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Reverting a bunch of bad -B type drops

This commit is contained in:
Mark DePristo 2011-08-08 16:57:38 -04:00
parent 383bb6f0e0
commit f8ad91b16f
15 changed files with 71 additions and 68 deletions
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19
public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java
View File

@ -23,9 +23,7 @@
*/
package org.broadinstitute.sting.gatk.walkers.phasing;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.Hidden;
import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.commandline.*;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.datasources.sample.Sample;
@ -64,6 +62,13 @@ import static org.broadinstitute.sting.utils.codecs.vcf.VCFUtils.getVCFHeadersFr
public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, PhasingStats> {
private static final boolean DEBUG = false;
/**
* The VCF file we are phasing variants from.
*
* All heterozygous variants found in this VCF file will be phased, where possible
*/
@Input(fullName="variants", shortName = "V", doc="Phase variants from this VCF file", required=true)
public RodBinding<VariantContext> variants;
@Output(doc = "File to which variants should be written", required = true)
protected VCFWriter writer = null;
@ -98,8 +103,6 @@ public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, Ph
private static PreciseNonNegativeDouble ZERO = new PreciseNonNegativeDouble(0.0);
private String rodName = "variant";
public static final String PQ_KEY = "PQ";
// In order to detect phase inconsistencies:
@ -172,8 +175,8 @@ public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, Ph
hInfo.add(new VCFInfoHeaderLine(PHASING_INCONSISTENT_KEY, 0, VCFHeaderLineType.Flag, "Are the reads significantly haplotype-inconsistent?"));
// todo -- fix samplesToPhase
Map<String, VCFHeader> rodNameToHeader = getVCFHeadersFromRods(getToolkit(), Arrays.asList(rodName));
Set<String> samples = new TreeSet<String>(samplesToPhase == null ? rodNameToHeader.get(rodName).getGenotypeSamples() : samplesToPhase);
Map<String, VCFHeader> rodNameToHeader = getVCFHeadersFromRods(getToolkit(), Arrays.asList(variants.getName()));
Set<String> samples = new TreeSet<String>(samplesToPhase == null ? rodNameToHeader.get(variants.getName()).getGenotypeSamples() : samplesToPhase);
writer.writeHeader(new VCFHeader(hInfo, samples));
}
@ -204,7 +207,7 @@ public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, Ph
PhasingStats phaseStats = new PhasingStats();
List<VariantContext> unprocessedList = new LinkedList<VariantContext>();
for (VariantContext vc : tracker.getValues(VariantContext.class, rodName, context.getLocation())) {
for (VariantContext vc : tracker.getValues(variants, context.getLocation())) {
if (samplesToPhase != null) vc = reduceVCToSamples(vc, samplesToPhase);
if (ReadBackedPhasingWalker.processVariantInPhasing(vc)) {

4
public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java
View File

@ -102,7 +102,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
@Test
public void testDBTagWithHapMap() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -B:compH3 " + validationDataLocation + "fakeHM3.vcf -G \"Standard\" --variants:VCF3 " + validationDataLocation + "vcfexample3empty.vcf -BTI variants", 1,
baseTestString() + " -B:compH3,VCF " + 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 " + validationDataLocation + "targetAnnotations.vcf -G \"Standard\" --variants:VCF3 " + validationDataLocation + "vcfexample3empty.vcf -E foo.AF -BTI variants", 1,
baseTestString() + " -B:foo,VCF " + 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
View File

@ -24,7 +24,7 @@ public class FastaAlternateReferenceIntegrationTest extends WalkerTest {
executeTest("testFastaReference", spec1b);
WalkerTestSpec spec2 = new WalkerTestSpec(
"-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",
"-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",
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 " + b36dbSNP129 +
" -B:dbsnp,VCF " + b36dbSNP129 +
" -o /dev/null",
0,
new ArrayList<String>(0));

2
public/java/test/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreatorIntegrationTest.java
View File

@ -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 " + validationDataLocation + "NA12878.chr1_10mb_11mb.slx.indels.vcf4 -BTI indels -o %s",
"-T RealignerTargetCreator -R " + b36KGReference + " -B:indels,VCF " + 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 " + fundamentalTestPBTVCF,
"-B:rbp " + fundamentalTestRBPVCF,
"-B:pbt,VCF " + fundamentalTestPBTVCF,
"-B:rbp,VCF " + 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 " + validationDataLocation + VCF +
" -B:variant,VCF " + 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 " + validationDataLocation + VCF +
" -B:variant,VCF " + 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 " + fundamentalTestVCF,
"-B:variant,VCF " + 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 " + validationDataLocation + VCF +
" -B:variant,VCF " + validationDataLocation + VCF +
" --cacheWindowSize " + cacheWindowSize +
" --maxPhaseSites " + maxPhaseSites +
" --phaseQualityThresh " + phaseQualityThresh +

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

@ -236,7 +236,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-R " + b36KGReference +
" -B:dbsnp " + validationDataLocation + "vcfexample3.vcf" +
" -B:dbsnp,VCF3 " + validationDataLocation + "vcfexample3.vcf" +
" -T CountCovariates" +
" -I " + bam +
" -L 1:10,000,000-10,200,000" +
@ -284,7 +284,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-R " + b36KGReference +
" -B:anyNameABCD " + validationDataLocation + "vcfexample3.vcf" +
" -B:anyNameABCD,VCF3 " + validationDataLocation + "vcfexample3.vcf" +
" -T CountCovariates" +
" -I " + bam +
" -B:dbsnp,vcf " + b36dbSNP129 +

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 " + GATKDataLocation + "dbsnp_132.hg18.vcf" +
" -B:dbsnp,VCF " + 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 " + GATKDataLocation + "dbsnp_132.hg18.vcf" +
" -B:dbsnp,VCF " + GATKDataLocation + "dbsnp_132.hg18.vcf" +
" -recalFile /dev/null" + moreArgs,
0,
new ArrayList<String>(0));

76
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 " + b37dbSNP132,
"-B:eval " + fundamentalTestVCF,
"-B:dbsnp,VCF " + b37dbSNP132,
"-B:eval,VCF " + fundamentalTestVCF,
"-noEV",
"-EV CountVariants",
"-noST",
@ -40,8 +40,8 @@ public class VariantEvalIntegrationTest extends WalkerTest {
buildCommandLine(
"-T VariantEval",
"-R " + b37KGReference,
"-B:dbsnp " + b37dbSNP132,
"-B:eval " + fundamentalTestVCF,
"-B:dbsnp,VCF " + b37dbSNP132,
"-B:eval,VCF " + fundamentalTestVCF,
"-noEV",
"-EV CountVariants",
"-noST",
@ -61,8 +61,8 @@ public class VariantEvalIntegrationTest extends WalkerTest {
buildCommandLine(
"-T VariantEval",
"-R " + b37KGReference,
"-B:dbsnp " + b37dbSNP132,
"-B:eval " + fundamentalTestVCF,
"-B:dbsnp,VCF " + b37dbSNP132,
"-B:eval,VCF " + fundamentalTestVCF,
"-noEV",
"-EV CountVariants",
"-noST",
@ -83,8 +83,8 @@ public class VariantEvalIntegrationTest extends WalkerTest {
buildCommandLine(
"-T VariantEval",
"-R " + b37KGReference,
"-B:dbsnp " + b37dbSNP132,
"-B:eval " + fundamentalTestVCF,
"-B:dbsnp,VCF " + b37dbSNP132,
"-B:eval,VCF " + fundamentalTestVCF,
"-noEV",
"-EV CountVariants",
"-noST",
@ -104,8 +104,8 @@ public class VariantEvalIntegrationTest extends WalkerTest {
buildCommandLine(
"-T VariantEval",
"-R " + b37KGReference,
"-B:dbsnp " + b37dbSNP132,
"-B:eval " + fundamentalTestVCF,
"-B:dbsnp,VCF " + b37dbSNP132,
"-B:eval,VCF " + fundamentalTestVCF,
"-noEV",
"-EV CountVariants",
"-noST",
@ -125,8 +125,8 @@ public class VariantEvalIntegrationTest extends WalkerTest {
buildCommandLine(
"-T VariantEval",
"-R " + b37KGReference,
"-B:dbsnp " + b37dbSNP132,
"-B:eval " + fundamentalTestVCF,
"-B:dbsnp,VCF " + b37dbSNP132,
"-B:eval,VCF " + fundamentalTestVCF,
"-noEV",
"-EV CountVariants",
"-noST",
@ -146,8 +146,8 @@ public class VariantEvalIntegrationTest extends WalkerTest {
buildCommandLine(
"-T VariantEval",
"-R " + b37KGReference,
"-B:dbsnp " + b37dbSNP132,
"-B:eval " + fundamentalTestVCF,
"-B:dbsnp,VCF " + b37dbSNP132,
"-B:eval,VCF " + fundamentalTestVCF,
"-noEV",
"-EV CountVariants",
"-noST",
@ -167,8 +167,8 @@ public class VariantEvalIntegrationTest extends WalkerTest {
buildCommandLine(
"-T VariantEval",
"-R " + b37KGReference,
"-B:dbsnp " + b37dbSNP132,
"-B:eval " + fundamentalTestVCF,
"-B:dbsnp,VCF " + b37dbSNP132,
"-B:eval,VCF " + fundamentalTestVCF,
"-noEV",
"-EV CountVariants",
"-noST",
@ -190,8 +190,8 @@ public class VariantEvalIntegrationTest extends WalkerTest {
buildCommandLine(
"-T VariantEval",
"-R " + b37KGReference,
"-B:dbsnp " + b37dbSNP132,
"-B:eval " + fundamentalTestVCF,
"-B:dbsnp,VCF " + b37dbSNP132,
"-B:eval,VCF " + fundamentalTestVCF,
"-noEV",
"-EV CountVariants",
"-noST",
@ -215,7 +215,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
buildCommandLine(
"-T VariantEval",
"-R " + b37KGReference,
"-B:eval " + fundamentalTestVCF,
"-B:eval,VCF " + fundamentalTestVCF,
"-noEV",
"-EV CountVariants",
"-noST",
@ -232,9 +232,9 @@ public class VariantEvalIntegrationTest extends WalkerTest {
public void testSelect1() {
String extraArgs = "-L 1:1-10,000,000";
String tests = cmdRoot +
" -B:dbsnp " + b36dbSNP129 +
" -B:eval " + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf" +
" -B:comp_genotypes " + validationDataLocation + "yri.trio.gatk.ug.head.vcf";
" -B:dbsnp,VCF " + 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",
1, Arrays.asList("14054badcd89b24c2375e1d09918f681"));
executeTestParallel("testSelect1", spec);
@ -244,7 +244,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
public void testVEGenotypeConcordance() {
String vcfFile = "GenotypeConcordanceEval.vcf";
WalkerTestSpec spec = new WalkerTestSpec(cmdRoot + " -ST CpG -B:eval " + validationDataLocation + vcfFile + " -B:comp " + validationDataLocation + "GenotypeConcordanceComp.vcf -noEV -EV GenotypeConcordance -o %s",
WalkerTestSpec spec = new WalkerTestSpec(cmdRoot + " -ST CpG -B:eval,VCF3 " + validationDataLocation + vcfFile + " -B:comp,VCF3 " + validationDataLocation + "GenotypeConcordanceComp.vcf -noEV -EV GenotypeConcordance -o %s",
1,
Arrays.asList("96f27163f16bb945f19c6623cd6db34e"));
executeTestParallel("testVEGenotypeConcordance" + vcfFile, spec);
@ -252,7 +252,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
@Test
public void testCompVsEvalAC() {
String extraArgs = "-T VariantEval -R "+b36KGReference+" -o %s -ST CpG -EV GenotypeConcordance -B:evalYRI " + validationDataLocation + "yri.trio.gatk.ug.very.few.lines.vcf -B:compYRI " + validationDataLocation + "yri.trio.gatk.fake.genotypes.ac.test.vcf";
String extraArgs = "-T VariantEval -R "+b36KGReference+" -o %s -ST CpG -EV GenotypeConcordance -B:evalYRI,VCF3 " + validationDataLocation + "yri.trio.gatk.ug.very.few.lines.vcf -B:compYRI,VCF3 " + validationDataLocation + "yri.trio.gatk.fake.genotypes.ac.test.vcf";
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("d1932be3748fcf6da77dc51aec323710"));
executeTestParallel("testCompVsEvalAC",spec);
}
@ -280,8 +280,8 @@ public class VariantEvalIntegrationTest extends WalkerTest {
String extraArgs = "-T VariantEval -R " +
b37KGReference +
" -L 20" +
" -B:dbsnp " + b37dbSNP132 +
" -B:evalBI " + validationDataLocation + "VariantEval/ALL.20100201.chr20.bi.sites.vcf" +
" -B:dbsnp,VCF " + b37dbSNP132 +
" -B:evalBI,VCF " + 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 " + b37dbSNP132 +
" -B:evalBI " + validationDataLocation + "VariantEval/ALL.20100201.chr20.bi.sites.vcf" +
" -B:evalBC " + validationDataLocation + "VariantEval/ALL.20100201.chr20.bc.sites.vcf" +
" -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" +
" -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 " + 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 +
" -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 +
" -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 " + b37dbSNP132,
"-B:eval " + fundamentalTestSNPsVCF,
"-B:dbsnp,VCF " + b37dbSNP132,
"-B:eval,VCF " + fundamentalTestSNPsVCF,
"-noEV",
"-EV CompOverlap",
"-sn HG00625",
@ -342,8 +342,8 @@ public class VariantEvalIntegrationTest extends WalkerTest {
buildCommandLine(
"-T VariantEval",
"-R " + b37KGReference,
"-B:dbsnp " + b37dbSNP132,
"-B:eval " + fundamentalTestSNPsOneSampleVCF,
"-B:dbsnp,VCF " + b37dbSNP132,
"-B:eval,VCF " + fundamentalTestSNPsOneSampleVCF,
"-noEV",
"-EV CompOverlap",
"-noST",
@ -363,8 +363,8 @@ public class VariantEvalIntegrationTest extends WalkerTest {
buildCommandLine(
"-T VariantEval",
"-R " + b37KGReference,
"-B:dbsnp " + b37dbSNP132,
"-B:eval " + fundamentalTestSNPsVCF,
"-B:dbsnp,VCF " + b37dbSNP132,
"-B:eval,VCF " + 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,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" +
" -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" +
" -T VariantRecalibrator" +
" -B:input " + params.inVCF +
" -B:input,VCF " + 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 " + params.inVCF +
" -B:input,VCF " + params.inVCF +
" -o %s" +
" -tranchesFile " + MD5DB.getMD5FilePath(params.tranchesMD5, null) +
" -recalFile " + MD5DB.getMD5FilePath(params.recalMD5, null),

4
public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextIntegrationTest.java
View File

@ -16,7 +16,7 @@ public class VariantContextIntegrationTest extends WalkerTest {
private static String root = cmdRoot +
" -L 1:1-1,000,000 -B:dbsnp,vcf " + b36dbSNP129 +
" -B:vcf " + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf";
" -B:vcf,VCF3 " + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf";
private static final class VCITTest extends TestDataProvider {
String args, md5;
@ -58,7 +58,7 @@ public class VariantContextIntegrationTest extends WalkerTest {
public void testToVCF() {
// this really just tests that we are seeing the same number of objects over all of chr1
WalkerTestSpec spec = new WalkerTestSpec( cmdRoot + " -NO_HEADER -B:vcf " + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.500.vcf -L 1:1-1000000 -o %s --outputVCF %s",
WalkerTestSpec spec = new WalkerTestSpec( cmdRoot + " -NO_HEADER -B:vcf,VCF3 " + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.500.vcf -L 1:1-1000000 -o %s --outputVCF %s",
2, // just one output file
Arrays.asList("e3c35d0c4b5d4935c84a270f9df0951f", "ff91731213fd0bbdc200ab6fd1c93e63"));
executeTest("testToVCF", spec);