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Final step (for now) in VA refactoring: update MD5's because, a) since it's not guaranteed that we'll iterate through reads/pileups in the same order, the rank sum dithering will change annotations, b) FS uses new generic threshold to distinguish uninformative reads (it used to use ad-hoc thresholds), c) AD definition changed and throws away uninformative reads, d) shortened general ploidy integration tests for quicker debugging. May have missed some MD5's in the update so there may be lingering test failures still

This commit is contained in:
Guillermo del Angel 2012-08-22 11:38:51 -04:00
parent 7df0abf49b
commit 901f47d8af
8 changed files with 55 additions and 52 deletions
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16
protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperGeneralPloidyIntegrationTest.java
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@ -18,8 +18,8 @@ public class UnifiedGenotyperGeneralPloidyIntegrationTest extends WalkerTest {
final String LSV_BAM = validationDataLocation +"93pools_NA12878_ref_chr20_40m_41m.bam";
final String REFSAMPLE_MT_CALLS = comparisonDataLocation + "Unvalidated/mtDNA/NA12878.snp.vcf";
final String REFSAMPLE_NAME = "NA12878";
final String MTINTERVALS = "MT:1-3000";
final String LSVINTERVALS = "20:40,000,000-41,000,000";
final String MTINTERVALS = "MT:1-1000";
final String LSVINTERVALS = "20:40,500,000-41,000,000";
final String NA12891_CALLS = comparisonDataLocation + "Unvalidated/mtDNA/NA12891.snp.vcf";
final String NA12878_WG_CALLS = comparisonDataLocation + "Unvalidated/NA12878/CEUTrio.HiSeq.WGS.b37_decoy.recal.ts_95.snp_indel_combined.vcf";
final String LSV_ALLELES = validationDataLocation + "ALL.chr20_40m_41m.largeScaleValidationSites.vcf";
@ -47,31 +47,31 @@ public class UnifiedGenotyperGeneralPloidyIntegrationTest extends WalkerTest {
@Test(enabled = true)
public void testBOTH_GGA_Pools() {
PC_LSV_Test(String.format(" -maxAltAlleles 2 -ploidy 24 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles %s",LSV_ALLELES),"LSV_BOTH_GGA","BOTH","0934f72865388999efec64bd9d4a9b93");
PC_LSV_Test(String.format(" -maxAltAlleles 2 -ploidy 24 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles %s",LSV_ALLELES),"LSV_BOTH_GGA","BOTH","077db83cf7dc5490f670c85856b408b2");
}
@Test(enabled = true)
public void testINDEL_GGA_Pools() {
PC_LSV_Test(String.format(" -maxAltAlleles 1 -ploidy 24 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles %s",LSV_ALLELES),"LSV_INDEL_GGA","INDEL","126581c72d287722437274d41b6fed7b");
PC_LSV_Test(String.format(" -maxAltAlleles 1 -ploidy 24 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles %s",LSV_ALLELES),"LSV_INDEL_GGA","INDEL","e460a17377b731ff4eab36fb56042ecd");
}
@Test(enabled = true)
public void testINDEL_maxAltAlleles2_ploidy3_Pools_noRef() {
PC_LSV_Test_NoRef(" -maxAltAlleles 2 -ploidy 3","LSV_INDEL_DISC_NOREF_p3","INDEL","b543aa1c3efedb301e525c1d6c50ed8d");
PC_LSV_Test_NoRef(" -maxAltAlleles 2 -ploidy 3","LSV_INDEL_DISC_NOREF_p3","INDEL","9514ed15c7030b6d47e04e6a3a2b0a3e");
}
@Test(enabled = true)
public void testINDEL_maxAltAlleles2_ploidy1_Pools_noRef() {
PC_LSV_Test_NoRef(" -maxAltAlleles 2 -ploidy 1","LSV_INDEL_DISC_NOREF_p1","INDEL","55b20557a836bb92688e68f12d7f5dc4");
PC_LSV_Test_NoRef(" -maxAltAlleles 2 -ploidy 1","LSV_INDEL_DISC_NOREF_p1","INDEL","26598044436c8044f22ffa767b06a0f0");
}
@Test(enabled = true)
public void testMT_SNP_DISCOVERY_sp4() {
PC_MT_Test(CEUTRIO_BAM, " -maxAltAlleles 1 -ploidy 8", "MT_SNP_DISCOVERY_sp4","7eb889e8e07182f4c3d64609591f9459");
PC_MT_Test(CEUTRIO_BAM, " -maxAltAlleles 1 -ploidy 8", "MT_SNP_DISCOVERY_sp4","da359fe7dd6dce045193198c264301ee");
}
@Test(enabled = true)
public void testMT_SNP_GGA_sp10() {
PC_MT_Test(CEUTRIO_BAM, String.format(" -maxAltAlleles 1 -ploidy 20 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles %s",NA12891_CALLS), "MT_SNP_GGA_sp10", "db8114877b99b14f7180fdcd24b040a7");
PC_MT_Test(CEUTRIO_BAM, String.format(" -maxAltAlleles 1 -ploidy 20 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles %s",NA12891_CALLS), "MT_SNP_GGA_sp10", "ad0eef3a9deaa098d79df62af7e5448a");
}
}

8
protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
View File

@ -20,17 +20,17 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void testHaplotypeCallerMultiSample() {
HCTest(CEUTRIO_BAM, "", "6b30c7e1b6bbe80d180d9d67441cec12");
HCTest(CEUTRIO_BAM, "", "e5b4a0627a1d69b9356f8a7cd2260e89");
}
@Test
public void testHaplotypeCallerSingleSample() {
HCTest(NA12878_BAM, "", "4cdfbfeadef00725974828310558d7d4");
HCTest(NA12878_BAM, "", "202d5b6edaf74f411c170099749f202f");
}
@Test
public void testHaplotypeCallerMultiSampleGGA() {
HCTest(CEUTRIO_BAM, "-gt_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "combined.phase1.chr20.raw.indels.sites.vcf", "6183fb6e374976d7087150009685e043");
HCTest(CEUTRIO_BAM, "-gt_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "combined.phase1.chr20.raw.indels.sites.vcf", "561931ba3919808ec471e745cb3148c7");
}
private void HCTestComplexVariants(String bam, String args, String md5) {
@ -41,7 +41,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void testHaplotypeCallerMultiSampleComplex() {
HCTestComplexVariants(CEUTRIO_BAM, "", "ab7593a7a60a2e9a66053572f1718df1");
HCTestComplexVariants(CEUTRIO_BAM, "", "316a0fb9c66c0a6aa40a170d5d8c0021");
}
}

2
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java
View File

@ -59,7 +59,7 @@ public class DepthPerAlleleBySample extends GenotypeAnnotation implements Standa
if (alleleLikelihoodMap != null && !alleleLikelihoodMap.isEmpty())
annotateWithLikelihoods(alleleLikelihoodMap, vc, gb);
else if ( vc.isSNP() && stratifiedContext != null)
else if ( stratifiedContext != null && (vc.isSNP()))
annotateWithPileup(stratifiedContext, vc, gb);
}

2
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java
View File

@ -71,7 +71,7 @@ public class HaplotypeScore extends InfoFieldAnnotation implements StandardAnnot
final Map<String, PerReadAlleleLikelihoodMap> stratifiedPerReadAlleleLikelihoodMap) {
if (vc.isSNP() && stratifiedContexts != null)
return annotatePileup(ref, stratifiedContexts, vc);
else if (stratifiedPerReadAlleleLikelihoodMap != null)
else if (stratifiedPerReadAlleleLikelihoodMap != null && vc.isVariant())
return annotateWithLikelihoods(stratifiedPerReadAlleleLikelihoodMap, vc);
else
return null;

4
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZero.java
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@ -34,9 +34,9 @@ public class MappingQualityZero extends InfoFieldAnnotation implements StandardA
final Map<String, AlignmentContext> stratifiedContexts,
final VariantContext vc,
final Map<String, PerReadAlleleLikelihoodMap> stratifiedPerReadAlleleLikelihoodMap) {
if (vc.isSNP() && stratifiedContexts != null)
if ((vc.isSNP() || !vc.isVariant()) && stratifiedContexts != null)
return annotatePileup(ref, stratifiedContexts, vc);
else if (stratifiedPerReadAlleleLikelihoodMap != null)
else if (stratifiedPerReadAlleleLikelihoodMap != null && vc.isVariant())
return annotateWithLikelihoods(stratifiedPerReadAlleleLikelihoodMap, vc);
else
return null;

3
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java
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@ -67,6 +67,9 @@ public abstract class RankSumTest extends InfoFieldAnnotation implements ActiveR
fillQualsFromPileup(vc.getAlleles(), vc.getStart(), pileup, indelLikelihoodMap, refQuals, altQuals );
}
if (refQuals.isEmpty() && altQuals.isEmpty())
return null;
final MannWhitneyU mannWhitneyU = new MannWhitneyU();
for (final Double qual : altQuals) {
mannWhitneyU.add(qual, MannWhitneyU.USet.SET1);

10
public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java
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@ -32,7 +32,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
public void testHasAnnotsAsking1() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -G Standard --variant " + privateTestDir + "vcfexample2.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
Arrays.asList("95b0627bfcac2191aed9908904e892ff"));
Arrays.asList("4a0318d0452d2dccde48ef081c431bf8"));
executeTest("test file has annotations, asking for annotations, #1", spec);
}
@ -40,7 +40,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
public void testHasAnnotsAsking2() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -G Standard --variant " + privateTestDir + "vcfexample3.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1,
Arrays.asList("0e2509349fd6c8a9e9408c918215e1de"));
Arrays.asList("da19c8e3c58340ba8bcc88e95ece4ac1"));
executeTest("test file has annotations, asking for annotations, #2", spec);
}
@ -66,7 +66,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
public void testNoAnnotsAsking1() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -G Standard --variant " + privateTestDir + "vcfexample2empty.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
Arrays.asList("32d81a7797605afb526983a2ab45efc2"));
Arrays.asList("cdefe79f46482a3d050ca2132604663a"));
executeTest("test file doesn't have annotations, asking for annotations, #1", spec);
}
@ -74,7 +74,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
public void testNoAnnotsAsking2() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -G Standard --variant " + privateTestDir + "vcfexample3empty.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1,
Arrays.asList("350539ccecea0d1f7fffd4ac29c015e7"));
Arrays.asList("5ec4c07b6801fca7013e3b0beb8b5418"));
executeTest("test file doesn't have annotations, asking for annotations, #2", spec);
}
@ -90,7 +90,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
public void testOverwritingHeader() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -G Standard --variant " + privateTestDir + "vcfexample4.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,001,292", 1,
Arrays.asList("c222361819fae035a0162f876990fdee"));
Arrays.asList("28c07151f5c5fae87c691d8f7d1a3929"));
executeTest("test overwriting header", spec);
}

62
public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
View File

@ -28,7 +28,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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,
Arrays.asList("0039fd0464c87e6ce66c4c8670fd8dfa"));
Arrays.asList("9a7fa3e9ec8350e3e9cfdce0c00ddcc3"));
executeTest("test MultiSample Pilot1", spec);
}
@ -36,7 +36,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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,
Arrays.asList("d1e68d4db6585ec00213b1d2d05e01a9"));
Arrays.asList("78693f3bf5d588e250507a596aa400da"));
executeTest("test MultiSample Pilot2 with alleles passed in", spec1);
}
@ -44,7 +44,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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,
Arrays.asList("b53860d209f8440f12b78d01606553e1"));
Arrays.asList("babf24ec8e5b5708d4a049629f7ea073"));
executeTest("test MultiSample Pilot2 with alleles passed in and emitting all sites", spec2);
}
@ -52,7 +52,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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,
Arrays.asList("61007c22c00a2871237280914a8f88f0"));
Arrays.asList("754187e70c1d117087e2270950a1c230"));
executeTest("test SingleSample Pilot2", spec);
}
@ -60,7 +60,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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,
Arrays.asList("feda4a38bba096f7b740a146055509c2"));
Arrays.asList("f9a2f882d050a90e6d8e6a1fba00f858"));
executeTest("test Multiple SNP alleles", spec);
}
@ -76,7 +76,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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,
Arrays.asList("0ff525e65c5836289c454c76ead5d80e"));
Arrays.asList("8a4ad38ec8015eea3461295148143428"));
executeTest("test reverse trim", spec);
}
@ -86,7 +86,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
//
// --------------------------------------------------------------------------------------------------------------
private final static String COMPRESSED_OUTPUT_MD5 = "e1a17f8f852c3d639f26e659d37bc1e5";
private final static String COMPRESSED_OUTPUT_MD5 = "ebb42960e115fb8dacd3edff5541b4da";
@Test
public void testCompressedOutput() {
@ -139,7 +139,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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,
Arrays.asList("b0b92abbaaa4c787dce6f1b302f983ee"));
Arrays.asList("91f7e112200ed2c3b0a5d0d9e16e9369"));
executeTest("test min_base_quality_score 26", spec);
}
@ -147,7 +147,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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,
Arrays.asList("186d33429756c89aad6cd89424d6dc94"));
Arrays.asList("b86e52b18496ab43a6b9a1bda632b5e6"));
executeTest("test SLOD", spec);
}
@ -155,7 +155,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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,
Arrays.asList("11b87f68b8530da168c1418513115f30"));
Arrays.asList("79b3e4f8b4476ce3c3acbc271d6ddcdc"));
executeTest("test NDA", spec);
}
@ -163,23 +163,23 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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,
Arrays.asList("d2be4b1af1f29579c4f96c08e1ddd871"));
Arrays.asList("bf7f21a600956eda0a357b97b21e3069"));
executeTest("test using comp track", spec);
}
@Test
public void testOutputParameterSitesOnly() {
testOutputParameters("-sites_only", "0055bd060e6ef53a6b836903d68953c9");
testOutputParameters("-sites_only", "976109543d8d97d94e0fe0521ff326e8");
}
@Test
public void testOutputParameterAllConfident() {
testOutputParameters("--output_mode EMIT_ALL_CONFIDENT_SITES", "235bec0a7b2d901442261104db18f5eb");
testOutputParameters("--output_mode EMIT_ALL_CONFIDENT_SITES", "8084a847f4a3c53a030e8c52eec35cea");
}
@Test
public void testOutputParameterAllSites() {
testOutputParameters("--output_mode EMIT_ALL_SITES", "7c57ede7019063c19aa9d2136045d84f");
testOutputParameters("--output_mode EMIT_ALL_SITES", "931e396f2a6903a291e813c64c18f8b5");
}
private void testOutputParameters(final String args, final String md5) {
@ -193,7 +193,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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,
Arrays.asList("3f8d724a5158adac4df38c4e2ed04167"));
Arrays.asList("e94be02fc5484c20b512840884e3d463"));
executeTest("test confidence 1", spec1);
}
@ -201,7 +201,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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,
Arrays.asList("3f8d724a5158adac4df38c4e2ed04167"));
Arrays.asList("e94be02fc5484c20b512840884e3d463"));
executeTest("test confidence 2", spec2);
}
@ -212,12 +212,12 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
// --------------------------------------------------------------------------------------------------------------
@Test
public void testHeterozyosity1() {
testHeterozosity( 0.01, "7e7384a3a52e19f76f368c2f4561d510" );
testHeterozosity( 0.01, "0dca2699f709793026b853c6f339bf08" );
}
@Test
public void testHeterozyosity2() {
testHeterozosity( 1.0 / 1850, "3d16366d870c086e894c07c9da411795" );
testHeterozosity( 1.0 / 1850, "35f14e436927e64712a8e28080e90c91" );
}
private void testHeterozosity(final double arg, final String md5) {
@ -241,7 +241,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
" -o %s" +
" -L 1:10,000,000-10,100,000",
1,
Arrays.asList("58abc4f504d3afd42271e290ac846c4b"));
Arrays.asList("0360b79163aa28ae66d0dde4c26b3d76"));
executeTest(String.format("test multiple technologies"), spec);
}
@ -260,7 +260,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
" -L 1:10,000,000-10,100,000" +
" -baq CALCULATE_AS_NECESSARY",
1,
Arrays.asList("e247f579f01eb698cfa1ae1e8a3995a8"));
Arrays.asList("59892388916bdfa544750ab76e43eabb"));
executeTest(String.format("test calling with BAQ"), spec);
}
@ -279,7 +279,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
" -o %s" +
" -L 1:10,000,000-10,500,000",
1,
Arrays.asList("cc2167dce156f70f5a31ac3dce499266"));
Arrays.asList("6aa034f669ec09ac4f5a28624cbe1830"));
executeTest(String.format("test indel caller in SLX"), spec);
}
@ -294,7 +294,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
" -minIndelCnt 1" +
" -L 1:10,000,000-10,100,000",
1,
Arrays.asList("1268bde77842e6bb6a4f337c1d589f4d"));
Arrays.asList("ba7a011d0c665acc4455d58a6ab28716"));
executeTest(String.format("test indel caller in SLX with low min allele count"), spec);
}
@ -307,7 +307,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
" -o %s" +
" -L 1:10,000,000-10,500,000",
1,
Arrays.asList("10c86ff98ad5ab800d208b435bcfbd7d"));
Arrays.asList("4f7d80f4f53ef0f0959414cb30097482"));
executeTest(String.format("test indel calling, multiple technologies"), spec);
}
@ -317,7 +317,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
baseCommandIndels + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + privateTestDir + "indelAllelesForUG.vcf -I " + validationDataLocation +
"pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,100,000", 1,
Arrays.asList("c0c4dbb050296633a3150b104b77e05a"));
Arrays.asList("95986d0c92436d3b9c1f1be9c768a368"));
executeTest("test MultiSample Pilot2 indels with alleles passed in", spec);
}
@ -327,7 +327,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
baseCommandIndels + " --output_mode EMIT_ALL_SITES --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles "
+ privateTestDir + "indelAllelesForUG.vcf -I " + validationDataLocation +
"pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,100,000", 1,
Arrays.asList("2472722f87f8718861698f60bbba2462"));
Arrays.asList("cecd3e35a817e299e97e8f7bbf083d2c"));
executeTest("test MultiSample Pilot2 indels with alleles passed in and emitting all sites", spec);
}
@ -335,13 +335,13 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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,
Arrays.asList("eeb64b261f0a44aa478d753dbbf9378e"));
Arrays.asList("c3f786a5228346b43a80aa80d22b1490"));
List<File> result = executeTest("test MultiSample Pilot1 CEU indels", spec1).getFirst();
WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
baseCommandIndels + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + result.get(0).getAbsolutePath() + " -I " + validationDataLocation +
"low_coverage_CEU.chr1.10k-11k.bam -o %s -L 1:10450700-10551000", 1,
Arrays.asList("d0a66c234056bb83dd84113bc2421f1e"));
Arrays.asList("1a4d856bfe53d9acee0ea303c4b83bb1"));
executeTest("test MultiSample Pilot1 CEU indels using GENOTYPE_GIVEN_ALLELES", spec2);
}
@ -351,7 +351,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
baseCommandIndelsb37 + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles " + privateTestDir + vcf + " -I " + validationDataLocation +
"NA12878.HiSeq.WGS.bwa.cleaned.recal.hg19.20.bam -o %s -L " + validationDataLocation + vcf, 1,
Arrays.asList("db0f91abb901e097714d8755058e1319"));
Arrays.asList("d76eacc4021b78ccc0a9026162e814a7"));
executeTest("test GENOTYPE_GIVEN_ALLELES with no evidence in reads", spec);
}
@ -363,7 +363,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
" -o %s" +
" -L 20:10,000,000-10,100,000",
1,
Arrays.asList("b3c923ed9efa04b85fc18a9b45c8d2a6"));
Arrays.asList("59ff26d7e5ca2503ebe9f74902251551"));
executeTest(String.format("test UG with base indel quality scores"), spec);
}
@ -397,7 +397,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testMinIndelFraction0() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
assessMinIndelFraction + " -minIndelFrac 0.0", 1,
Arrays.asList("160600dfa8e46f91dbb5d574517aac74"));
Arrays.asList("f99f9a917529bfef717fad97f725d5df"));
executeTest("test minIndelFraction 0.0", spec);
}
@ -405,7 +405,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testMinIndelFraction25() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
assessMinIndelFraction + " -minIndelFrac 0.25", 1,
Arrays.asList("aa58dc9f77132c30363562bcdc321f6e"));
Arrays.asList("eac2cd649bd5836068350eb4260aaea7"));
executeTest("test minIndelFraction 0.25", spec);
}