From c53c55da12ebf95141f3645ab3197d67e1ca0fb5 Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Thu, 25 Oct 2012 09:37:08 -0400 Subject: [PATCH] Re-enable tests --- .../UnifiedGenotyperIntegrationTest.java | 80 +++++++++---------- 1 file changed, 40 insertions(+), 40 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 9e50a8556..8eb1c4657 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 + " -nosl --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 + " -nosl --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 + " -nosl --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 + " -nosl --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 = "fd236bd635d514e4214d364f45ec4d10"; - //@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, @@ -112,7 +112,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { // // -------------------------------------------------------------------------------------------------------------- - //@Test + @Test public void testParallelization() { // Note that we need to turn off any randomization for this to work, so no downsampling and no annotations @@ -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 + " --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", "97ba874eafc9884a4de027a84c036311"); } - //@Test + @Test public void testOutputParameterAllConfident() { testOutputParameters("--output_mode EMIT_ALL_CONFIDENT_SITES", "f9ea04d96eeef29e71d37e60518c2579"); } - //@Test + @Test public void testOutputParameterAllSites() { testOutputParameters("--output_mode EMIT_ALL_SITES", "41c046d38ea328421df924e37e017645"); } @@ -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, @@ -215,7 +215,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { executeTest("test confidence 1", spec1); } - //@Test + @Test public void testConfidence2() { 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, @@ -228,12 +228,12 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { // testing heterozygosity // // -------------------------------------------------------------------------------------------------------------- - //@Test + @Test public void testHeterozyosity1() { testHeterozosity( 0.01, "986923de51c71635d47e3d06fe3794a1" ); } - //@Test + @Test public void testHeterozyosity2() { testHeterozosity( 1.0 / 1850, "fb12b1553f813004a394a391a8540873" ); } @@ -251,7 +251,7 @@ 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 + @@ -269,7 +269,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { // testing calls with BAQ // // -------------------------------------------------------------------------------------------------------------- - //@Test + @Test public void testCallingWithBAQ() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( baseCommand + @@ -289,7 +289,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { // // -------------------------------------------------------------------------------------------------------------- // Basic indel testing with SLX data - //@Test + @Test public void testSimpleIndels() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( baseCommandIndels + @@ -303,7 +303,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { } // Basic indel testing with SLX data - //@Test + @Test public void testIndelsWithLowMinAlleleCnt() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( baseCommandIndels + @@ -317,7 +317,7 @@ 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 + @@ -330,7 +330,7 @@ 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 + @@ -339,7 +339,7 @@ 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 " @@ -349,7 +349,7 @@ 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, @@ -363,7 +363,7 @@ 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( @@ -373,7 +373,7 @@ 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 + @@ -392,7 +392,7 @@ 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 " + @@ -411,7 +411,7 @@ 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, @@ -419,7 +419,7 @@ 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, @@ -427,7 +427,7 @@ 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, @@ -441,7 +441,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { // // -------------------------------------------------------------------------------------------------------------- - //@Test + @Test public void testNsInCigar() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-T UnifiedGenotyper -R " + b37KGReference + " -nosl --no_cmdline_in_header -I " + validationDataLocation + "testWithNs.bam -o %s -L 8:141799600-141814700", 1, @@ -455,7 +455,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { // // -------------------------------------------------------------------------------------------------------------- - //@Test + @Test public void testReducedBam() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-T UnifiedGenotyper -R " + b37KGReference + " -nosl --no_cmdline_in_header -I " + privateTestDir + "bamExample.ReducedRead.ADAnnotation.bam -o %s -L 1:67,225,396-67,288,518", 1, @@ -463,12 +463,12 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { executeTest("test calling on a ReducedRead BAM", spec); } - //@Test + @Test public void testReducedBamSNPs() { testReducedCalling("SNP", "1d4a826b144723ff0766c36aa0239287"); } - //@Test + @Test public void testReducedBamINDELs() { testReducedCalling("INDEL", "68ef51d5c98480e0c0192e0eecb95bca"); }