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Updated IntegrationTests to use the new type free format for VCF files

This commit is contained in:
Mark DePristo 2011-08-08 15:04:38 -04:00
parent 0810c42309
commit ba7353c561
14 changed files with 61 additions and 61 deletions
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2
public/java/src/org/broadinstitute/sting/commandline/ArgumentTypeDescriptor.java
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@ -333,7 +333,7 @@ class RodBindingArgumentTypeDescriptor extends ArgumentTypeDescriptor {
FeatureManager.FeatureDescriptor featureDescriptor = manager.getByFiletype(file);
if ( featureDescriptor != null ) {
tribbleType = featureDescriptor.getName();
logger.warn("Dynamically determined of " + file + " to be " + tribbleType);
logger.warn("Dynamically determined type of " + file + " to be " + tribbleType);
if ( tags.getPositionalTags().size() == 1 ) {
// -X:type style is a name when we can determine the type dynamically

4
public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java
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@ -102,7 +102,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
@Test
public void testDBTagWithHapMap() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -B:compH3,VCF " + validationDataLocation + "fakeHM3.vcf -G \"Standard\" --variants:VCF3 " + validationDataLocation + "vcfexample3empty.vcf -BTI variants", 1,
baseTestString() + " -B:compH3 " + validationDataLocation + "fakeHM3.vcf -G \"Standard\" --variants:VCF3 " + validationDataLocation + "vcfexample3empty.vcf -BTI variants", 1,
Arrays.asList("1bc01c5b3bd0b7aef75230310c3ce688"));
executeTest("getting DB tag with HM3", spec);
}
@ -110,7 +110,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
@Test
public void testUsingExpression() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -B:foo,VCF " + validationDataLocation + "targetAnnotations.vcf -G \"Standard\" --variants:VCF3 " + validationDataLocation + "vcfexample3empty.vcf -E foo.AF -BTI variants", 1,
baseTestString() + " -B:foo " + validationDataLocation + "targetAnnotations.vcf -G \"Standard\" --variants:VCF3 " + validationDataLocation + "vcfexample3empty.vcf -E foo.AF -BTI variants", 1,
Arrays.asList("e9c0d832dc6b4ed06c955060f830c140"));
executeTest("using expression", spec);
}

2
public/java/test/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceIntegrationTest.java
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@ -24,7 +24,7 @@ public class FastaAlternateReferenceIntegrationTest extends WalkerTest {
executeTest("testFastaReference", spec1b);
WalkerTestSpec spec2 = new WalkerTestSpec(
"-T FastaAlternateReferenceMaker -R " + b36KGReference + " -B:indels,VCF " + validationDataLocation + "NA12878.chr1_10mb_11mb.slx.indels.vcf4 --snpmask:vcf " + b36dbSNP129 + " -L 1:10,075,000-10,075,380;1:10,093,447-10,093,847;1:10,271,252-10,271,452 -o %s",
"-T FastaAlternateReferenceMaker -R " + b36KGReference + " -B:indels " + validationDataLocation + "NA12878.chr1_10mb_11mb.slx.indels.vcf4 --snpmask:vcf " + b36dbSNP129 + " -L 1:10,075,000-10,075,380;1:10,093,447-10,093,847;1:10,271,252-10,271,452 -o %s",
1,
Arrays.asList("0567b32ebdc26604ddf2a390de4579ac"));
executeTest("testFastaAlternateReferenceIndels", spec2);

2
public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperPerformanceTest.java
View File

@ -15,7 +15,7 @@ public class UnifiedGenotyperPerformanceTest extends WalkerTest {
" -glm BOTH" +
" -I " + evaluationDataLocation + "NA12878.GAII.chr1.50MB.bam" +
" -L chr1:1-50,000,000" +
" -B:dbsnp,VCF " + b36dbSNP129 +
" -B:dbsnp " + b36dbSNP129 +
" -o /dev/null",
0,
new ArrayList<String>(0));

2
public/java/test/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreatorIntegrationTest.java
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@ -23,7 +23,7 @@ public class RealignerTargetCreatorIntegrationTest extends WalkerTest {
executeTest("test dbsnp", spec2);
WalkerTest.WalkerTestSpec spec3 = new WalkerTest.WalkerTestSpec(
"-T RealignerTargetCreator -R " + b36KGReference + " -B:indels,VCF " + validationDataLocation + "NA12878.chr1_10mb_11mb.slx.indels.vcf4 -BTI indels -o %s",
"-T RealignerTargetCreator -R " + b36KGReference + " -B:indels " + validationDataLocation + "NA12878.chr1_10mb_11mb.slx.indels.vcf4 -BTI indels -o %s",
1,
Arrays.asList("5206cee6c01b299417bf2feeb8b3dc96"));
executeTest("test rods only", spec3);

4
public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/MergeAndMatchHaplotypesIntegrationTest.java
View File

@ -16,8 +16,8 @@ public class MergeAndMatchHaplotypesIntegrationTest extends WalkerTest {
buildCommandLine(
"-T MergeAndMatchHaplotypes",
"-R " + b37KGReference,
"-B:pbt,VCF " + fundamentalTestPBTVCF,
"-B:rbp,VCF " + fundamentalTestRBPVCF,
"-B:pbt " + fundamentalTestPBTVCF,
"-B:rbp " + fundamentalTestRBPVCF,
"-o %s"
),
1,

2
public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/MergeMNPsIntegrationTest.java
View File

@ -10,7 +10,7 @@ public class MergeMNPsIntegrationTest extends WalkerTest {
public static String baseTestString(String reference, String VCF, int maxDistMNP) {
return "-T MergeMNPs" +
" -R " + reference +
" -B:variant,VCF " + validationDataLocation + VCF +
" -B:variant " + validationDataLocation + VCF +
" --maxGenomicDistanceForMNP " + maxDistMNP +
" -o %s" +
" -NO_HEADER";

2
public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesIntegrationTest.java
View File

@ -10,7 +10,7 @@ public class MergeSegregatingAlternateAllelesIntegrationTest extends WalkerTest
public static String baseTestString(String reference, String VCF, int maxDist) {
return "-T MergeSegregatingAlternateAlleles" +
" -R " + reference +
" -B:variant,VCF " + validationDataLocation + VCF +
" -B:variant " + validationDataLocation + VCF +
" --maxGenomicDistance " + maxDist +
" -o %s" +
" -NO_HEADER";

2
public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmissionIntegrationTest.java
View File

@ -16,7 +16,7 @@ public class PhaseByTransmissionIntegrationTest extends WalkerTest {
"-T PhaseByTransmission",
"-NO_HEADER",
"-R " + b37KGReference,
"-B:variant,VCF " + fundamentalTestVCF,
"-B:variant " + fundamentalTestVCF,
"-f NA12892+NA12891=NA12878",
"-o %s"
),

2
public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingIntegrationTest.java
View File

@ -11,7 +11,7 @@ public class ReadBackedPhasingIntegrationTest extends WalkerTest {
return "-T ReadBackedPhasing" +
" -R " + reference +
" -I " + validationDataLocation + reads +
" -B:variant,VCF " + validationDataLocation + VCF +
" -B:variant " + validationDataLocation + VCF +
" --cacheWindowSize " + cacheWindowSize +
" --maxPhaseSites " + maxPhaseSites +
" --phaseQualityThresh " + phaseQualityThresh +

4
public/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersPerformanceTest.java
View File

@ -16,7 +16,7 @@ public class RecalibrationWalkersPerformanceTest extends WalkerTest {
" -L chr1:1-50,000,000" +
" -standard" +
" -OQ" +
" -B:dbsnp,VCF " + GATKDataLocation + "dbsnp_132.hg18.vcf" +
" -B:dbsnp " + GATKDataLocation + "dbsnp_132.hg18.vcf" +
" -recalFile /dev/null" + moreArgs,
0,
new ArrayList<String>(0));
@ -31,7 +31,7 @@ public class RecalibrationWalkersPerformanceTest extends WalkerTest {
" -L " + evaluationDataLocation + "whole_exome_agilent_designed_120.targets.chr1.interval_list" +
" -standard" +
" -OQ" +
" -B:dbsnp,VCF " + GATKDataLocation + "dbsnp_132.hg18.vcf" +
" -B:dbsnp " + GATKDataLocation + "dbsnp_132.hg18.vcf" +
" -recalFile /dev/null" + moreArgs,
0,
new ArrayList<String>(0));

68
public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java
View File

@ -20,8 +20,8 @@ public class VariantEvalIntegrationTest extends WalkerTest {
buildCommandLine(
"-T VariantEval",
"-R " + b37KGReference,
"-B:dbsnp,VCF " + b37dbSNP132,
"-B:eval,VCF " + fundamentalTestVCF,
"-B:dbsnp " + b37dbSNP132,
"-B:eval " + fundamentalTestVCF,
"-noEV",
"-EV CountVariants",
"-noST",
@ -40,8 +40,8 @@ public class VariantEvalIntegrationTest extends WalkerTest {
buildCommandLine(
"-T VariantEval",
"-R " + b37KGReference,
"-B:dbsnp,VCF " + b37dbSNP132,
"-B:eval,VCF " + fundamentalTestVCF,
"-B:dbsnp " + b37dbSNP132,
"-B:eval " + fundamentalTestVCF,
"-noEV",
"-EV CountVariants",
"-noST",
@ -61,8 +61,8 @@ public class VariantEvalIntegrationTest extends WalkerTest {
buildCommandLine(
"-T VariantEval",
"-R " + b37KGReference,
"-B:dbsnp,VCF " + b37dbSNP132,
"-B:eval,VCF " + fundamentalTestVCF,
"-B:dbsnp " + b37dbSNP132,
"-B:eval " + fundamentalTestVCF,
"-noEV",
"-EV CountVariants",
"-noST",
@ -83,8 +83,8 @@ public class VariantEvalIntegrationTest extends WalkerTest {
buildCommandLine(
"-T VariantEval",
"-R " + b37KGReference,
"-B:dbsnp,VCF " + b37dbSNP132,
"-B:eval,VCF " + fundamentalTestVCF,
"-B:dbsnp " + b37dbSNP132,
"-B:eval " + fundamentalTestVCF,
"-noEV",
"-EV CountVariants",
"-noST",
@ -104,8 +104,8 @@ public class VariantEvalIntegrationTest extends WalkerTest {
buildCommandLine(
"-T VariantEval",
"-R " + b37KGReference,
"-B:dbsnp,VCF " + b37dbSNP132,
"-B:eval,VCF " + fundamentalTestVCF,
"-B:dbsnp " + b37dbSNP132,
"-B:eval " + fundamentalTestVCF,
"-noEV",
"-EV CountVariants",
"-noST",
@ -125,8 +125,8 @@ public class VariantEvalIntegrationTest extends WalkerTest {
buildCommandLine(
"-T VariantEval",
"-R " + b37KGReference,
"-B:dbsnp,VCF " + b37dbSNP132,
"-B:eval,VCF " + fundamentalTestVCF,
"-B:dbsnp " + b37dbSNP132,
"-B:eval " + fundamentalTestVCF,
"-noEV",
"-EV CountVariants",
"-noST",
@ -146,8 +146,8 @@ public class VariantEvalIntegrationTest extends WalkerTest {
buildCommandLine(
"-T VariantEval",
"-R " + b37KGReference,
"-B:dbsnp,VCF " + b37dbSNP132,
"-B:eval,VCF " + fundamentalTestVCF,
"-B:dbsnp " + b37dbSNP132,
"-B:eval " + fundamentalTestVCF,
"-noEV",
"-EV CountVariants",
"-noST",
@ -167,8 +167,8 @@ public class VariantEvalIntegrationTest extends WalkerTest {
buildCommandLine(
"-T VariantEval",
"-R " + b37KGReference,
"-B:dbsnp,VCF " + b37dbSNP132,
"-B:eval,VCF " + fundamentalTestVCF,
"-B:dbsnp " + b37dbSNP132,
"-B:eval " + fundamentalTestVCF,
"-noEV",
"-EV CountVariants",
"-noST",
@ -190,8 +190,8 @@ public class VariantEvalIntegrationTest extends WalkerTest {
buildCommandLine(
"-T VariantEval",
"-R " + b37KGReference,
"-B:dbsnp,VCF " + b37dbSNP132,
"-B:eval,VCF " + fundamentalTestVCF,
"-B:dbsnp " + b37dbSNP132,
"-B:eval " + fundamentalTestVCF,
"-noEV",
"-EV CountVariants",
"-noST",
@ -215,7 +215,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
buildCommandLine(
"-T VariantEval",
"-R " + b37KGReference,
"-B:eval,VCF " + fundamentalTestVCF,
"-B:eval " + fundamentalTestVCF,
"-noEV",
"-EV CountVariants",
"-noST",
@ -232,7 +232,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
public void testSelect1() {
String extraArgs = "-L 1:1-10,000,000";
String tests = cmdRoot +
" -B:dbsnp,VCF " + b36dbSNP129 +
" -B:dbsnp " + b36dbSNP129 +
" -B:eval,VCF3 " + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf" +
" -B:comp_genotypes,VCF3 " + validationDataLocation + "yri.trio.gatk.ug.head.vcf";
WalkerTestSpec spec = new WalkerTestSpec(withSelect(tests, "DP < 50", "DP50") + " " + extraArgs + " -ST CpG -o %s",
@ -280,8 +280,8 @@ public class VariantEvalIntegrationTest extends WalkerTest {
String extraArgs = "-T VariantEval -R " +
b37KGReference +
" -L 20" +
" -B:dbsnp,VCF " + b37dbSNP132 +
" -B:evalBI,VCF " + validationDataLocation + "VariantEval/ALL.20100201.chr20.bi.sites.vcf" +
" -B:dbsnp " + b37dbSNP132 +
" -B:evalBI " + validationDataLocation + "VariantEval/ALL.20100201.chr20.bi.sites.vcf" +
" -noST -ST Novelty -o %s";
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("0897dfba2f4a245faddce38000555cce"));
executeTestParallel("testEvalTrackWithoutGenotypes",spec);
@ -291,9 +291,9 @@ public class VariantEvalIntegrationTest extends WalkerTest {
public void testMultipleEvalTracksWithoutGenotypes() {
String extraArgs = "-T VariantEval -R " + b37KGReference +
" -L 20" +
" -B:dbsnp,VCF " + b37dbSNP132 +
" -B:evalBI,VCF " + validationDataLocation + "VariantEval/ALL.20100201.chr20.bi.sites.vcf" +
" -B:evalBC,VCF " + validationDataLocation + "VariantEval/ALL.20100201.chr20.bc.sites.vcf" +
" -B:dbsnp " + b37dbSNP132 +
" -B:evalBI " + validationDataLocation + "VariantEval/ALL.20100201.chr20.bi.sites.vcf" +
" -B:evalBC " + validationDataLocation + "VariantEval/ALL.20100201.chr20.bc.sites.vcf" +
" -noST -ST Novelty -o %s";
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("ead3602e14ec2944b5d9e4dacc08c819"));
executeTestParallel("testMultipleEvalTracksWithoutGenotypes",spec);
@ -305,9 +305,9 @@ public class VariantEvalIntegrationTest extends WalkerTest {
String extraArgs = "-T VariantEval" +
" -R " + b37KGReference +
" -B:comp,VCF " + validationDataLocation + "/VariantEval/ALL.phase1.chr20.broad.snps.genotypes.subset.vcf" +
" -B:eval,VCF " + validationDataLocation + "/VariantEval/NA12878.hg19.HiSeq.WGS.cleaned.ug.snpfiltered.indelfiltered.optimized.cut.subset.vcf" +
" -B:dbsnp,VCF " + dbsnp +
" -B:comp " + validationDataLocation + "/VariantEval/ALL.phase1.chr20.broad.snps.genotypes.subset.vcf" +
" -B:eval " + validationDataLocation + "/VariantEval/NA12878.hg19.HiSeq.WGS.cleaned.ug.snpfiltered.indelfiltered.optimized.cut.subset.vcf" +
" -B:dbsnp " + dbsnp +
" -L 20:10000000-10100000" +
" -noST -noEV -ST Novelty -EV CompOverlap" +
" -o %s";
@ -324,8 +324,8 @@ public class VariantEvalIntegrationTest extends WalkerTest {
buildCommandLine(
"-T VariantEval",
"-R " + b37KGReference,
"-B:dbsnp,VCF " + b37dbSNP132,
"-B:eval,VCF " + fundamentalTestSNPsVCF,
"-B:dbsnp " + b37dbSNP132,
"-B:eval " + fundamentalTestSNPsVCF,
"-noEV",
"-EV CompOverlap",
"-sn HG00625",
@ -342,8 +342,8 @@ public class VariantEvalIntegrationTest extends WalkerTest {
buildCommandLine(
"-T VariantEval",
"-R " + b37KGReference,
"-B:dbsnp,VCF " + b37dbSNP132,
"-B:eval,VCF " + fundamentalTestSNPsOneSampleVCF,
"-B:dbsnp " + b37dbSNP132,
"-B:eval " + fundamentalTestSNPsOneSampleVCF,
"-noEV",
"-EV CompOverlap",
"-noST",
@ -363,8 +363,8 @@ public class VariantEvalIntegrationTest extends WalkerTest {
buildCommandLine(
"-T VariantEval",
"-R " + b37KGReference,
"-B:dbsnp,VCF " + b37dbSNP132,
"-B:eval,VCF " + fundamentalTestSNPsVCF,
"-B:dbsnp " + b37dbSNP132,
"-B:eval " + fundamentalTestSNPsVCF,
"-noEV",
"-EV CountVariants",
"-noST",

10
public/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java
View File

@ -41,11 +41,11 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
//System.out.printf("PARAMS FOR %s is %s%n", vcf, clusterFile);
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-R " + b37KGReference +
" -B:dbsnp,VCF,known=true,training=false,truth=false,prior=10.0 " + GATKDataLocation + "dbsnp_132_b37.leftAligned.vcf" +
" -B:hapmap,VCF,known=false,training=true,truth=true,prior=15.0 " + comparisonDataLocation + "Validated/HapMap/3.3/sites_r27_nr.b37_fwd.vcf" +
" -B:omni,VCF,known=false,training=true,truth=true,prior=12.0 " + comparisonDataLocation + "Validated/Omni2.5_chip/Omni25_sites_1525_samples.b37.vcf" +
" -B:dbsnp,known=true,training=false,truth=false,prior=10.0 " + GATKDataLocation + "dbsnp_132_b37.leftAligned.vcf" +
" -B:hapmap,known=false,training=true,truth=true,prior=15.0 " + comparisonDataLocation + "Validated/HapMap/3.3/sites_r27_nr.b37_fwd.vcf" +
" -B:omni,known=false,training=true,truth=true,prior=12.0 " + comparisonDataLocation + "Validated/Omni2.5_chip/Omni25_sites_1525_samples.b37.vcf" +
" -T VariantRecalibrator" +
" -B:input,VCF " + params.inVCF +
" -B:input " + params.inVCF +
" -L 20:1,000,000-40,000,000" +
" -an QD -an HaplotypeScore -an HRun" +
" -percentBad 0.07" +
@ -64,7 +64,7 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
" -T ApplyRecalibration" +
" -L 20:12,000,000-30,000,000" +
" -NO_HEADER" +
" -B:input,VCF " + params.inVCF +
" -B:input " + params.inVCF +
" -o %s" +
" -tranchesFile " + MD5DB.getMD5FilePath(params.tranchesMD5, null) +
" -recalFile " + MD5DB.getMD5FilePath(params.recalMD5, null),

16
public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java
View File

@ -63,8 +63,8 @@ public class CombineVariantsIntegrationTest extends WalkerTest {
String file2 = "hapmap_3.3.b37.sites.vcf";
WalkerTestSpec spec = new WalkerTestSpec(
"-T CombineVariants -NO_HEADER -o %s -R " + b37KGReference
+ " -L 1:1-10,000,000 -V:omni,VCF " + validationDataLocation + file1
+ " -V:hm3,VCF " + validationDataLocation + file2 + args,
+ " -L 1:1-10,000,000 -V:omni " + validationDataLocation + file1
+ " -V:hm3 " + validationDataLocation + file2 + args,
1,
Arrays.asList(md5));
executeTest("combineSites 1:" + new File(file1).getName() + " 2:" + new File(file2).getName() + " args = " + args, spec);
@ -91,10 +91,10 @@ public class CombineVariantsIntegrationTest extends WalkerTest {
@Test public void threeWayWithRefs() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString(" -V:NA19240_BGI,VCF "+validationDataLocation+"NA19240.BGI.RG.vcf" +
" -V:NA19240_ILLUMINA,VCF "+validationDataLocation+"NA19240.ILLUMINA.RG.vcf" +
" -V:NA19240_WUGSC,VCF "+validationDataLocation+"NA19240.WUGSC.RG.vcf" +
" -V:denovoInfo,VCF "+validationDataLocation+"yri_merged_validation_data_240610.annotated.b36.vcf" +
baseTestString(" -V:NA19240_BGI "+validationDataLocation+"NA19240.BGI.RG.vcf" +
" -V:NA19240_ILLUMINA "+validationDataLocation+"NA19240.ILLUMINA.RG.vcf" +
" -V:NA19240_WUGSC "+validationDataLocation+"NA19240.WUGSC.RG.vcf" +
" -V:denovoInfo "+validationDataLocation+"yri_merged_validation_data_240610.annotated.b36.vcf" +
" -setKey centerSet" +
" -filteredRecordsMergeType KEEP_IF_ANY_UNFILTERED" +
" -priority NA19240_BGI,NA19240_ILLUMINA,NA19240_WUGSC,denovoInfo" +
@ -110,8 +110,8 @@ public class CombineVariantsIntegrationTest extends WalkerTest {
String file2 = "combine.2.vcf";
WalkerTestSpec spec = new WalkerTestSpec(
"-T CombineVariants -NO_HEADER -o %s -R " + b37KGReference
+ " -V:one,VCF " + validationDataLocation + file1
+ " -V:two,VCF " + validationDataLocation + file2 + args,
+ " -V:one " + validationDataLocation + file1
+ " -V:two " + validationDataLocation + file2 + args,
1,
Arrays.asList(md5));
executeTest("combineComplexSites 1:" + new File(file1).getName() + " 2:" + new File(file2).getName() + " args = " + args, spec);