From aa8b2ab5353eccb87879cca6ec29a2e0488c3335 Mon Sep 17 00:00:00 2001 From: Ernesto Brau Date: Fri, 18 Aug 2017 22:51:33 -0400 Subject: [PATCH] Change to GKL 0.5.5, which fixes a bug in FPGA 'private' mode (#1623) Update GKL to version 0.5.5, which fixes a bug in FPGA 'private' mode. Integration test results were updated to reflect different fallback behavior when AVX is not available. --- .../walkers/bqsr/BQSRIntegrationTest.java | 12 ++++---- .../cancer/m2/MuTect2IntegrationTest.java | 2 +- .../HaplotypeCallerIntegrationTest.java | 6 ++-- .../SplitNCigarReadsIntegrationTest.java | 10 +++---- ...mulateReadsForVariantsIntegrationTest.java | 14 +++++----- .../engine/EngineFeaturesIntegrationTest.java | 8 +++--- .../engine/arguments/CramIntegrationTest.java | 8 +++--- .../arguments/IntervalIntegrationTest.java | 6 ++-- public/gatk-root/pom.xml | 2 +- .../tools/walkers/BAQIntegrationTest.java | 4 +-- .../ClipReadsWalkersIntegrationTest.java | 26 ++++++++--------- .../readutils/PrintReadsIntegrationTest.java | 28 +++++++++---------- .../SplitSamFileIntegrationTest.java | 6 ++-- 13 files changed, 66 insertions(+), 66 deletions(-) diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/bqsr/BQSRIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/bqsr/BQSRIntegrationTest.java index 8d35c0135..4c9eba380 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/bqsr/BQSRIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/bqsr/BQSRIntegrationTest.java @@ -198,13 +198,13 @@ public class BQSRIntegrationTest extends WalkerTest { public Object[][] createPRTestData() { List tests = new ArrayList(); - tests.add(new Object[]{1, new PRTest(" -qq -1", "8a38828e3b14ce067614d4248e3ea95a")}); - tests.add(new Object[]{1, new PRTest(" -qq 6", "e4f23250b2c87f0d68d042cc3d2ec1d3")}); - tests.add(new Object[]{1, new PRTest(" -DIQ", "2dfa45f004d3a371fd290ed67fbdf573")}); - tests.add(new Object[]{1, new PRTest(" --useOriginalQualities -SQQ 10 -SQQ 20 -SQQ 30", "4882354d9e603f9bbe7c9591bba0a573")}); - tests.add(new Object[]{1, new PRTest(" --useOriginalQualities -SQQ 10 -SQQ 20 -SQQ 30 -RDQ", "6ffdfc4593e83f7c234b6249412433af")}); + tests.add(new Object[]{1, new PRTest(" -qq -1", "e9969c6d7fd35d96b82c691b4ced5443")}); + tests.add(new Object[]{1, new PRTest(" -qq 6", "b4b271acac003b8504b530c5526d43ad")}); + tests.add(new Object[]{1, new PRTest(" -DIQ", "ec795d16746c3bdf5e54c57337e6eed6")}); + tests.add(new Object[]{1, new PRTest(" --useOriginalQualities -SQQ 10 -SQQ 20 -SQQ 30", "d50df5a7bcc8f195479f64285c124d18")}); + tests.add(new Object[]{1, new PRTest(" --useOriginalQualities -SQQ 10 -SQQ 20 -SQQ 30 -RDQ", "58b9df85e49eb3ee228f0d581c168791")}); for ( final int nct : Arrays.asList(1, 2, 4) ) { - tests.add(new Object[]{nct, new PRTest("", "6451093cadfc14d7359617b2a7ea6db8")}); + tests.add(new Object[]{nct, new PRTest("", "f4704ba2894ec0aec8a55ce6b361f768")}); } return tests.toArray(new Object[][]{}); diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/cancer/m2/MuTect2IntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/cancer/m2/MuTect2IntegrationTest.java index ae5b9d47c..41c35c375 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/cancer/m2/MuTect2IntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/cancer/m2/MuTect2IntegrationTest.java @@ -138,7 +138,7 @@ public class MuTect2IntegrationTest extends WalkerTest { public void testTruePositivesDream3TrackedDropped() { M2TestWithDroppedReads(DREAM3_TUMOR_BAM, DREAM3_NORMAL_BAM, "21:10935369", "", "48a446d47bb10434cb7f0ee726d15721", - "6ecaeb74893249dfa5723b2266c957e2"); + "265a72d3f79bb0fe054a847ab0c01c67"); } /** diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java index c95fd9f86..200c8010c 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java @@ -133,7 +133,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { @Test public void testHaplotypeBAMOutFlags() throws IOException { - final String md5BAMOut = "69aae17f8cd384666ec7c3c1f3d3eb57"; + final String md5BAMOut = "0934466fa2b8648af9e6267286a57151"; HCTestWithBAMOut(NA12878_BAM, " -L 20:10000000-10100000 ", "df622103b0a6917f2299b1acfd0ed0ac", md5BAMOut); validateForwardedProgramRecords(new ArrayList<>(Arrays.asList(new File(NA12878_BAM))), md5BAMOut); } @@ -330,7 +330,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { @Test public void testLeftAlignmentBamOutBugFix() throws IOException { final String outputVCF = createTempFile("temp", ".vcf").getAbsolutePath(); - final String md5BAMOut = "27e729df3b166c81792a62a5b57ef7b3"; + final String md5BAMOut = "60db3996cd37a863d8b93218fcbf1c8b"; final String base = String.format("-T HaplotypeCaller -R %s -I %s", REF, LEFT_ALIGNMENT_BAMOUT_TEST_INPUT) + " --no_cmdline_in_header -bamout %s -o " + outputVCF + " -L 1:11740000-11740700 --allowNonUniqueKmersInRef"; final WalkerTestSpec spec = new WalkerTestSpec(base, 1, Arrays.asList(md5BAMOut)); @@ -541,7 +541,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { public void testHaplotypeCallerReadPosRankSum() throws IOException { final File testBAM = new File(privateTestDir + "testReadPos.snippet.bam"); final String md5Variants = "e664b7a9da71cf81e14648ac7e698eea"; - final String md5BAMOut = "3ef35732e49980093ad445e3ac5731fa"; + final String md5BAMOut = "74f2cab2d2d0d999b54456b73e597d6c"; 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"; final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList(md5Variants, md5BAMOut)); diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/rnaseq/SplitNCigarReadsIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/rnaseq/SplitNCigarReadsIntegrationTest.java index 5386c2b16..9233d30d0 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/rnaseq/SplitNCigarReadsIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/rnaseq/SplitNCigarReadsIntegrationTest.java @@ -87,7 +87,7 @@ public class SplitNCigarReadsIntegrationTest extends WalkerTest { public void testSplitsWithOverhangs() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-T SplitNCigarReads -R " + b37KGReference + " -I " + privateTestDir + "NA12878.RNAseq.bam -o %s --no_pg_tag -U ALLOW_N_CIGAR_READS", 1, - Arrays.asList("72fbeb2043f005e1698e21563f0625a9")); + Arrays.asList("b721d997bd09873a244fee97c1e58af1")); executeTest("test splits with overhangs", spec); } @@ -95,7 +95,7 @@ public class SplitNCigarReadsIntegrationTest extends WalkerTest { public void testSplitsFixNDN() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-T SplitNCigarReads -R " + b37KGReference + " -I " + privateTestDir + "splitNCigarReadsSnippet.bam -o %s --no_pg_tag -U ALLOW_N_CIGAR_READS -fixNDN", 1, - Arrays.asList("add7012d5e814d6cfd32f6cac1eb8ce3")); + Arrays.asList("9aa80944c2c7ee8a1f259907e3d8b51c")); executeTest("test fix NDN", spec); } @@ -103,7 +103,7 @@ public class SplitNCigarReadsIntegrationTest extends WalkerTest { public void testSplitsWithOverhangsNotClipping() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-T SplitNCigarReads --doNotFixOverhangs -R " + b37KGReference + " -I " + privateTestDir + "NA12878.RNAseq.bam -o %s --no_pg_tag -U ALLOW_N_CIGAR_READS", 1, - Arrays.asList("6a55ac0a945e010bf03e1dd8f7749417")); + Arrays.asList("4134e1ff0eaaa9986e19526a7c3a8319")); executeTest("test splits with overhangs not clipping", spec); } @@ -111,7 +111,7 @@ public class SplitNCigarReadsIntegrationTest extends WalkerTest { public void testSplitsWithOverhangs0Mismatches() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-T SplitNCigarReads --maxMismatchesInOverhang 0 -R " + b37KGReference + " -I " + privateTestDir + "NA12878.RNAseq.bam -o %s --no_pg_tag -U ALLOW_N_CIGAR_READS", 1, - Arrays.asList("8a577047955ff9edca3caf1f6e545d3e")); + Arrays.asList("94ebc9fbd64684e50c5f54ad5ff042b6")); executeTest("test splits with overhangs 0 mismatches", spec); } @@ -119,7 +119,7 @@ public class SplitNCigarReadsIntegrationTest extends WalkerTest { public void testSplitsWithOverhangs5BasesInOverhang() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-T SplitNCigarReads --maxBasesInOverhang 5 -R " + b37KGReference + " -I " + privateTestDir + "NA12878.RNAseq.bam -o %s --no_pg_tag -U ALLOW_N_CIGAR_READS", 1, - Arrays.asList("bdd822868b88063cf50c6336ed1a5e64")); + Arrays.asList("b737b2dfb22a608ee3def6137fed9414")); executeTest("test splits with overhangs 5 bases in overhang", spec); } } diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/simulatereads/SimulateReadsForVariantsIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/simulatereads/SimulateReadsForVariantsIntegrationTest.java index 4a105aa96..37e87196f 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/simulatereads/SimulateReadsForVariantsIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/simulatereads/SimulateReadsForVariantsIntegrationTest.java @@ -64,7 +64,7 @@ public class SimulateReadsForVariantsIntegrationTest extends WalkerTest { WalkerTestSpec spec = new WalkerTestSpec( "-T SimulateReadsForVariants --no_pg_tag -R " + b37KGReference + " -V " + publicTestDir + "forSimulation.vcf -o %s", 1, - Arrays.asList("d929369b9095420a8aaff2595ec2f80a")); + Arrays.asList("b5680f835aff1da6e1e60123d39f2371")); executeTest("testVariants", spec); } @@ -74,7 +74,7 @@ public class SimulateReadsForVariantsIntegrationTest extends WalkerTest { WalkerTestSpec spec = new WalkerTestSpec( "-RL 70 -T SimulateReadsForVariants --no_pg_tag -R " + b37KGReference + " -V " + publicTestDir + "forSimulation.vcf -o %s", 1, - Arrays.asList("bbc65e4f8bd3a1656616476a1e190ecf")); + Arrays.asList("177d32e0b13bd40aaeef71e8e5ffefe7")); executeTest("testReadLength", spec); } @@ -84,7 +84,7 @@ public class SimulateReadsForVariantsIntegrationTest extends WalkerTest { WalkerTestSpec spec = new WalkerTestSpec( "-ER 40 -T SimulateReadsForVariants --no_pg_tag -R " + b37KGReference + " -V " + publicTestDir + "forSimulation.vcf -o %s", 1, - Arrays.asList("cb0e4b11bbd1b5a154ad6c99541cd017")); + Arrays.asList("7353b4d148221f4f4975f07712413e18")); executeTest("testErrorRate", spec); } @@ -94,7 +94,7 @@ public class SimulateReadsForVariantsIntegrationTest extends WalkerTest { WalkerTestSpec spec = new WalkerTestSpec( "-RGPL SOLID -T SimulateReadsForVariants --no_pg_tag -R " + b37KGReference + " -V " + publicTestDir + "forSimulation.vcf -o %s", 1, - Arrays.asList("2b5c6cda9a434c9e25e5da5599eeae51")); + Arrays.asList("6f7a2ff3aa3c2e24a00f04dc770a4140")); executeTest("testPlatformTag", spec); } @@ -105,7 +105,7 @@ public class SimulateReadsForVariantsIntegrationTest extends WalkerTest { WalkerTestSpec spec = new WalkerTestSpec( "-T SimulateReadsForVariants --no_pg_tag --useAFAsAlleleFraction -DP 100 -R " + b37KGReference + " -V " + publicTestDir + "forAlleleFractionSimulation.vcf -o %s", 1, - Arrays.asList("1ae2c354718b470e30b44d5e59cb9944")); + Arrays.asList("f19d4b62269512fff0dcce21874c0d43")); executeTest("testAlleleFraction", spec); } @@ -116,7 +116,7 @@ public class SimulateReadsForVariantsIntegrationTest extends WalkerTest { WalkerTestSpec spec = new WalkerTestSpec( "-T SimulateReadsForVariants --no_pg_tag -R " + b37KGReference + " -V " + publicTestDir + "forLongInsert.vcf -o %s", 1, - Arrays.asList("5c069bff8efb988660c7f6d28a3117fc")); + Arrays.asList("052f1b644848cfd058cd2aeb0b6f2fd2")); executeTest("testLongInsertFailure", spec); } @@ -126,7 +126,7 @@ public class SimulateReadsForVariantsIntegrationTest extends WalkerTest { WalkerTestSpec spec = new WalkerTestSpec( "-RL 269 -T SimulateReadsForVariants --no_pg_tag -R " + b37KGReference + " -V " + publicTestDir + "forLongInsert.vcf -o %s", 1, - Arrays.asList("0657f6a692d22b5e2b7f5832710042e4")); + Arrays.asList("33f7da2e0b711a9ad28cb49c60e648be")); executeTest("testLongInsertSuccess", spec); } diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/EngineFeaturesIntegrationTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/EngineFeaturesIntegrationTest.java index ed86e55cf..59d840c66 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/EngineFeaturesIntegrationTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/EngineFeaturesIntegrationTest.java @@ -324,12 +324,12 @@ public class EngineFeaturesIntegrationTest extends WalkerTest { @Test() public void testDefaultBaseQualities20() { - executeTest("testDefaultBaseQualities20", testDefaultBaseQualities(20, "90a450f74554bbd2cc3a9e0f9de68e26")); + executeTest("testDefaultBaseQualities20", testDefaultBaseQualities(20, "da5a4293e125f00ecbdfd450b80d8357")); } @Test() public void testDefaultBaseQualities30() { - executeTest("testDefaultBaseQualities30", testDefaultBaseQualities(30, "ec11db4173ce3b8e43997f00dab5ae26")); + executeTest("testDefaultBaseQualities30", testDefaultBaseQualities(30, "c82e72ee08d545266927a7f2e8ab24c3")); } @Test(expectedExceptions = Exception.class) @@ -732,10 +732,10 @@ public class EngineFeaturesIntegrationTest extends WalkerTest { public void testSAMWriterFeatures() { testBAMFeatures("-compress 0", "49228d4f5b14c4cfed4a09372eb71139"); testBAMFeatures("-compress 9", "bc61a1b2b53a2ec7c63b533fa2f8701b"); - testBAMFeatures("-simplifyBAM", "a1127bab46674b165496b79bb9fa7964"); + testBAMFeatures("-simplifyBAM", "f66b671b32d1bbbf65a88585a64b556a"); //Validate MD5 - final String expectedMD5 = "c58b9114fc15b53655f2c03c819c29fd"; + final String expectedMD5 = "a0c0f1fafc248ac82a84b8ca71292caf"; final File md5Target = testBAMFeatures("--generate_md5", expectedMD5); final File md5File = new File(md5Target.getAbsoluteFile() + ".md5"); md5File.deleteOnExit(); diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/arguments/CramIntegrationTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/arguments/CramIntegrationTest.java index 244f67daf..44ae88ba1 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/arguments/CramIntegrationTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/arguments/CramIntegrationTest.java @@ -41,16 +41,16 @@ public class CramIntegrationTest extends WalkerTest { return new Object[][] { {"PrintReads", "exampleBAM.bam", "", "cram", ""}, // Bypass MD5 check since the CRAM header stores the file name {"PrintReads", "exampleCRAM.cram", "", "cram", ""}, - {"PrintReads", "exampleCRAM.cram", "", "bam", "e7834d5992a69143d7c463275213bbf8"}, - {"PrintReads", "exampleCRAM.cram", " -L chr1:200", "bam", "d362fbf30a2c77a2653f1c8eb2dd8fc1"}, + {"PrintReads", "exampleCRAM.cram", "", "bam", "50c55e1040aa0ffd4036aa581fcfe8af"}, + {"PrintReads", "exampleCRAM.cram", " -L chr1:200", "bam", "f74f78bd16aed8a395f0e79e3898ab19"}, {"CountLoci", "exampleCRAM.cram", "", "txt", "ade93df31a6150321c1067e749cae9be"}, {"CountLoci", "exampleCRAM.cram", " -L chr1:200", "txt", "b026324c6904b2a9cb4b88d6d61c81d1"}, {"CountReads", "exampleCRAM.cram", "", "txt", "4fbafd6948b6529caa2b78e476359875"}, {"CountReads", "exampleCRAM.cram", " -L chr1:200", "txt", "b026324c6904b2a9cb4b88d6d61c81d1"}, - {"PrintReads", "exampleCRAM.cram", " -L chr1:200 -L chr1:89597", "bam", "a11bd125b69f651aaa2ae68c8ccab22f"}, + {"PrintReads", "exampleCRAM.cram", " -L chr1:200 -L chr1:89597", "bam", "1a6331f0e7afdccd07425df251d28811"}, {"CountLoci", "exampleCRAM.cram", " -L chr1:200 -L chr1:89597", "txt", "26ab0db90d72e28ad0ba1e22ee510510"}, {"CountReads", "exampleCRAM.cram", " -L chr1:200 -L chr1:89597", "txt", "6d7fce9fee471194aa8b5b6e47267f03"}, - {"PrintReads", "exampleCRAM-nobai-withcrai.cram", " -L chr1:200 -L chr1:89597", "bam", "9e3e8b5a58dfcb50f5b270547c01d56a"}, + {"PrintReads", "exampleCRAM-nobai-withcrai.cram", " -L chr1:200 -L chr1:89597", "bam", "41f8ebb256120befc6ea7d228915b349"}, {"CountLoci", "exampleCRAM-nobai-withcrai.cram", " -L chr1:200 -L chr1:89597", "txt", "26ab0db90d72e28ad0ba1e22ee510510"}, {"CountReads", "exampleCRAM-nobai-withcrai.cram", " -L chr1:200 -L chr1:89597", "txt", "6d7fce9fee471194aa8b5b6e47267f03"}, }; diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/arguments/IntervalIntegrationTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/arguments/IntervalIntegrationTest.java index 954cbc0a6..a2b6c4486 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/arguments/IntervalIntegrationTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/arguments/IntervalIntegrationTest.java @@ -62,7 +62,7 @@ public class IntervalIntegrationTest extends WalkerTest { // our base file File baseOutputFile = createTempFile("testUnmappedReadInclusion",".bam"); spec.setOutputFileLocation(baseOutputFile); - spec.addAuxFile("c66bb2c3c5382e2acff09b2b359562bb",createTempFileFromBase(baseOutputFile.getAbsolutePath())); + spec.addAuxFile("4eeb9b07d3c9ddd4ea9eada7805903a2",createTempFileFromBase(baseOutputFile.getAbsolutePath())); spec.addAuxFile("fadcdf88597b9609c5f2a17f4c6eb455", createTempFileFromBase(baseOutputFile.getAbsolutePath().substring(0,baseOutputFile.getAbsolutePath().indexOf(".bam"))+".bai")); executeTest("testUnmappedReadInclusion",spec); @@ -109,8 +109,8 @@ public class IntervalIntegrationTest extends WalkerTest { // our base file File baseOutputFile = createTempFile("testMixedMappedAndUnmapped",".bam"); spec.setOutputFileLocation(baseOutputFile); - spec.addAuxFile("c64cff3ed376bc8f2977078dbdac4518",createTempFileFromBase(baseOutputFile.getAbsolutePath())); - spec.addAuxFile("fa90ff91ac0cc689c71a3460a3530b8b", createTempFileFromBase(baseOutputFile.getAbsolutePath().substring(0,baseOutputFile.getAbsolutePath().indexOf(".bam"))+".bai")); + spec.addAuxFile("70ac0317c0c13d885e6c2de4f837cdd3",createTempFileFromBase(baseOutputFile.getAbsolutePath())); + spec.addAuxFile("df469db01610ddb731868dfb28917142", createTempFileFromBase(baseOutputFile.getAbsolutePath().substring(0,baseOutputFile.getAbsolutePath().indexOf(".bam"))+".bai")); executeTest("testMixedMappedAndUnmapped",spec); } diff --git a/public/gatk-root/pom.xml b/public/gatk-root/pom.xml index 4440b32c1..a7d20025c 100644 --- a/public/gatk-root/pom.xml +++ b/public/gatk-root/pom.xml @@ -89,7 +89,7 @@ com.intel.gkl gkl - 0.5.2 + 0.5.5 log4j diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/BAQIntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/BAQIntegrationTest.java index 540f350ab..2522b0f84 100644 --- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/BAQIntegrationTest.java +++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/BAQIntegrationTest.java @@ -44,13 +44,13 @@ public class BAQIntegrationTest extends WalkerTest { // -------------------------------------------------------------------------------------------------------------- @Test public void testPrintReadsNoBAQ() { - WalkerTestSpec spec = new WalkerTestSpec( baseCommand +" -baq OFF", 1, Arrays.asList("e33187ca383c7f5c75c5d547ec79e1cb")); + WalkerTestSpec spec = new WalkerTestSpec( baseCommand +" -baq OFF", 1, Arrays.asList("526dbbb390dbd36daa70ac35a8eddc36")); executeTest(String.format("testPrintReadsNoBAQ"), spec); } @Test public void testPrintReadsRecalBAQ() { - WalkerTestSpec spec = new WalkerTestSpec( baseCommand +" -baq RECALCULATE", 1, Arrays.asList("a25043edfbfa4f21a13cc21064b460df")); + WalkerTestSpec spec = new WalkerTestSpec( baseCommand +" -baq RECALCULATE", 1, Arrays.asList("25cb8f91e31a07cca2e141a119c9e020")); executeTest(String.format("testPrintReadsRecalBAQ"), spec); } } diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/ClipReadsWalkersIntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/ClipReadsWalkersIntegrationTest.java index 17cc7c367..e35815c6a 100644 --- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/ClipReadsWalkersIntegrationTest.java +++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/ClipReadsWalkersIntegrationTest.java @@ -47,22 +47,22 @@ public class ClipReadsWalkersIntegrationTest extends WalkerTest { } final static String Q10ClipOutput = "b29c5bc1cb9006ed9306d826a11d444f"; - @Test public void testQClip0() { testClipper("clipQSum0", "-QT 0", "117a4760b54308f81789c39b1c9de578", "bcf0d1e13537f764f006ef6d9b401ea7"); } - @Test public void testQClip2() { testClipper("clipQSum2", "-QT 2", Q10ClipOutput, "27847d330b962e60650df23b6efc8c3c"); } - @Test public void testQClip10() { testClipper("clipQSum10", "-QT 10", "b29c5bc1cb9006ed9306d826a11d444f", "27847d330b962e60650df23b6efc8c3c"); } - @Test public void testQClip20() { testClipper("clipQSum20", "-QT 20", "6c3434dce66ae5c9eeea502f10fb9bee", "f89ec5439e88f5a75433150da0069034"); } + @Test public void testQClip0() { testClipper("clipQSum0", "-QT 0", "117a4760b54308f81789c39b1c9de578", "2e617e0f0b4a1bf45dbb666da0a6a16c"); } + @Test public void testQClip2() { testClipper("clipQSum2", "-QT 2", Q10ClipOutput, "1b0d2317dfd1fd5a4d14eea3f560ac17"); } + @Test public void testQClip10() { testClipper("clipQSum10", "-QT 10", "b29c5bc1cb9006ed9306d826a11d444f", "1b0d2317dfd1fd5a4d14eea3f560ac17"); } + @Test public void testQClip20() { testClipper("clipQSum20", "-QT 20", "6c3434dce66ae5c9eeea502f10fb9bee", "3a9a10966cce58baf9e9400a2c5f99ca"); } - @Test public void testClipRange1() { testClipper("clipRange1", "-CT 1-5", "b5acd753226e25b1e088838c1aab9117", "987007f6e430cad4cb4a8d1cc1f45d91"); } - @Test public void testClipRange2() { testClipper("clipRange2", "-CT 1-5,11-15", "be4fcad5b666a5540028b774169cbad7", "ec4cf54ed50a6baf69dbf98782c19aeb"); } + @Test public void testClipRange1() { testClipper("clipRange1", "-CT 1-5", "b5acd753226e25b1e088838c1aab9117", "701f03388ffaeb0f92be1e719e2477df"); } + @Test public void testClipRange2() { testClipper("clipRange2", "-CT 1-5,11-15", "be4fcad5b666a5540028b774169cbad7", "7dc5da735c437b6523e0823a1ed0e981"); } - @Test public void testClipSeq() { testClipper("clipSeqX", "-X CCCCC", "db199bd06561c9f2122f6ffb07941fbc", "a9cf540e4ed2514061248a878e09a09c"); } - @Test public void testClipSeqFile() { testClipper("clipSeqXF", "-XF " + privateTestDir + "seqsToClip.fasta", "22cd33dbd06cc425ce3626360367bfca", "906871df304dd966682e5798d59fc86b"); } + @Test public void testClipSeq() { testClipper("clipSeqX", "-X CCCCC", "db199bd06561c9f2122f6ffb07941fbc", "daa41acd8c9f1a75c8107d0fd0db8cf0"); } + @Test public void testClipSeqFile() { testClipper("clipSeqXF", "-XF " + privateTestDir + "seqsToClip.fasta", "22cd33dbd06cc425ce3626360367bfca", "b1812de69c967059362139a269044362"); } - @Test public void testClipMulti() { testClipper("clipSeqMulti", "-QT 10 -CT 1-5 -XF " + privateTestDir + "seqsToClip.fasta -X CCCCC", "e4a88276a6f76ccc2b05a06c76305a1c", "b41995fea04034ca0427c4a71504ef83"); } + @Test public void testClipMulti() { testClipper("clipSeqMulti", "-QT 10 -CT 1-5 -XF " + privateTestDir + "seqsToClip.fasta -X CCCCC", "e4a88276a6f76ccc2b05a06c76305a1c", "9f999ed70684fdfb8dba019ff71741fe"); } - @Test public void testClipNs() { testClipper("testClipNs", "-QT 10 -CR WRITE_NS", Q10ClipOutput, "27847d330b962e60650df23b6efc8c3c"); } - @Test public void testClipQ0s() { testClipper("testClipQs", "-QT 10 -CR WRITE_Q0S", Q10ClipOutput, "195b8bdfc0186fdca742764aa9b06363"); } - @Test public void testClipSoft() { testClipper("testClipSoft", "-QT 10 -CR SOFTCLIP_BASES", Q10ClipOutput, "08d16051be0b3fa3453eb1e6ca48b098"); } + @Test public void testClipNs() { testClipper("testClipNs", "-QT 10 -CR WRITE_NS", Q10ClipOutput, "1b0d2317dfd1fd5a4d14eea3f560ac17"); } + @Test public void testClipQ0s() { testClipper("testClipQs", "-QT 10 -CR WRITE_Q0S", Q10ClipOutput, "b7ce95f277d5f66b7f5a60ffbf9692cf"); } + @Test public void testClipSoft() { testClipper("testClipSoft", "-QT 10 -CR SOFTCLIP_BASES", Q10ClipOutput, "55c9d86c18c5a59a98429e8a5076e871"); } @Test public void testUseOriginalQuals() { @@ -74,7 +74,7 @@ public class ClipReadsWalkersIntegrationTest extends WalkerTest { " -OQ -QT 4 -CR WRITE_Q0S" + " -o %s -os %s", 2, - Arrays.asList("a2819d54b2110150e38511f5a55db91d", "55c01ccc2e84481b22d3632cdb06c8ba")); + Arrays.asList("0e4c116fa07c3d8190eefe6968a0b819", "55c01ccc2e84481b22d3632cdb06c8ba")); executeTest("clipOriginalQuals", spec); } } diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/PrintReadsIntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/PrintReadsIntegrationTest.java index d013d0c42..eccd968ad 100644 --- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/PrintReadsIntegrationTest.java +++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/PrintReadsIntegrationTest.java @@ -59,27 +59,27 @@ public class PrintReadsIntegrationTest extends WalkerTest { @DataProvider(name = "PRTest") public Object[][] createPrintReadsTestData() { return new Object[][]{ - {new PRTest(hg18Reference, new String[]{"HiSeq.1mb.bam"}, "", "0aa3505ba61e05663e629011dd54e423")}, + {new PRTest(hg18Reference, new String[]{"HiSeq.1mb.bam"}, "", "83d1454dc01cd2e7458dad4012695f64")}, {new PRTest(hg18Reference, new String[]{"HiSeq.1mb.bam"}, " -compress 0", "0aec10d19e0dbdfe1d0cbb3eddaf623a")}, - {new PRTest(hg18Reference, new String[]{"HiSeq.1mb.bam"}, " -simplifyBAM", "c565d9cd4838a313e7bdb30530c0cf71")}, - {new PRTest(hg18Reference, new String[]{"HiSeq.1mb.bam"}, " -n 10", "917440a38aba707ec0e012168590981a")}, + {new PRTest(hg18Reference, new String[]{"HiSeq.1mb.bam"}, " -simplifyBAM", "60255a68df1b8f2fbba373d75274f0de")}, + {new PRTest(hg18Reference, new String[]{"HiSeq.1mb.bam"}, " -n 10", "eb7c6bacca5fee09b8df50880eb81ee6")}, // See: GATKBAMIndex.getStartOfLastLinearBin(), BAMScheduler.advance(), IntervalOverlapFilteringIterator.advance() - {new PRTest(b37KGReference, new String[]{"unmappedFlagReadsInLastLinearBin.bam"}, "", "0b58c903f54e8543a8b2ce1439aa769b")}, - {new PRTest(b37KGReference, new String[]{"unmappedFlagReadsInLastLinearBin.bam"}, " -L 1", "5b1154cc81dba6bcfe76188e4df8d79c")}, - {new PRTest(b37KGReference, new String[]{"unmappedFlagReadsInLastLinearBin.cram"}, " -L 1:10001 -L GL000192.1:500204", "a84efdc3d4a8d6329b5f0b494dd280d2")}, - {new PRTest(b37KGReference, new String[]{"unmappedFlagReadsInLastLinearBin.bam"}, " -L unmapped", "cbd3d1d50c8674f79033aa8c36aa3cd1")}, - {new PRTest(b37KGReference, new String[]{"unmappedFlagReadsInLastLinearBin.bam"}, " -L 1 -L unmapped", "5b1154cc81dba6bcfe76188e4df8d79c")}, - {new PRTest(b37KGReference, new String[]{"oneReadAllInsertion.bam"}, "", "e212d1799ae797e781b17e630656a9a1")}, - {new PRTest(b37KGReference, new String[]{"NA12878.1_10mb_2_10mb.bam"}, "", "0387c61303140d8899fcbfdd3e72ed80")}, + {new PRTest(b37KGReference, new String[]{"unmappedFlagReadsInLastLinearBin.bam"}, "", "3d67c398ce2ac1deeddbccbd850380a7")}, + {new PRTest(b37KGReference, new String[]{"unmappedFlagReadsInLastLinearBin.bam"}, " -L 1", "37cdd8871843693f2650d7b48c8ae1d4")}, + {new PRTest(b37KGReference, new String[]{"unmappedFlagReadsInLastLinearBin.cram"}, " -L 1:10001 -L GL000192.1:500204", "4d63fd6e977a53e5d9590bd030b40bd0")}, + {new PRTest(b37KGReference, new String[]{"unmappedFlagReadsInLastLinearBin.bam"}, " -L unmapped", "a834400e3bd69045eb8a9e94131633f5")}, + {new PRTest(b37KGReference, new String[]{"unmappedFlagReadsInLastLinearBin.bam"}, " -L 1 -L unmapped", "37cdd8871843693f2650d7b48c8ae1d4")}, + {new PRTest(b37KGReference, new String[]{"oneReadAllInsertion.bam"}, "", "6c04aac25e2136fee395897aac96bea8")}, + {new PRTest(b37KGReference, new String[]{"NA12878.1_10mb_2_10mb.bam"}, "", "57a9bc1f7dd4e7717ee796c484bcf45a")}, // Tests for filtering options {new PRTest(b37KGReference, new String[]{"NA12878.1_10mb_2_10mb.bam", "NA20313.highCoverageRegion.bam"}, - "", "ad56da66be0bdab5a8992de9617ae6a5")}, + "", "e691d61df10f7614d73c8ecb46c75ee1")}, {new PRTest(b37KGReference, new String[]{"NA12878.1_10mb_2_10mb.bam", "NA20313.highCoverageRegion.bam"}, - " -readGroup SRR359098", "c3bfe28722a665e666098dbb7048a9f1")}, + " -readGroup SRR359098", "7644eab114bf537411218f782d75a6a6")}, {new PRTest(b37KGReference, new String[]{"NA12878.1_10mb_2_10mb.bam", "NA20313.highCoverageRegion.bam"}, - " -readGroup 20FUK.3 -sn NA12878", "8191f8d635d00b1f4d0993b785cc46c5")}, + " -readGroup 20FUK.3 -sn NA12878", "351d5da29874033e50d29c5c36575a6c")}, {new PRTest(b37KGReference, new String[]{"NA12878.1_10mb_2_10mb.bam", "NA20313.highCoverageRegion.bam"}, - " -sn na12878", "92a85b4223ec45e114f12a1fe6ebbaeb")}, + " -sn na12878", "9056d852418dd2083f38e3eac1551fcd")}, }; } diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/SplitSamFileIntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/SplitSamFileIntegrationTest.java index a316dffe7..526605f61 100644 --- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/SplitSamFileIntegrationTest.java +++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/SplitSamFileIntegrationTest.java @@ -43,9 +43,9 @@ public class SplitSamFileIntegrationTest extends WalkerTest { " --outputRoot " + prefix, Collections.emptyList() ); - addSplitOutput(spec, prefix, "NA12878", "3e28b666fb673be138eca9bd3db9520b"); - addSplitOutput(spec, prefix, "NA12891", "af01069bc3da4252ce8417a03d11f48b"); - addSplitOutput(spec, prefix, "NA12892", "cfa1cb6aaca03900160bd5627f4f698b"); + addSplitOutput(spec, prefix, "NA12878", "356bddf614a44a0234f7b116f5cde998"); + addSplitOutput(spec, prefix, "NA12891", "5dd92a0089e3f781e77d94010264b9fd"); + addSplitOutput(spec, prefix, "NA12892", "ea8f16c18c89b49ce9d32d76c6af75f9"); executeTest("testSplitSamFile", spec); }