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Re-enable tests

This commit is contained in:
Eric Banks 2012-10-25 09:37:08 -04:00
parent e6652f7777
commit c53c55da12
1 changed files with 40 additions and 40 deletions
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80
public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
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@ -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");
}