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Fix some of the broken integration tests

This commit is contained in:
Eric Banks 2012-10-26 11:23:44 -04:00
parent ebebec7fdb
commit 7a706ed345
3 changed files with 45 additions and 46 deletions
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10
protected/java/src/org/broadinstitute/sting/gatk/downsampling/AlleleBiasedDownsamplingUtils.java
View File

@ -37,12 +37,6 @@ import java.util.*;
public class AlleleBiasedDownsamplingUtils {
private static final ArrayList<PileupElement>[] alleleStratifiedElements = new ArrayList[4];
static {
for ( int i = 0; i < 4; i++ )
alleleStratifiedElements[i] = new ArrayList<PileupElement>();
}
/**
* Computes an allele biased version of the given pileup
*
@ -58,6 +52,10 @@ public class AlleleBiasedDownsamplingUtils {
if ( downsamplingFraction >= 1.0 )
return new ReadBackedPileupImpl(pileup.getLocation(), new ArrayList<PileupElement>());
final ArrayList<PileupElement>[] alleleStratifiedElements = new ArrayList[4];
for ( int i = 0; i < 4; i++ )
alleleStratifiedElements[i] = new ArrayList<PileupElement>();
// start by stratifying the reads by the alleles they represent at this position
for( final PileupElement pe : pileup ) {
// abort if we have a reduced read - we do not want to remove it!

78
public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
View File

@ -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,
@ -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,

3
public/java/test/org/broadinstitute/sting/utils/nanoScheduler/NanoSchedulerIntegrationTest.java
View File

@ -32,11 +32,12 @@ public class NanoSchedulerIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
buildCommandLine(
"-T UnifiedGenotyper -R " + b37KGReference,
"-nosl --no_cmdline_in_header -G",
"--no_cmdline_in_header -G",
//"--dbsnp " + b37dbSNP132,
"-I " + privateTestDir + "NA12878.HiSeq.b37.chr20.10_11mb.bam",
"-L 20:10,000,000-10,100,000",
"-glm " + glm,
"--contamination_fraction_to_filter 0.0",
"-nt " + nt,
"-nct " + nct,
"-o %s"