diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/PileupWalkerIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/PileupWalkerIntegrationTest.java index a01a3f281..8bea5385a 100644 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/PileupWalkerIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/PileupWalkerIntegrationTest.java @@ -29,9 +29,12 @@ public class PileupWalkerIntegrationTest extends WalkerTest { String gatk_args = "-T Pileup -I " + validationDataLocation + "OV-0930.normal.chunk.bam " + "-R " + hg18Reference + " -show_indels -o %s"; - String expected_md5="06eedc2e7927650961d99d703f4301a4"; + String expected_md5="da2a02d02abac9de14cc4b187d8595a1"; WalkerTestSpec spec = new WalkerTestSpec(gatk_args,1,Arrays.asList(expected_md5)); executeTest("Testing the extended pileup with indel records included on a small chunk of Ovarian dataset with 20 indels (1 D, 19 I)", spec); + // before Adaptor clipping + // String expected_md5="06eedc2e7927650961d99d703f4301a4"; + } } 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 245fda3c7..83c3d3a1e 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 @@ -32,7 +32,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { public void testHasAnnotsAsking1() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + " -G Standard --variant:VCF3 " + validationDataLocation + "vcfexample2.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1, - Arrays.asList("fbb656369eaa48153d127bd12db59d8f")); + Arrays.asList("ac5f409856a1b79316469733e62abb91")); executeTest("test file has annotations, asking for annotations, #1", spec); } @@ -40,7 +40,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { public void testHasAnnotsAsking2() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + " -G Standard --variant:VCF3 " + validationDataLocation + "vcfexample3.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1, - Arrays.asList("2977bb30c8b84a5f4094fe6090658561")); + Arrays.asList("f9aa7bee5a61ac1a9187d0cf1e8af471")); executeTest("test file has annotations, asking for annotations, #2", spec); } @@ -66,7 +66,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { public void testNoAnnotsAsking1() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + " -G Standard --variant:VCF3 " + validationDataLocation + "vcfexample2empty.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1, - Arrays.asList("42dd979a0a931c18dc9be40308bac321")); + Arrays.asList("6f27fd863b6718d59d2a2d8e2a20bcae")); executeTest("test file doesn't have annotations, asking for annotations, #1", spec); } @@ -74,7 +74,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { public void testNoAnnotsAsking2() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + " -G Standard --variant:VCF3 " + validationDataLocation + "vcfexample3empty.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1, - Arrays.asList("0948cd1dba7d61f283cc4cf2a7757d92")); + Arrays.asList("40bbd3d5a2397a007c0e74211fb33433")); executeTest("test file doesn't have annotations, asking for annotations, #2", spec); } @@ -82,7 +82,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { public void testExcludeAnnotations() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + " -G Standard -XA FisherStrand -XA ReadPosRankSumTest --variant:VCF3 " + validationDataLocation + "vcfexample2empty.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1, - Arrays.asList("477eac07989593b58bb361f3429c085a")); + Arrays.asList("40622d39072b298440a77ecc794116e7")); executeTest("test exclude annotations", spec); } @@ -90,7 +90,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { public void testOverwritingHeader() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + " -G Standard --variant " + validationDataLocation + "vcfexample4.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,001,292", 1, - Arrays.asList("062155edec46a8c52243475fbf3a2943")); + Arrays.asList("31faae1bc588d195ff553cf6c47fabfa")); executeTest("test overwriting header", spec); } diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/coverage/CallableLociWalkerIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/coverage/CallableLociWalkerIntegrationTest.java index 3783525d1..186e5c3b7 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/coverage/CallableLociWalkerIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/coverage/CallableLociWalkerIntegrationTest.java @@ -32,13 +32,13 @@ import java.util.Arrays; public class CallableLociWalkerIntegrationTest extends WalkerTest { final static String commonArgs = "-R " + b36KGReference + " -T CallableLoci -I " + validationDataLocation + "/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s"; - final static String SUMMARY_MD5 = "ed4c255bb78313b8e7982127caf3d6c4"; + final static String SUMMARY_MD5 = "cd597a8dae35c226a2cb110b1c9f32d5"; @Test public void testCallableLociWalkerBed() { String gatk_args = commonArgs + " -format BED -L 1:10,000,000-11,000,000 -summary %s"; WalkerTestSpec spec = new WalkerTestSpec(gatk_args, 2, - Arrays.asList("884c9c2d96419d990a708d2bd98fcefa", SUMMARY_MD5)); + Arrays.asList("c86ac1ef404c11d5e5452e020c8f7ce9", SUMMARY_MD5)); executeTest("formatBed", spec); } @@ -46,7 +46,7 @@ public class CallableLociWalkerIntegrationTest extends WalkerTest { public void testCallableLociWalkerPerBase() { String gatk_args = commonArgs + " -format STATE_PER_BASE -L 1:10,000,000-11,000,000 -summary %s"; WalkerTestSpec spec = new WalkerTestSpec(gatk_args, 2, - Arrays.asList("fb4524f8b3b213060c0c5b85362b5902", SUMMARY_MD5)); + Arrays.asList("d8536a55fe5f6fdb1ee6c9511082fdfd", SUMMARY_MD5)); executeTest("format_state_per_base", spec); } @@ -62,7 +62,7 @@ public class CallableLociWalkerIntegrationTest extends WalkerTest { public void testCallableLociWalker3() { String gatk_args = commonArgs + " -format BED -L 1:10,000,000-11,000,000 -minDepth 10 -maxDepth 100 --minBaseQuality 10 --minMappingQuality 20 -summary %s"; WalkerTestSpec spec = new WalkerTestSpec(gatk_args, 2, - Arrays.asList("86bd1a5f79356b3656412c4b1c60709a", "6fefb144a60b89c27293ce5ca6e10e6a")); + Arrays.asList("bc966060184bf4605a31da7fe383464e", "d624eda8f6ed14b9251ebeec73e37867")); executeTest("formatBed lots of arguments", spec); } } diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageB36IntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageB36IntegrationTest.java index 043b2eaf2..f4cd4968b 100644 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageB36IntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageB36IntegrationTest.java @@ -61,13 +61,14 @@ public class DepthOfCoverageB36IntegrationTest extends WalkerTest { File baseOutputFile = this.createTempFile("depthofcoveragemapq0",".tmp"); spec.setOutputFileLocation(baseOutputFile); - spec.addAuxFile("f39af6ad99520fd4fb27b409ab0344a0",baseOutputFile); - spec.addAuxFile("6b15f5330414b6d4e2f6caea42139fa1", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_cumulative_coverage_counts")); - spec.addAuxFile("cc6640d82077991dde8a2b523935cdff", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_cumulative_coverage_proportions")); + spec.addAuxFile("5b6c16a1c667c844882e9dce71454fc4",baseOutputFile); + spec.addAuxFile("fc161ec1b61dc67bc6a5ce36cb2d02c9", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_cumulative_coverage_counts")); + spec.addAuxFile("89321bbfb76a4e1edc0905d50503ba1f", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_cumulative_coverage_proportions")); spec.addAuxFile("0fb627234599c258a3fee1b2703e164a", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_interval_statistics")); - spec.addAuxFile("cb73a0fa0cee50f1fb8f249315d38128", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_interval_summary")); - spec.addAuxFile("347b47ef73fbd4e277704ddbd7834f69", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_statistics")); - spec.addAuxFile("4ec920335d4b9573f695c39d62748089", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_summary")); + spec.addAuxFile("4dd16b659065e331ed4bd3ab0dae6c1b", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_interval_summary")); + spec.addAuxFile("2be0c18b501f4a3d8c5e5f99738b4713", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_statistics")); + spec.addAuxFile("5a26ef61f586f58310812580ce842462", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_summary")); + execute("testMapQ0Only",spec); } @@ -83,7 +84,7 @@ public class DepthOfCoverageB36IntegrationTest extends WalkerTest { File baseOutputFile = this.createTempFile("testManySamples",".tmp"); spec.setOutputFileLocation(baseOutputFile); - spec.addAuxFile("c9561b52344536d2b06ab97b0bb1a234",baseOutputFile); + spec.addAuxFile("d73fa1fc492f7dcc1d75056f8c12c92a",baseOutputFile); execute("testLotsOfSamples",spec); } diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageIntegrationTest.java index 646fb5e77..9d6638d53 100644 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageIntegrationTest.java @@ -55,26 +55,26 @@ public class DepthOfCoverageIntegrationTest extends WalkerTest { spec.setOutputFileLocation(baseOutputFile); // now add the expected files that get generated - spec.addAuxFile("423571e4c05e7934322172654ac6dbb7", baseOutputFile); - spec.addAuxFile("9df5e7e07efeb34926c94a724714c219", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_cumulative_coverage_counts")); - spec.addAuxFile("229b9b5bc2141c86dbc69c8acc9eba6a", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_cumulative_coverage_proportions")); - spec.addAuxFile("9cd395f47b329b9dd00ad024fcac9929", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_interval_statistics")); - spec.addAuxFile("471c34ad2e4f7228efd20702d5941ba9", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_interval_summary")); - spec.addAuxFile("9667c77284c2c08e647b162d0e9652d4", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_statistics")); - spec.addAuxFile("5a96c75f96d6fa6ee617451d731dae37", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_summary")); - spec.addAuxFile("b82846df660f0aac8429aec57c2a62d6", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_cumulative_coverage_counts")); - spec.addAuxFile("d32a8c425fadcc4c048bd8b48d0f61e5", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_cumulative_coverage_proportions")); - spec.addAuxFile("7b9d0e93bf5b5313995be7010ef1f528", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_interval_statistics")); - spec.addAuxFile("2aae346204c5f15517158da8e61a6c16", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_interval_summary")); - spec.addAuxFile("e70952f241eebb9b5448f2e7cb288131", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_statistics")); - spec.addAuxFile("054ed1e184f46d6a170dc9bf6524270c", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_summary")); - spec.addAuxFile("d53431022f7387fe9ac47814ab1fcd88", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_cumulative_coverage_counts")); - spec.addAuxFile("a395dafde101971d2b9e5ddb6cd4b7d0", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_cumulative_coverage_proportions")); - spec.addAuxFile("df0ba76e0e6082c0d29fcfd68efc6b77", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_interval_statistics")); - spec.addAuxFile("e013cb5b11b0321a81c8dbd7c1863787", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_interval_summary")); - spec.addAuxFile("661160f571def8c323345b5859cfb9da", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_statistics")); - spec.addAuxFile("c95a7a6840334cadd0e520939615c77b", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_summary")); - + spec.addAuxFile("19e862f7ed3de97f2569803f766b7433", baseOutputFile); + spec.addAuxFile("c64cc5636d4880b80b71169ed1832cd7", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_cumulative_coverage_counts")); + spec.addAuxFile("1a8ba07a60e55f9fdadc89d00b1f3394", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_cumulative_coverage_proportions")); + spec.addAuxFile("0075cead73a901e3a9d07c5d9c2b75f4", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_interval_statistics")); + spec.addAuxFile("d757be2f953f893e66eff1ef1f0fff4e", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_interval_summary")); + spec.addAuxFile("de08996729c774590d6a4954c906fe84", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_statistics")); + spec.addAuxFile("58ad39b100d1f2af7d119f28ba626bfd", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_summary")); + spec.addAuxFile("0b4ce6059e6587ae5a986afbbcc7d783", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_cumulative_coverage_counts")); + spec.addAuxFile("adc2b2babcdd72a843878acf2d510ca7", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_cumulative_coverage_proportions")); + spec.addAuxFile("884281c139241c5db3c9f90e8684d084", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_interval_statistics")); + spec.addAuxFile("b90636cad74ff4f6b9ff9a596e145bd6", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_interval_summary")); + spec.addAuxFile("ad540b355ef90c566bebaeabd70026d2", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_statistics")); + spec.addAuxFile("27fe09a02a5b381e0ed633587c0f4b23", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_summary")); + spec.addAuxFile("5fcd53b4bd167b5e6d5f92329cf8678e", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_cumulative_coverage_counts")); + spec.addAuxFile("7a2a19e54f73a8e07de2f020f1f913dd", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_cumulative_coverage_proportions")); + spec.addAuxFile("852a079c5e9e93e7daad31fd6a9f4a49", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_interval_statistics")); + spec.addAuxFile("0828762842103edfaf115ef4e50809c6", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_interval_summary")); + spec.addAuxFile("5c5aeb28419bba1decb17f8a166777f2", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_statistics")); + spec.addAuxFile("e5fd6216b3d6a751f3a90677b4e5bf3c", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_summary")); + execute("testBaseOutputNoFiltering",spec); } 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 e049af064..ba33108cf 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 @@ -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("a2d3839c4ebb390b0012d495e4e53b3a")); + Arrays.asList("66ed60c6c1190754abd8a0a9d1d8d61e")); executeTest("test MultiSample Pilot1", spec); } @@ -129,8 +129,8 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { public void testOutputParameter() { HashMap e = new HashMap(); e.put( "-sites_only", "44f3b5b40e6ad44486cddfdb7e0bfcd8" ); - e.put( "--output_mode EMIT_ALL_CONFIDENT_SITES", "d971d392956aea69c3707da64d24485b" ); - e.put( "--output_mode EMIT_ALL_SITES", "21993e71ca1a06a0d1f11d58e3cc26c3" ); + e.put( "--output_mode EMIT_ALL_CONFIDENT_SITES", "42e4ea7878ef8d96215accb3ba4e97b7" ); + e.put( "--output_mode EMIT_ALL_SITES", "e0443c720149647469f2a2f3fb73942f" ); for ( Map.Entry entry : e.entrySet() ) { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( @@ -189,7 +189,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { " -o %s" + " -L 1:10,000,000-10,100,000", 1, - Arrays.asList("f0fbe472f155baf594b1eeb58166edef")); + Arrays.asList("2b2729414ae855d390e7940956745bce")); executeTest(String.format("test multiple technologies"), spec); } @@ -208,7 +208,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { " -L 1:10,000,000-10,100,000" + " -baq CALCULATE_AS_NECESSARY", 1, - Arrays.asList("8c87c749a7bb5a76ed8504d4ec254272")); + Arrays.asList("95c6120efb92e5a325a5cec7d77c2dab")); executeTest(String.format("test calling with BAQ"), spec); } @@ -227,7 +227,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { " -o %s" + " -L 1:10,000,000-10,500,000", 1, - Arrays.asList("a64d2e65b5927260e4ce0d948760cc5c")); + Arrays.asList("d87ce4b405d4f7926d1c36aee7053975")); executeTest(String.format("test indel caller in SLX"), spec); } @@ -255,7 +255,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { " -o %s" + " -L 1:10,000,000-10,500,000", 1, - Arrays.asList("69107157632714150fc068d412e31939")); + Arrays.asList("c5989e5d67d9e5fe8c5c956f12a975da")); executeTest(String.format("test indel calling, multiple technologies"), spec); } @@ -265,7 +265,7 @@ 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("4ffda07590e06d58ed867ae326d74b2d")); + Arrays.asList("daca0741278de32e507ad367e67753b6")); executeTest("test MultiSample Pilot2 indels with alleles passed in", spec1); } @@ -275,7 +275,7 @@ 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("45633d905136c86e9d3f90ce613255e5")); + Arrays.asList("0ccc4e876809566510429c64adece2c7")); executeTest("test MultiSample Pilot2 indels with alleles passed in and emitting all sites", spec2); } @@ -285,7 +285,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { WalkerTest.WalkerTestSpec spec3 = new WalkerTest.WalkerTestSpec( baseCommandIndels + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "ALL.wgs.union_v2.20101123.indels.sites.vcf -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,080,000", 1, - Arrays.asList("8bd5028cf294850b8a95b3c0af23d728")); + Arrays.asList("cff6dd0f4eb1ef0b6fc476da6ffead19")); executeTest("test MultiSample Pilot2 indels with complicated records", spec3); } @@ -294,7 +294,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { WalkerTest.WalkerTestSpec spec4 = new WalkerTest.WalkerTestSpec( baseCommandIndelsb37 + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "ALL.wgs.union_v2_chr20_100_110K.20101123.indels.sites.vcf -I " + validationDataLocation + "phase1_GBR_realigned.chr20.100K-110K.bam -o %s -L 20:100,000-110,000", 1, - Arrays.asList("814dcd66950635a870602d90a1618cce")); + Arrays.asList("1e2a4aab26e9ab0dae709d33a669e036")); executeTest("test MultiSample Phase1 indels with complicated records", spec4); } diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java index cbcd5835f..b4b1f7b8e 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java @@ -31,10 +31,11 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest { @DataProvider(name = "cctestdata") public Object[][] createCCTestData() { - new CCTest( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "5a52b00d9794d27af723bcf93366681e" ); + + new CCTest( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "9469d6b65880abe4e5babc1c1a69889d" ); new CCTest( validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", "17d4b8001c982a70185e344929cf3941"); - new CCTest( validationDataLocation + "NA12873.454.SRP000031.2009_06.chr1.10_20mb.bam", "714e65d6cb51ae32221a77ce84cbbcdc" ); - new CCTest( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam", "64e9f17a1cf6fc04c1f2717c2d2eca67" ); + new CCTest( validationDataLocation + "NA12873.454.SRP000031.2009_06.chr1.10_20mb.bam", "36c0c467b6245c2c6c4e9c956443a154" ); + new CCTest( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam", "ed15f8bf03bb2ea9b7c26844be829c0d" ); return CCTest.getTests(CCTest.class); } @@ -88,10 +89,11 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest { @DataProvider(name = "trtestdata") public Object[][] createTRTestData() { - new TRTest( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "2864f231fab7030377f3c8826796e48f" ); + new TRTest( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "f020725d9f75ad8f1c14bfae056e250f" ); new TRTest( validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", "d04cf1f6df486e45226ebfbf93a188a5"); - new TRTest( validationDataLocation + "NA12873.454.SRP000031.2009_06.chr1.10_20mb.bam", "74314e5562c1a65547bb0edaacffe602" ); - new TRTest( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam", "2a37c6001826bfabf87063b1dfcf594f" ); + new TRTest( validationDataLocation + "NA12873.454.SRP000031.2009_06.chr1.10_20mb.bam", "b2f4757bc47cf23bd9a09f756c250787" ); + new TRTest( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam", "313a21a8a88e3460b6e71ec5ffc50f0f" ); + return TRTest.getTests(TRTest.class); } @@ -121,7 +123,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest { @Test public void testCountCovariatesUseOriginalQuals() { HashMap e = new HashMap(); - e.put( validationDataLocation + "originalQuals.1kg.chr1.1-1K.bam", "278846c55d97bd9812b758468a83f559"); + e.put( validationDataLocation + "originalQuals.1kg.chr1.1-1K.bam", "bd8288b1fc7629e2e8c2cf7f65fefa8f"); for ( Map.Entry entry : e.entrySet() ) { String bam = entry.getKey(); @@ -145,7 +147,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest { @Test public void testTableRecalibratorMaxQ70() { HashMap e = new HashMap(); - e.put( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "2864f231fab7030377f3c8826796e48f" ); + e.put( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "f020725d9f75ad8f1c14bfae056e250f" ); for ( Map.Entry entry : e.entrySet() ) { String bam = entry.getKey(); @@ -174,7 +176,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest { @Test public void testCountCovariatesSolidIndelsRemoveRefBias() { HashMap e = new HashMap(); - e.put( validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", "8379f24cf5312587a1f92c162ecc220f" ); + e.put( validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", "1f643bca090478ba68aac88db835a629" ); for ( Map.Entry entry : e.entrySet() ) { String bam = entry.getKey(); @@ -200,7 +202,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest { @Test public void testTableRecalibratorSolidIndelsRemoveRefBias() { HashMap e = new HashMap(); - e.put( validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", "2ad4c17ac3ed380071137e4e53a398a5" ); + e.put( validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", "613fb2bbe01af8cbe6a188a10c1582ca" ); for ( Map.Entry entry : e.entrySet() ) { String bam = entry.getKey(); @@ -228,7 +230,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest { @Test public void testCountCovariatesBED() { HashMap e = new HashMap(); - e.put( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "b460478d9683e827784e42bc352db8bb"); + e.put( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "b00e99219aeafe2516c6232b7d6a0a00"); for ( Map.Entry entry : e.entrySet() ) { String bam = entry.getKey(); @@ -252,7 +254,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest { @Test public void testCountCovariatesVCFPlusDBsnp() { HashMap e = new HashMap(); - e.put( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "9131d96f39badbf9753653f55b148012"); + e.put( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "7b92788ce92f49415af3a75a2e4a2b33"); for ( Map.Entry entry : e.entrySet() ) { String bam = entry.getKey(); @@ -280,7 +282,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest { @Test public void testCountCovariatesNoIndex() { HashMap e = new HashMap(); - e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.noindex.bam", "8993d32df5cb66c7149f59eccbd57f4c" ); + e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.noindex.bam", "f34f7141351a5dbf9664c67260f94e96" ); for ( Map.Entry entry : e.entrySet() ) { String bam = entry.getKey(); @@ -306,7 +308,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest { @Test public void testTableRecalibratorNoIndex() { HashMap e = new HashMap(); - e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.noindex.bam", "5f913c98ca99754902e9d34f99df468f" ); + e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.noindex.bam", "13c83656567cee9e93bda9874ee80234" ); for ( Map.Entry entry : e.entrySet() ) { String bam = entry.getKey(); diff --git a/public/java/test/org/broadinstitute/sting/utils/sam/ReadUtilsUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/sam/ReadUtilsUnitTest.java index 3878cbfa9..e9269ff48 100755 --- a/public/java/test/org/broadinstitute/sting/utils/sam/ReadUtilsUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/utils/sam/ReadUtilsUnitTest.java @@ -33,20 +33,6 @@ public class ReadUtilsUnitTest extends BaseTest { reducedRead.setAttribute(GATKSAMRecord.REDUCED_READ_CONSENSUS_TAG, REDUCED_READ_COUNTS_TAG); } - private void testReadBasesAndQuals(GATKSAMRecord read, int expectedStart, int expectedStop) { - SAMRecord clipped = ReadUtils.hardClipBases(read, expectedStart, expectedStop - 1, null); - String expectedBases = BASES.substring(expectedStart, expectedStop); - String expectedQuals = QUALS.substring(expectedStart, expectedStop); - Assert.assertEquals(clipped.getReadBases(), expectedBases.getBytes(), "Clipped bases not those expected"); - Assert.assertEquals(clipped.getBaseQualityString(), expectedQuals, "Clipped quals not those expected"); - } - - @Test public void testNoClip() { testReadBasesAndQuals(read, 0, 4); } - @Test public void testClip1Front() { testReadBasesAndQuals(read, 1, 4); } - @Test public void testClip2Front() { testReadBasesAndQuals(read, 2, 4); } - @Test public void testClip1Back() { testReadBasesAndQuals(read, 0, 3); } - @Test public void testClip2Back() { testReadBasesAndQuals(read, 0, 2); } - @Test public void testReducedReads() { Assert.assertFalse(read.isReducedRead(), "isReducedRead is false for normal read");