From ed11b7dab25c87c34942698ba10c6cb77ed2da4f Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Fri, 26 Oct 2012 12:10:44 -0400 Subject: [PATCH] Fix UG parallelization test --- .../AlleleBiasedDownsamplingUtils.java | 2 +- .../UnifiedGenotyperIntegrationTest.java | 86 +++++++++---------- 2 files changed, 44 insertions(+), 44 deletions(-) diff --git a/protected/java/src/org/broadinstitute/sting/gatk/downsampling/AlleleBiasedDownsamplingUtils.java b/protected/java/src/org/broadinstitute/sting/gatk/downsampling/AlleleBiasedDownsamplingUtils.java index b84cde58e..59357e1c4 100755 --- a/protected/java/src/org/broadinstitute/sting/gatk/downsampling/AlleleBiasedDownsamplingUtils.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/downsampling/AlleleBiasedDownsamplingUtils.java @@ -45,7 +45,7 @@ public class AlleleBiasedDownsamplingUtils { * @param log logging output * @return allele biased pileup */ - public synchronized static ReadBackedPileup createAlleleBiasedBasePileup(final ReadBackedPileup pileup, final double downsamplingFraction, final PrintStream log) { + public static ReadBackedPileup createAlleleBiasedBasePileup(final ReadBackedPileup pileup, final double downsamplingFraction, final PrintStream log) { // special case removal of all or no reads if ( downsamplingFraction <= 0.0 ) return pileup; 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 ea2f0fb97..2a17435aa 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 @@ -26,7 +26,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { // testing normal calling // // -------------------------------------------------------------------------------------------------------------- - //@Test + @Test 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, @@ -34,7 +34,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { executeTest("test MultiSample Pilot1", spec); } - //@Test + @Test public void testWithAllelesPassedIn1() { WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec( baseCommand + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + privateTestDir + "allelesForUG.vcf -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,025,000", 1, @@ -42,7 +42,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { executeTest("test MultiSample Pilot2 with alleles passed in", spec1); } - //@Test + @Test public void testWithAllelesPassedIn2() { WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec( baseCommand + " --output_mode EMIT_ALL_SITES --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + privateTestDir + "allelesForUG.vcf -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,025,000", 1, @@ -50,7 +50,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { executeTest("test MultiSample Pilot2 with alleles passed in and emitting all sites", spec2); } - //@Test + @Test 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, @@ -58,7 +58,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { executeTest("test SingleSample Pilot2", spec); } - //@Test + @Test public void testMultipleSNPAlleles() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-T UnifiedGenotyper -R " + b37KGReference + " --no_cmdline_in_header -glm BOTH --dbsnp " + b37dbSNP129 + " -I " + privateTestDir + "multiallelic.snps.bam -o %s -L " + privateTestDir + "multiallelic.snps.intervals", 1, @@ -66,7 +66,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { executeTest("test Multiple SNP alleles", spec); } - //@Test + @Test public void testBadRead() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-T UnifiedGenotyper -R " + b37KGReference + " --no_cmdline_in_header -glm BOTH -I " + privateTestDir + "badRead.test.bam -o %s -L 1:22753424-22753464", 1, @@ -74,7 +74,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { executeTest("test bad read", spec); } - //@Test + @Test public void testReverseTrim() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-T UnifiedGenotyper -R " + b37KGReference + " --no_cmdline_in_header -glm INDEL -I " + validationDataLocation + "CEUTrio.HiSeq.b37.chr20.10_11mb.bam -o %s -L 20:10289124 -L 20:10090289", 1, @@ -82,7 +82,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { executeTest("test reverse trim", spec); } - //@Test + @Test public void testMismatchedPLs() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-T UnifiedGenotyper -R " + b37KGReference + " --no_cmdline_in_header -glm INDEL -I " + privateTestDir + "mismatchedPLs.bam -o %s -L 1:24020341", 1, @@ -98,7 +98,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { private final static String COMPRESSED_OUTPUT_MD5 = "6792419c482e767a3deb28913ed2b1ad"; - //@Test + @Test public void testCompressedOutput() { 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, @@ -117,24 +117,24 @@ 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 = "3d25ea660275a455ca443a786bff3d32"; + String md5 = "d408b4661b820ed86272415b8ea08780"; 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, + baseCommand + " -dt NONE -G none --contamination_fraction_to_filter 0.0 -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,075,000", 1, Arrays.asList(md5)); executeTest("test parallelization (single thread)", spec1); GenomeAnalysisEngine.resetRandomGenerator(); WalkerTest.WalkerTestSpec spec2 = 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 -nt 2", 1, + baseCommand + " -dt NONE -G none --contamination_fraction_to_filter 0.0 -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,075,000 -nt 2", 1, Arrays.asList(md5)); executeTest("test parallelization (2 threads)", spec2); GenomeAnalysisEngine.resetRandomGenerator(); WalkerTest.WalkerTestSpec spec3 = 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 -nt 4", 1, + baseCommand + " -dt NONE -G none --contamination_fraction_to_filter 0.0 -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,075,000 -nt 4", 1, Arrays.asList(md5)); executeTest("test parallelization (4 threads)", spec3); } @@ -145,7 +145,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { // // -------------------------------------------------------------------------------------------------------------- - //@Test + @Test public void testMinBaseQualityScore() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000 --min_base_quality_score 26", 1, @@ -153,7 +153,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { executeTest("test min_base_quality_score 26", spec); } - //@Test + @Test public void testSLOD() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-T UnifiedGenotyper -R " + b36KGReference + " --computeSLOD --no_cmdline_in_header -glm BOTH --dbsnp " + b36dbSNP129 + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000", 1, @@ -161,7 +161,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { executeTest("test SLOD", spec); } - //@Test + @Test public void testNDA() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( baseCommand + " --annotateNDA -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000", 1, @@ -169,7 +169,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { executeTest("test NDA", spec); } - //@Test + @Test public void testCompTrack() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-T UnifiedGenotyper -R " + b36KGReference + " --no_cmdline_in_header -glm BOTH -comp:FOO " + b36dbSNP129 + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000", 1, @@ -177,7 +177,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { executeTest("test using comp track", spec); } - //@Test + @Test public void testNoCmdLineHeaderStdout() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( baseCommandNoCmdLineHeaderStdout + " -glm INDEL -L 1:67,225,396-67,288,518", 0, @@ -185,17 +185,17 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { executeTest("testNoCmdLineHeaderStdout", spec); } - //@Test + @Test public void testOutputParameterSitesOnly() { testOutputParameters("-sites_only", "40aeb4c9e31fe7046b72afc58e7599cb"); } - //@Test + @Test public void testOutputParameterAllConfident() { testOutputParameters("--output_mode EMIT_ALL_CONFIDENT_SITES", "c706ca93b25ff83613cb4e95dcac567c"); } - //@Test + @Test public void testOutputParameterAllSites() { testOutputParameters("--output_mode EMIT_ALL_SITES", "8a263fd0a94463ce1de9990f2b8ec841"); } @@ -207,7 +207,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { executeTest(String.format("testParameter[%s]", args), spec); } - //@Test + @Test 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, @@ -220,12 +220,12 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { // testing heterozygosity // // -------------------------------------------------------------------------------------------------------------- - //@Test + @Test public void testHeterozyosity1() { testHeterozosity( 0.01, "8e61498ca03a8d805372a64c466b3b42" ); } - //@Test + @Test public void testHeterozyosity2() { testHeterozosity( 1.0 / 1850, "668d06b5173cf3b97d052726988e1d7b" ); } @@ -243,7 +243,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { // testing calls with SLX, 454, and SOLID data // // -------------------------------------------------------------------------------------------------------------- - //@Test + @Test public void testMultiTechnologies() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( baseCommand + @@ -261,7 +261,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { // testing calls with BAQ // // -------------------------------------------------------------------------------------------------------------- - //@Test + @Test public void testCallingWithBAQ() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( baseCommand + @@ -281,7 +281,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { // // -------------------------------------------------------------------------------------------------------------- // Basic indel testing with SLX data - //@Test + @Test public void testSimpleIndels() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( baseCommandIndels + @@ -295,7 +295,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { } // Basic indel testing with SLX data - //@Test + @Test public void testIndelsWithLowMinAlleleCnt() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( baseCommandIndels + @@ -309,7 +309,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { executeTest(String.format("test indel caller in SLX with low min allele count"), spec); } - //@Test + @Test public void testMultiTechnologyIndels() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( baseCommandIndels + @@ -322,7 +322,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { executeTest(String.format("test indel calling, multiple technologies"), spec); } - //@Test + @Test public void testWithIndelAllelesPassedIn1() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( baseCommandIndels + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + privateTestDir + "indelAllelesForUG.vcf -I " + validationDataLocation + @@ -331,7 +331,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { executeTest("test MultiSample Pilot2 indels with alleles passed in", spec); } - //@Test + @Test public void testWithIndelAllelesPassedIn2() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( baseCommandIndels + " --output_mode EMIT_ALL_SITES --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " @@ -341,7 +341,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { executeTest("test MultiSample Pilot2 indels with alleles passed in and emitting all sites", spec); } - //@Test + @Test public void testMultiSampleIndels1() { WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec( baseCommandIndels + " -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -o %s -L 1:10450700-10551000", 1, @@ -355,7 +355,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { executeTest("test MultiSample Pilot1 CEU indels using GENOTYPE_GIVEN_ALLELES", spec2); } - //@Test + @Test public void testGGAwithNoEvidenceInReads() { final String vcf = "small.indel.test.vcf"; WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( @@ -365,7 +365,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { executeTest("test GENOTYPE_GIVEN_ALLELES with no evidence in reads", spec); } - //@Test + @Test public void testBaseIndelQualityScores() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( baseCommandIndelsb37 + @@ -384,7 +384,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { // // -------------------------------------------------------------------------------------------------------------- - //@Test + @Test public void testSnpEffAnnotationRequestedWithoutRodBinding() { 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 " + @@ -403,7 +403,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { final static String assessMinIndelFraction = baseCommandIndelsb37 + " -I " + validationDataLocation + "978604.bam -L 1:978,586-978,626 -o %s --sites_only -rf Sample -goodSM 7377 -goodSM 22-0022 -goodSM 134 -goodSM 344029-53 -goodSM 14030"; - //@Test + @Test public void testMinIndelFraction0() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( assessMinIndelFraction + " -minIndelFrac 0.0", 1, @@ -411,7 +411,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { executeTest("test minIndelFraction 0.0", spec); } - //@Test + @Test public void testMinIndelFraction25() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( assessMinIndelFraction + " -minIndelFrac 0.25", 1, @@ -419,7 +419,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { executeTest("test minIndelFraction 0.25", spec); } - //@Test + @Test public void testMinIndelFraction100() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( assessMinIndelFraction + " -minIndelFrac 1", 1, @@ -433,7 +433,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { // // -------------------------------------------------------------------------------------------------------------- - //@Test + @Test public void testNsInCigar() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-T UnifiedGenotyper -R " + b37KGReference + " --no_cmdline_in_header -I " + validationDataLocation + "testWithNs.bam -o %s -L 8:141799600-141814700", 1, @@ -447,7 +447,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { // // -------------------------------------------------------------------------------------------------------------- - //@Test + @Test public void testReducedBam() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-T UnifiedGenotyper -R " + b37KGReference + " --no_cmdline_in_header -I " + privateTestDir + "bamExample.ReducedRead.ADAnnotation.bam -o %s -L 1:67,225,396-67,288,518", 1, @@ -455,12 +455,12 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { executeTest("test calling on a ReducedRead BAM", spec); } - //@Test + @Test public void testReducedBamSNPs() { testReducedCalling("SNP", "9ba4867cadb366746ee63e7a4afdb95e"); } - //@Test + @Test public void testReducedBamINDELs() { testReducedCalling("INDEL", "132a4e0ccf9230b5bb4b56c649e2bdd5"); } @@ -479,7 +479,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { // // -------------------------------------------------------------------------------------------------------------- - //@Test + @Test public void testContaminationDownsampling() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000 --contamination_fraction_to_filter 0.20", 1,