72005cd863a" ); - e.put( "--output_mode EMIT_ALL_CONFIDENT_SITES", "55d09bf13149bddc06cc36be0801507b" ); - e.put( "--output_mode EMIT_ALL_SITES", "727f49dcb2439b18446829efc3b1561c" ); + e.put( "-sites_only", "d40114aa201aa33ff5f174f15b6b73af" ); + e.put( "--output_mode EMIT_ALL_CONFIDENT_SITES", "3c681b053fd2280f3c42041d24243752" ); + e.put( "--output_mode EMIT_ALL_SITES", "eafa6d71c5ecd64dfee5d7a3f60e392e" ); for ( Map.Entry entry : e.entrySet() ) { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( @@ -170,12 +169,12 @@ 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("51bfdf777123bf49de5d92ffde5c74e7")); + Arrays.asList("c71ca370947739cb7d87b59452be7a07")); executeTest("test confidence 1", spec1); WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec( baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000 -stand_emit_conf 10 ", 1, - Arrays.asList("c67c285e70fd4457c9f9ce7bd878ddca")); + Arrays.asList("1c0a599d475cc7d5e745df6e9b6c0d29")); executeTest("test confidence 2", spec2); } @@ -187,8 +186,8 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { @Test public void testHeterozyosity() { HashMap e = new HashMap(); - e.put( 0.01, "7ecc564d4db97d5932cef2e558550ed2" ); - e.put( 1.0 / 1850, "aa9e101bb9f9e111fe292fec467d915a" ); + e.put( 0.01, "af5199fbc0853cf5888acdcc88f012bc" ); + e.put( 1.0 / 1850, "4e6938645ccde1fdf204ffbf4e88170f" ); for ( Map.Entry entry : e.entrySet() ) { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( @@ -212,7 +211,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { " -o %s" + " -L 1:10,000,000-10,100,000", 1, - Arrays.asList("2efd686186b2c5129be4cf89274a24dd")); + Arrays.asList("213ebaaaacf850312d885e918eb33500")); executeTest(String.format("test multiple technologies"), spec); } @@ -231,7 +230,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { " -L 1:10,000,000-10,100,000" + " -baq CALCULATE_AS_NECESSARY", 1, - Arrays.asList("2892d35331fe9fc141ba19269ec7caed")); + Arrays.asList("3aecba34a89f3525afa57a38dc20e6cd")); executeTest(String.format("test calling with BAQ"), spec); } @@ -250,7 +249,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { " -o %s" + " -L 1:10,000,000-10,500,000", 1, - Arrays.asList("8c2afb4289ed44521933d1a74c8d6c7f")); + Arrays.asList("043973c719a85de29a35a33a674616fb")); executeTest(String.format("test indel caller in SLX"), spec); } @@ -265,7 +264,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { " -minIndelCnt 1" + " -L 1:10,000,000-10,100,000", 1, - Arrays.asList("b6fb70590a10e1c27fb611732916f27d")); + Arrays.asList("68d4e6c1849e892467aed61c33e7bf24")); executeTest(String.format("test indel caller in SLX witn low min allele count"), spec); } @@ -278,7 +277,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { " -o %s" + " -L 1:10,000,000-10,500,000", 1, - Arrays.asList("61642502bd08cc03cdaaeb83a5426b46")); + Arrays.asList("f86d453c5d2d2f33fb28ae2050658a5e")); executeTest(String.format("test indel calling, multiple technologies"), spec); } @@ -288,14 +287,14 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { WalkerTest.WalkerTestSpec spec1 = 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("69b0b3f089c80b9864294d838a061336")); + Arrays.asList("408d3aba4d094c067fc00a43992c2292")); executeTest("test MultiSample Pilot2 indels with alleles passed in", spec1); WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec( 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("c90174cfd7dd68bdef36fe2c60145e10")); + Arrays.asList("94977d6e42e764280e9deaf4e3ac8c80")); executeTest("test MultiSample Pilot2 indels with alleles passed in and emitting all sites", spec2); }