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Cleanup of VCF header lines and constants, BCF2 bugfixes 

-- Created public static UnifiedGenotyper.getHeaderInfo that loads UG standard header lines, and use this in tools like PoolCaller
-- Created VCFStandardHeaderLines class that keeps standard header lines in the GATK in a single place.  Provides convenient methods to add these to a header, as well as functionality to repair standard lines in incoming VCF headers
-- VCF parsers now automatically repair standard VCF header lines when reading the header
-- Updating integration tests to reflect header changes
-- Created private and public testdata directories (public/testdata and private/testdata).  Updated tests to use test
-- SelectHeaders now always updates the header to include the contig lines
-- SelectVariants add UG header lines when in regenotype mode
-- Renamed PHRED_GENOTYPE_LIKELIHOODS_KEY to GENOTYPE_PL_KEY
-- Bugfix in BCF2 to handle lists of null elements (can happen in genotype field values from VCFs)
-- Throw error when VCF has unbounded non-flag values that don't have = value bindings
-- By default we no longer allow writing of BCF2 files without contig lines in the header
This commit is contained in:
Mark DePristo 2012-06-20 15:35:36 -04:00
parent c4e0233ba3
commit 567dba0f76
84 changed files with 802 additions and 336 deletions
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7
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java
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@ -55,9 +55,10 @@ import java.util.*;
public class ChromosomeCounts extends InfoFieldAnnotation implements StandardAnnotation, ActiveRegionBasedAnnotation {
public static final String[] keyNames = { VCFConstants.ALLELE_NUMBER_KEY, VCFConstants.ALLELE_COUNT_KEY, VCFConstants.ALLELE_FREQUENCY_KEY };
public static final VCFInfoHeaderLine[] descriptions = { new VCFInfoHeaderLine(VCFConstants.ALLELE_FREQUENCY_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Float, "Allele Frequency, for each ALT allele, in the same order as listed"),
new VCFInfoHeaderLine(VCFConstants.ALLELE_COUNT_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Integer, "Allele count in genotypes, for each ALT allele, in the same order as listed"),
new VCFInfoHeaderLine(VCFConstants.ALLELE_NUMBER_KEY, 1, VCFHeaderLineType.Integer, "Total number of alleles in called genotypes") };
public static final VCFInfoHeaderLine[] descriptions = {
VCFStandardHeaderLines.getInfoLine(VCFConstants.ALLELE_FREQUENCY_KEY),
VCFStandardHeaderLines.getInfoLine(VCFConstants.ALLELE_COUNT_KEY),
VCFStandardHeaderLines.getInfoLine(VCFConstants.ALLELE_NUMBER_KEY) };
private Set<String> founderIds = new HashSet<String>();

6
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java
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@ -8,8 +8,8 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompa
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.codecs.vcf.VCFStandardHeaderLines;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.sting.utils.variantcontext.Allele;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
@ -68,5 +68,7 @@ public class DepthOfCoverage extends InfoFieldAnnotation implements StandardAnno
public List<String> getKeyNames() { return Arrays.asList(VCFConstants.DEPTH_KEY); }
public List<VCFInfoHeaderLine> getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine(getKeyNames().get(0), 1, VCFHeaderLineType.Integer, "Approximate read depth; some reads may have been filtered")); }
public List<VCFInfoHeaderLine> getDescriptions() {
return Arrays.asList(VCFStandardHeaderLines.getInfoLine(getKeyNames().get(0)));
}
}

12
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java
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@ -6,10 +6,7 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatibleWalker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
import org.broadinstitute.sting.utils.codecs.vcf.VCFFormatHeaderLine;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineCount;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
import org.broadinstitute.sting.utils.codecs.vcf.*;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.variantcontext.Allele;
@ -136,11 +133,6 @@ public class DepthPerAlleleBySample extends GenotypeAnnotation implements Standa
public List<String> getKeyNames() { return Arrays.asList(VCFConstants.GENOTYPE_ALLELE_DEPTHS); }
public List<VCFFormatHeaderLine> getDescriptions() {
return Arrays.asList(
new VCFFormatHeaderLine(
getKeyNames().get(0),
VCFHeaderLineCount.UNBOUNDED,
VCFHeaderLineType.Integer,
"Allelic depths for the ref and alt alleles in the order listed"));
return Arrays.asList(VCFStandardHeaderLines.getFormatLine(getKeyNames().get(0)));
}
}

6
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZero.java
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@ -7,8 +7,8 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompa
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.codecs.vcf.VCFStandardHeaderLines;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
@ -44,5 +44,7 @@ public class MappingQualityZero extends InfoFieldAnnotation implements StandardA
public List<String> getKeyNames() { return Arrays.asList(VCFConstants.MAPPING_QUALITY_ZERO_KEY); }
public List<VCFInfoHeaderLine> getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine(getKeyNames().get(0), 1, VCFHeaderLineType.Integer, "Total Mapping Quality Zero Reads")); }
public List<VCFInfoHeaderLine> getDescriptions() {
return Arrays.asList(VCFStandardHeaderLines.getInfoLine(getKeyNames().get(0)));
}
}

4
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java
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@ -63,7 +63,9 @@ public class QualByDepth extends InfoFieldAnnotation implements StandardAnnotati
public List<String> getKeyNames() { return Arrays.asList("QD"); }
public List<VCFInfoHeaderLine> getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine(getKeyNames().get(0), 1, VCFHeaderLineType.Float, "Variant Confidence/Quality by Depth")); }
public List<VCFInfoHeaderLine> getDescriptions() {
return Arrays.asList(new VCFInfoHeaderLine(getKeyNames().get(0), 1, VCFHeaderLineType.Float, "Variant Confidence/Quality by Depth"));
}
public Map<String, Object> annotate(Map<String, Map<Allele, List<GATKSAMRecord>>> stratifiedContexts, VariantContext vc) {
if ( stratifiedContexts.size() == 0 )

6
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java
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@ -10,8 +10,8 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnota
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.QualityUtils;
import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.codecs.vcf.VCFStandardHeaderLines;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
@ -85,5 +85,7 @@ public class RMSMappingQuality extends InfoFieldAnnotation implements StandardAn
public List<String> getKeyNames() { return Arrays.asList(VCFConstants.RMS_MAPPING_QUALITY_KEY); }
public List<VCFInfoHeaderLine> getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine(getKeyNames().get(0), 1, VCFHeaderLineType.Float, "RMS Mapping Quality")); }
public List<VCFInfoHeaderLine> getDescriptions() {
return Arrays.asList(VCFStandardHeaderLines.getInfoLine(getKeyNames().get(0)));
}
}

12
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java
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@ -41,8 +41,8 @@ import java.util.*;
public class VariantAnnotatorEngine {
private List<InfoFieldAnnotation> requestedInfoAnnotations;
private List<GenotypeAnnotation> requestedGenotypeAnnotations;
private List<InfoFieldAnnotation> requestedInfoAnnotations = Collections.emptyList();
private List<GenotypeAnnotation> requestedGenotypeAnnotations = Collections.emptyList();
private List<VAExpression> requestedExpressions = new ArrayList<VAExpression>();
private final HashMap<RodBinding<VariantContext>, String> dbAnnotations = new HashMap<RodBinding<VariantContext>, String>();
@ -164,8 +164,12 @@ public class VariantAnnotatorEngine {
descriptions.addAll(annotation.getDescriptions());
for ( GenotypeAnnotation annotation : requestedGenotypeAnnotations )
descriptions.addAll(annotation.getDescriptions());
for ( String db : dbAnnotations.values() )
descriptions.add(new VCFInfoHeaderLine(db, 0, VCFHeaderLineType.Flag, (db.equals(VCFConstants.DBSNP_KEY) ? "dbSNP" : db) + " Membership"));
for ( String db : dbAnnotations.values() ) {
if ( VCFStandardHeaderLines.getInfoLine(db, false) != null )
descriptions.add(VCFStandardHeaderLines.getInfoLine(db));
else
descriptions.add(new VCFInfoHeaderLine(db, 0, VCFHeaderLineType.Flag, db + " Membership"));
}
return descriptions;
}

6
public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/ThresHolder.java
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@ -128,13 +128,13 @@ class ThresHolder {
Set<VCFHeaderLine> headerLines = new HashSet<VCFHeaderLine>();
// INFO fields for overall data
headerLines.add(new VCFInfoHeaderLine(VCFConstants.END_KEY, 1, VCFHeaderLineType.Integer, "Stop position of the interval"));
headerLines.add(new VCFInfoHeaderLine(VCFConstants.DEPTH_KEY, 1, VCFHeaderLineType.Float, "Average depth across the interval. Sum of the depth in a loci divided by interval size."));
headerLines.add(VCFStandardHeaderLines.getInfoLine(VCFConstants.END_KEY));
headerLines.add(new VCFInfoHeaderLine("AVG_INTERVAL_DP", 1, VCFHeaderLineType.Float, "Average depth across the interval. Sum of the depth in a loci divided by interval size."));
headerLines.add(new VCFInfoHeaderLine("Diagnose Targets", 0, VCFHeaderLineType.Flag, "DiagnoseTargets mode"));
// FORMAT fields for each genotype
// todo -- find the appropriate VCF constants
headerLines.add(new VCFFormatHeaderLine(VCFConstants.DEPTH_KEY, 1, VCFHeaderLineType.Float, "Average depth across the interval. Sum of the depth in a loci divided by interval size."));
headerLines.add(new VCFFormatHeaderLine("AVG_INTERVAL_DP", 1, VCFHeaderLineType.Float, "Average depth across the interval. Sum of the depth in a loci divided by interval size."));
headerLines.add(new VCFFormatHeaderLine("Q1", 1, VCFHeaderLineType.Float, "Lower Quartile of depth distribution."));
headerLines.add(new VCFFormatHeaderLine("MED", 1, VCFHeaderLineType.Float, "Median of depth distribution."));
headerLines.add(new VCFFormatHeaderLine("Q3", 1, VCFHeaderLineType.Float, "Upper Quartile of depth Distribution."));

44
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
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@ -241,7 +241,7 @@ public class UnifiedGenotyper extends LocusWalker<List<VariantCallContext>, Unif
UG_engine = new UnifiedGenotyperEngine(getToolkit(), UAC, logger, verboseWriter, annotationEngine, samples, VariantContextUtils.DEFAULT_PLOIDY);
// initialize the header
Set<VCFHeaderLine> headerInfo = getHeaderInfo();
Set<VCFHeaderLine> headerInfo = getHeaderInfo(UAC, annotationEngine, dbsnp);
// invoke initialize() method on each of the annotation classes, allowing them to add their own header lines
// and perform any necessary initialization/validation steps
@ -250,27 +250,37 @@ public class UnifiedGenotyper extends LocusWalker<List<VariantCallContext>, Unif
writer.writeHeader(new VCFHeader(headerInfo, samples));
}
private Set<VCFHeaderLine> getHeaderInfo() {
public static Set<VCFHeaderLine> getHeaderInfo(final UnifiedArgumentCollection UAC,
final VariantAnnotatorEngine annotationEngine,
final DbsnpArgumentCollection dbsnp) {
Set<VCFHeaderLine> headerInfo = new HashSet<VCFHeaderLine>();
// all annotation fields from VariantAnnotatorEngine
headerInfo.addAll(annotationEngine.getVCFAnnotationDescriptions());
if ( annotationEngine != null )
headerInfo.addAll(annotationEngine.getVCFAnnotationDescriptions());
// annotation (INFO) fields from UnifiedGenotyper
if ( !UAC.NO_SLOD )
headerInfo.add(new VCFInfoHeaderLine(VCFConstants.STRAND_BIAS_KEY, 1, VCFHeaderLineType.Float, "Strand Bias"));
VCFStandardHeaderLines.addStandardInfoLines(headerInfo, true, VCFConstants.STRAND_BIAS_KEY);
if ( UAC.ANNOTATE_NUMBER_OF_ALLELES_DISCOVERED )
headerInfo.add(new VCFInfoHeaderLine(UnifiedGenotyperEngine.NUMBER_OF_DISCOVERED_ALLELES_KEY, 1, VCFHeaderLineType.Integer, "Number of alternate alleles discovered (but not necessarily genotyped) at this site"));
headerInfo.add(new VCFInfoHeaderLine(VCFConstants.DOWNSAMPLED_KEY, 0, VCFHeaderLineType.Flag, "Were any of the samples downsampled?"));
headerInfo.add(new VCFInfoHeaderLine(VCFConstants.MLE_ALLELE_COUNT_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Integer, "Maximum likelihood expectation (MLE) for the allele counts (not necessarily the same as the AC), for each ALT allele, in the same order as listed"));
headerInfo.add(new VCFInfoHeaderLine(VCFConstants.MLE_ALLELE_FREQUENCY_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Float, "Maximum likelihood expectation (MLE) for the allele frequency (not necessarily the same as the AF), for each ALT allele, in the same order as listed"));
VCFStandardHeaderLines.addStandardInfoLines(headerInfo, true,
VCFConstants.DOWNSAMPLED_KEY,
VCFConstants.MLE_ALLELE_COUNT_KEY,
VCFConstants.MLE_ALLELE_FREQUENCY_KEY);
// also, check to see whether comp rods were included
if ( dbsnp.dbsnp.isBound() )
headerInfo.add(new VCFInfoHeaderLine(VCFConstants.DBSNP_KEY, 0, VCFHeaderLineType.Flag, "dbSNP Membership"));
if ( dbsnp != null && dbsnp.dbsnp.isBound() )
VCFStandardHeaderLines.addStandardInfoLines(headerInfo, true, VCFConstants.DBSNP_KEY);
// FORMAT fields
headerInfo.addAll(getSupportedHeaderStrings());
VCFStandardHeaderLines.addStandardFormatLines(headerInfo, true,
VCFConstants.GENOTYPE_KEY,
VCFConstants.GENOTYPE_QUALITY_KEY,
VCFConstants.DEPTH_KEY,
VCFConstants.GENOTYPE_PL_KEY);
// FILTER fields are added unconditionally as it's not always 100% certain the circumstances
// where the filters are used. For example, in emitting all sites the lowQual field is used
@ -279,20 +289,6 @@ public class UnifiedGenotyper extends LocusWalker<List<VariantCallContext>, Unif
return headerInfo;
}
/**
* return a set of supported format lines; what we currently support for output in the genotype fields of a VCF
* @return a set of VCF format lines
*/
private static Set<VCFFormatHeaderLine> getSupportedHeaderStrings() {
Set<VCFFormatHeaderLine> result = new HashSet<VCFFormatHeaderLine>();
result.add(VCFConstants.GENOTYPE_KEY_HEADER_LINE);
result.add(new VCFFormatHeaderLine(VCFConstants.GENOTYPE_QUALITY_KEY, 1, VCFHeaderLineType.Integer, "Genotype Quality"));
result.add(new VCFFormatHeaderLine(VCFConstants.DEPTH_KEY, 1, VCFHeaderLineType.Integer, "Approximate read depth (reads with MQ=255 or with bad mates are filtered)"));
result.add(new VCFFormatHeaderLine(VCFConstants.PHRED_GENOTYPE_LIKELIHOODS_KEY, VCFHeaderLineCount.G, VCFHeaderLineType.Integer, "Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification"));
return result;
}
/**
* Compute at a given locus.
*

2
public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetectorWalker.java
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@ -316,7 +316,7 @@ public class SomaticIndelDetectorWalker extends ReadWalker<Integer,Integer> {
// first, the basic info
headerInfo.add(new VCFHeaderLine("source", "SomaticIndelDetector"));
headerInfo.add(new VCFHeaderLine("reference", getToolkit().getArguments().referenceFile.getName()));
headerInfo.add(VCFConstants.GENOTYPE_KEY_HEADER_LINE);
headerInfo.add(VCFStandardHeaderLines.getFormatLine(VCFConstants.GENOTYPE_KEY));
// FORMAT and INFO fields
// headerInfo.addAll(VCFUtils.getSupportedHeaderStrings());

9
public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java
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@ -150,8 +150,7 @@ public class ApplyRecalibration extends RodWalker<Integer, Integer> implements T
// setup the header fields
final Set<VCFHeaderLine> hInfo = new HashSet<VCFHeaderLine>();
hInfo.addAll(VCFUtils.getHeaderFields(getToolkit(), inputNames));
hInfo.add(new VCFInfoHeaderLine(VariantRecalibrator.VQS_LOD_KEY, 1, VCFHeaderLineType.Float, "Log odds ratio of being a true variant versus being false under the trained gaussian mixture model"));
hInfo.add(new VCFInfoHeaderLine(VariantRecalibrator.CULPRIT_KEY, 1, VCFHeaderLineType.String, "The annotation which was the worst performing in the Gaussian mixture model, likely the reason why the variant was filtered out"));
addVQSRStandardHeaderLines(hInfo);
final TreeSet<String> samples = new TreeSet<String>();
samples.addAll(SampleUtils.getUniqueSamplesFromRods(getToolkit(), inputNames));
@ -173,6 +172,12 @@ public class ApplyRecalibration extends RodWalker<Integer, Integer> implements T
vcfWriter.writeHeader(vcfHeader);
}
public static final void addVQSRStandardHeaderLines(final Set<VCFHeaderLine> hInfo) {
hInfo.add(VCFStandardHeaderLines.getInfoLine(VCFConstants.END_KEY));
hInfo.add(new VCFInfoHeaderLine(VariantRecalibrator.VQS_LOD_KEY, 1, VCFHeaderLineType.Float, "Log odds ratio of being a true variant versus being false under the trained gaussian mixture model"));
hInfo.add(new VCFInfoHeaderLine(VariantRecalibrator.CULPRIT_KEY, 1, VCFHeaderLineType.String, "The annotation which was the worst performing in the Gaussian mixture model, likely the reason why the variant was filtered out"));
}
//---------------------------------------------------------------------------------------------------------------
//
// map

7
public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
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@ -37,7 +37,9 @@ import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.QualityUtils;
import org.broadinstitute.sting.utils.R.RScriptExecutor;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine;
import org.broadinstitute.sting.utils.collections.ExpandingArrayList;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.io.Resource;
@ -229,7 +231,10 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
throw new UserException.CommandLineException( "No truth set found! Please provide sets of known polymorphic loci marked with the truth=true ROD binding tag. For example, -B:hapmap,VCF,known=false,training=true,truth=true,prior=12.0 hapmapFile.vcf" );
}
recalWriter.writeHeader( new VCFHeader() );
final Set<VCFHeaderLine> hInfo = new HashSet<VCFHeaderLine>();
ApplyRecalibration.addVQSRStandardHeaderLines(hInfo);
recalWriter.writeHeader( new VCFHeader(hInfo) );
}
//---------------------------------------------------------------------------------------------------------------

7
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectHeaders.java
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@ -34,9 +34,7 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.RodWalker;
import org.broadinstitute.sting.gatk.walkers.TreeReducible;
import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine;
import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
import org.broadinstitute.sting.utils.codecs.vcf.*;
import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
import org.broadinstitute.sting.utils.text.ListFileUtils;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
@ -202,6 +200,9 @@ public class SelectHeaders extends RodWalker<Integer, Integer> implements TreeRe
// Remove any excluded headers.
if (XLheaderNames != null)
selectedHeaders = ListFileUtils.excludeMatching(selectedHeaders, headerKey, XLheaderNames, true);
// always include the contig lines
selectedHeaders = VCFUtils.withUpdatedContigsAsLines(selectedHeaders, getToolkit().getArguments().referenceFile, getToolkit().getMasterSequenceDictionary());
return selectedHeaders;
}

7
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
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@ -36,6 +36,7 @@ import org.broadinstitute.sting.gatk.walkers.TreeReducible;
import org.broadinstitute.sting.gatk.walkers.annotator.ChromosomeCounts;
import org.broadinstitute.sting.gatk.walkers.genotyper.GenotypeLikelihoodsCalculationModel;
import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedArgumentCollection;
import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyper;
import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine;
import org.broadinstitute.sting.utils.MendelianViolation;
import org.broadinstitute.sting.utils.SampleUtils;
@ -432,8 +433,7 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
headerLines.add(new VCFInfoHeaderLine("AN_Orig", 1, VCFHeaderLineType.Integer, "Original AN"));
}
headerLines.addAll(Arrays.asList(ChromosomeCounts.descriptions));
headerLines.add(new VCFInfoHeaderLine(VCFConstants.DEPTH_KEY, 1, VCFHeaderLineType.Integer, "Depth of coverage"));
vcfWriter.writeHeader(new VCFHeader(headerLines, samples));
headerLines.add(VCFStandardHeaderLines.getInfoLine(VCFConstants.DEPTH_KEY));
for (int i = 0; i < SELECT_EXPRESSIONS.size(); i++) {
// It's not necessary that the user supply select names for the JEXL expressions, since those
@ -469,6 +469,7 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
UAC.OutputMode = UnifiedGenotyperEngine.OUTPUT_MODE.EMIT_ALL_SITES;
UAC.NO_SLOD = true;
UG_engine = new UnifiedGenotyperEngine(getToolkit(), UAC, logger, null, null, samples, VariantContextUtils.DEFAULT_PLOIDY);
headerLines.addAll(UnifiedGenotyper.getHeaderInfo(UAC, null, null));
}
/** load in the IDs file to a hashset for matching */
@ -483,6 +484,8 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
throw new UserException.CouldNotReadInputFile(rsIDFile, e);
}
}
vcfWriter.writeHeader(new VCFHeader(headerLines, samples));
}
/**

4
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantValidationAssessor.java
View File

@ -170,8 +170,8 @@ public class VariantValidationAssessor extends RodWalker<VariantContext,Integer>
hInfo.add(new VCFInfoHeaderLine("HetPct", 1, VCFHeaderLineType.Float, "Percent of heterozygous genotypes"));
hInfo.add(new VCFInfoHeaderLine("HomVarPct", 1, VCFHeaderLineType.Float, "Percent homozygous variant genotypes"));
hInfo.add(new VCFInfoHeaderLine("HW", 1, VCFHeaderLineType.Float, "Phred-scaled Hardy-Weinberg violation p-value"));
hInfo.add(new VCFInfoHeaderLine(VCFConstants.ALLELE_COUNT_KEY, 1, VCFHeaderLineType.Integer, "Allele count in genotypes, for each ALT allele, in the same order as listed"));
hInfo.add(new VCFInfoHeaderLine(VCFConstants.ALLELE_NUMBER_KEY, 1, VCFHeaderLineType.Integer, "Total number of alleles in called genotypes"));
hInfo.add(VCFStandardHeaderLines.getInfoLine(VCFConstants.ALLELE_COUNT_KEY));
hInfo.add(VCFStandardHeaderLines.getInfoLine(VCFConstants.ALLELE_NUMBER_KEY));
hInfo.add(new VCFFilterHeaderLine("HardyWeinbergViolation", "The validation is in Hardy-Weinberg violation"));
hInfo.add(new VCFFilterHeaderLine("HighNoCallRate", "The validation no-call rate is too high"));
hInfo.add(new VCFFilterHeaderLine("TooManyHomVars", "The validation homozygous variant rate is too high"));

4
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java
View File

@ -219,10 +219,8 @@ public class VariantsToVCF extends RodWalker<Integer, Integer> {
// setup the header fields
Set<VCFHeaderLine> hInfo = new HashSet<VCFHeaderLine>();
hInfo.addAll(VCFUtils.getHeaderFields(getToolkit(), Arrays.asList(variants.getName())));
//hInfo.add(new VCFHeaderLine("source", "VariantsToVCF"));
//hInfo.add(new VCFHeaderLine("reference", getToolkit().getArguments().referenceFile.getID()));
hInfo.add(VCFStandardHeaderLines.getFormatLine(VCFConstants.GENOTYPE_KEY));
hInfo.add(VCFConstants.GENOTYPE_KEY_HEADER_LINE);
allowedGenotypeFormatStrings.add(VCFConstants.GENOTYPE_KEY);
for ( VCFHeaderLine field : hInfo ) {
if ( field instanceof VCFFormatHeaderLine) {

2
public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2GenotypeFieldDecoders.java
View File

@ -60,7 +60,7 @@ public class BCF2GenotypeFieldDecoders {
genotypeFieldDecoder.put(VCFConstants.GENOTYPE_FILTER_KEY, new FTDecoder());
genotypeFieldDecoder.put(VCFConstants.DEPTH_KEY, new DPDecoder());
genotypeFieldDecoder.put(VCFConstants.GENOTYPE_ALLELE_DEPTHS, new ADDecoder());
genotypeFieldDecoder.put(VCFConstants.PHRED_GENOTYPE_LIKELIHOODS_KEY, new PLDecoder());
genotypeFieldDecoder.put(VCFConstants.GENOTYPE_PL_KEY, new PLDecoder());
genotypeFieldDecoder.put(VCFConstants.GENOTYPE_QUALITY_KEY, new GQDecoder());
}

6
public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Utils.java
View File

@ -164,8 +164,10 @@ public final class BCF2Utils {
public static final String collapseStringList(final List<String> strings) {
final StringBuilder b = new StringBuilder();
for ( final String s : strings ) {
assert s.indexOf(",") == -1; // no commas in individual strings
b.append(",").append(s);
if ( s != null ) {
assert s.indexOf(",") == -1; // no commas in individual strings
b.append(",").append(s);
}
}
return b.toString();
}

9
public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java
View File

@ -23,7 +23,7 @@ import java.util.zip.GZIPInputStream;
public abstract class AbstractVCFCodec extends AsciiFeatureCodec<VariantContext> implements NameAwareCodec {
public final static int MAX_ALLELE_SIZE_BEFORE_WARNING = (int)Math.pow(2, 20);
protected final static Logger log = Logger.getLogger(VCFCodec.class);
protected final static Logger log = Logger.getLogger(AbstractVCFCodec.class);
protected final static int NUM_STANDARD_FIELDS = 8; // INFO is the 8th column
// we have to store the list of strings that make up the header until they're needed
@ -168,6 +168,7 @@ public abstract class AbstractVCFCodec extends AsciiFeatureCodec<VariantContext>
}
this.header = new VCFHeader(metaData, sampleNames);
this.header = VCFStandardHeaderLines.repairStandardHeaderLines(this.header);
return this.header;
}
@ -433,6 +434,10 @@ public abstract class AbstractVCFCodec extends AsciiFeatureCodec<VariantContext>
}
} else {
key = infoFieldArray[i];
final VCFInfoHeaderLine headerLine = header.getInfoHeaderLine(key);
if ( headerLine != null && headerLine.getType() != VCFHeaderLineType.Flag )
generateException("Found info key " + key + " without a = value, but the header says the field is of type "
+ headerLine.getType() + " but this construct is only value for FLAG type fields");
value = true;
}
@ -780,7 +785,7 @@ public abstract class AbstractVCFCodec extends AsciiFeatureCodec<VariantContext>
gb.GQ((int)Math.round(Double.valueOf(GTValueArray[i])));
} else if (gtKey.equals(VCFConstants.GENOTYPE_ALLELE_DEPTHS)) {
gb.AD(decodeInts(GTValueArray[i]));
} else if (gtKey.equals(VCFConstants.PHRED_GENOTYPE_LIKELIHOODS_KEY)) {
} else if (gtKey.equals(VCFConstants.GENOTYPE_PL_KEY)) {
gb.PL(decodeInts(GTValueArray[i]));
} else if (gtKey.equals(VCFConstants.GENOTYPE_LIKELIHOODS_KEY)) {
gb.PL(GenotypeLikelihoods.fromGLField(GTValueArray[i]).getAsPLs());

3
public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFCodec.java
View File

@ -114,7 +114,8 @@ public class VCFCodec extends AbstractVCFCodec {
* @param headerForRepairs
*/
public void setHeaderForRepairs(final VCFHeader headerForRepairs) {
log.info("Using master VCF header to repair missing files from incoming VCFs");
if ( headerForRepairs != null )
log.info("Using master VCF header to repair missing files from incoming VCFs");
this.headerForRepairs = headerForRepairs;
}

15
public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFConstants.java
View File

@ -44,20 +44,21 @@ public final class VCFConstants {
public static final String DOWNSAMPLED_KEY = "DS";
public static final String EXPECTED_ALLELE_COUNT_KEY = "EC";
public static final String END_KEY = "END";
public static final String GENOTYPE_FILTER_KEY = "FT";
public static final String GENOTYPE_KEY = "GT";
@Deprecated
public static final String GENOTYPE_LIKELIHOODS_KEY = "GL"; // log10 scaled genotype likelihoods
public static final String GENOTYPE_POSTERIORS_KEY = "GP";
public static final String GENOTYPE_QUALITY_KEY = "GQ";
public static final String GENOTYPE_ALLELE_DEPTHS = "AD";
public static final String GENOTYPE_PL_KEY = "PL"; // phred-scaled genotype likelihoods
@Deprecated public static final String GENOTYPE_LIKELIHOODS_KEY = "GL"; // log10 scaled genotype likelihoods
public static final String HAPMAP2_KEY = "H2";
public static final String HAPMAP3_KEY = "H3";
public static final String HAPLOTYPE_QUALITY_KEY = "HQ";
public static final String RMS_MAPPING_QUALITY_KEY = "MQ";
public static final String MAPPING_QUALITY_ZERO_KEY = "MQ0";
public static final String SAMPLE_NUMBER_KEY = "NS";
public static final String PHRED_GENOTYPE_LIKELIHOODS_KEY = "PL"; // phred-scaled genotype likelihoods
public static final String PHASE_QUALITY_KEY = "PQ";
public static final String PHASE_SET_KEY = "PS";
public static final String OLD_DEPTH_KEY = "RD";
@ -88,7 +89,8 @@ public final class VCFConstants {
public static final String FORMAT_HEADER_START = "##FORMAT";
public static final String INFO_HEADER_START = "##INFO";
public static final String ALT_HEADER_START = "##ALT";
public static final String CONTIG_HEADER_START = "##contig";
public static final String CONTIG_HEADER_KEY = "contig";
public static final String CONTIG_HEADER_START = "##" + CONTIG_HEADER_KEY;
// old indel alleles
public static final char DELETION_ALLELE_v3 = 'D';
@ -117,9 +119,4 @@ public final class VCFConstants {
public static final int MAX_GENOTYPE_QUAL = 99;
public static final Double VCF_ENCODING_EPSILON = 0.00005; // when we consider fields equal(), used in the Qual compare
//
// VCF header line constants
//
public static final VCFFormatHeaderLine GENOTYPE_KEY_HEADER_LINE = new VCFFormatHeaderLine(VCFConstants.GENOTYPE_KEY, 1, VCFHeaderLineType.String, "Genotype");
}

6
public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeader.java
View File

@ -195,11 +195,11 @@ public class VCFHeader {
}
}
if ( hasFormatLine(VCFConstants.GENOTYPE_LIKELIHOODS_KEY) && ! hasFormatLine(VCFConstants.PHRED_GENOTYPE_LIKELIHOODS_KEY) ) {
if ( hasFormatLine(VCFConstants.GENOTYPE_LIKELIHOODS_KEY) && ! hasFormatLine(VCFConstants.GENOTYPE_PL_KEY) ) {
logger.warn("Found " + VCFConstants.GENOTYPE_LIKELIHOODS_KEY + " format, but no "
+ VCFConstants.PHRED_GENOTYPE_LIKELIHOODS_KEY + " field. As the GATK now only manages PL fields internally"
+ VCFConstants.GENOTYPE_PL_KEY + " field. As the GATK now only manages PL fields internally"
+ " automatically adding a corresponding PL field to your VCF header");
addMetaDataLine(new VCFFormatHeaderLine(VCFConstants.PHRED_GENOTYPE_LIKELIHOODS_KEY, VCFHeaderLineCount.G, VCFHeaderLineType.Integer, "Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification"));
addMetaDataLine(new VCFFormatHeaderLine(VCFConstants.GENOTYPE_PL_KEY, VCFHeaderLineCount.G, VCFHeaderLineType.Integer, "Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification"));
loadMetaDataMaps();
}
}

264
public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFStandardHeaderLines.java 100644
View File

@ -0,0 +1,264 @@
/*
* Copyright (c) 2012, The Broad Institute
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.utils.codecs.vcf;
import com.google.java.contract.Ensures;
import com.google.java.contract.Invariant;
import com.google.java.contract.Requires;
import org.apache.log4j.Logger;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import java.util.*;
/**
* Manages header lines for standard VCF INFO and FORMAT fields
*
* Provides simple mechanisms for registering standard lines,
* looking them up, and adding them to headers
*
* @author Mark DePristo
* @since 6/12
*/
public class VCFStandardHeaderLines {
/**
* Enabling this causes us to repair header lines even if only their descriptions differ
*/
private final static boolean REPAIR_BAD_DESCRIPTIONS = false;
protected final static Logger logger = Logger.getLogger(VCFStandardHeaderLines.class);
private static Standards<VCFFormatHeaderLine> formatStandards = new Standards<VCFFormatHeaderLine>();
private static Standards<VCFInfoHeaderLine> infoStandards = new Standards<VCFInfoHeaderLine>();
/**
* Walks over the VCF header and repairs the standard VCF header lines in it, returning a freshly
* allocated VCFHeader with standard VCF header lines repaired as necessary
*
* @param header
* @return
*/
@Requires("header != null")
@Ensures("result != null")
public static VCFHeader repairStandardHeaderLines(final VCFHeader header) {
final Set<VCFHeaderLine> newLines = new LinkedHashSet<VCFHeaderLine>(header.getMetaData().size());
for ( VCFHeaderLine line : header.getMetaData() ) {
if ( line instanceof VCFFormatHeaderLine ) {
line = formatStandards.repair((VCFFormatHeaderLine) line);
} else if ( line instanceof VCFInfoHeaderLine) {
line = infoStandards.repair((VCFInfoHeaderLine) line);
}
newLines.add(line);
}
return new VCFHeader(newLines, header.getGenotypeSamples());
}
/**
* Adds header lines for each of the format fields in IDs to header, returning the set of
* IDs without standard descriptions, unless throwErrorForMissing is true, in which
* case this situation results in a ReviewedStingException
*
* @param IDs
* @return
*/
public static Set<String> addStandardFormatLines(final Set<VCFHeaderLine> headerLines, final boolean throwErrorForMissing, final Collection<String> IDs) {
return formatStandards.addToHeader(headerLines, IDs, throwErrorForMissing);
}
/**
* @see #addStandardFormatLines(java.util.Set, boolean, java.util.Collection)
*
* @param headerLines
* @param throwErrorForMissing
* @param IDs
* @return
*/
public static Set<String> addStandardFormatLines(final Set<VCFHeaderLine> headerLines, final boolean throwErrorForMissing, final String ... IDs) {
return addStandardFormatLines(headerLines, throwErrorForMissing, Arrays.asList(IDs));
}
/**
* Returns the standard format line for ID. If none exists, return null or throw an exception, depending
* on throwErrorForMissing
*
* @param ID
* @param throwErrorForMissing
* @return
*/
public static VCFFormatHeaderLine getFormatLine(final String ID, final boolean throwErrorForMissing) {
return formatStandards.get(ID, throwErrorForMissing);
}
/**
* Returns the standard format line for ID. If none exists throw an exception
*
* @param ID
* @return
*/
public static VCFFormatHeaderLine getFormatLine(final String ID) {
return formatStandards.get(ID, true);
}
private static void registerStandard(final VCFFormatHeaderLine line) {
formatStandards.add(line);
}
/**
* Adds header lines for each of the info fields in IDs to header, returning the set of
* IDs without standard descriptions, unless throwErrorForMissing is true, in which
* case this situation results in a ReviewedStingException
*
* @param IDs
* @return
*/
public static Set<String> addStandardInfoLines(final Set<VCFHeaderLine> headerLines, final boolean throwErrorForMissing, final Collection<String> IDs) {
return infoStandards.addToHeader(headerLines, IDs, throwErrorForMissing);
}
/**
* @see #addStandardFormatLines(java.util.Set, boolean, java.util.Collection)
*
* @param IDs
* @return
*/
public static Set<String> addStandardInfoLines(final Set<VCFHeaderLine> headerLines, final boolean throwErrorForMissing, final String ... IDs) {
return addStandardInfoLines(headerLines, throwErrorForMissing, Arrays.asList(IDs));
}
/**
* Returns the standard info line for ID. If none exists, return null or throw an exception, depending
* on throwErrorForMissing
*
* @param ID
* @param throwErrorForMissing
* @return
*/
public static VCFInfoHeaderLine getInfoLine(final String ID, final boolean throwErrorForMissing) {
return infoStandards.get(ID, throwErrorForMissing);
}
/**
* Returns the standard info line for ID. If none exists throw an exception
*
* @param ID
* @return
*/
public static VCFInfoHeaderLine getInfoLine(final String ID) {
return getInfoLine(ID, true);
}
private static void registerStandard(final VCFInfoHeaderLine line) {
infoStandards.add(line);
}
//
// VCF header line constants
//
static {
// FORMAT lines
registerStandard(new VCFFormatHeaderLine(VCFConstants.GENOTYPE_KEY, 1, VCFHeaderLineType.String, "Genotype"));
registerStandard(new VCFFormatHeaderLine(VCFConstants.GENOTYPE_QUALITY_KEY, 1, VCFHeaderLineType.Integer, "Genotype Quality"));
registerStandard(new VCFFormatHeaderLine(VCFConstants.DEPTH_KEY, 1, VCFHeaderLineType.Integer, "Approximate read depth (reads with MQ=255 or with bad mates are filtered)"));
registerStandard(new VCFFormatHeaderLine(VCFConstants.GENOTYPE_PL_KEY, VCFHeaderLineCount.G, VCFHeaderLineType.Integer, "Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification"));
registerStandard(new VCFFormatHeaderLine(VCFConstants.GENOTYPE_ALLELE_DEPTHS, VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.Integer, "Allelic depths for the ref and alt alleles in the order listed"));
// INFO lines
registerStandard(new VCFInfoHeaderLine(VCFConstants.END_KEY, 1, VCFHeaderLineType.Integer, "Stop position of the interval"));
registerStandard(new VCFInfoHeaderLine(VCFConstants.MLE_ALLELE_COUNT_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Integer, "Maximum likelihood expectation (MLE) for the allele counts (not necessarily the same as the AC), for each ALT allele, in the same order as listed"));
registerStandard(new VCFInfoHeaderLine(VCFConstants.MLE_ALLELE_FREQUENCY_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Float, "Maximum likelihood expectation (MLE) for the allele frequency (not necessarily the same as the AF), for each ALT allele, in the same order as listed"));
registerStandard(new VCFInfoHeaderLine(VCFConstants.DOWNSAMPLED_KEY, 0, VCFHeaderLineType.Flag, "Were any of the samples downsampled?"));
registerStandard(new VCFInfoHeaderLine(VCFConstants.DBSNP_KEY, 0, VCFHeaderLineType.Flag, "dbSNP Membership"));
registerStandard(new VCFInfoHeaderLine(VCFConstants.DEPTH_KEY, 1, VCFHeaderLineType.Integer, "Approximate read depth; some reads may have been filtered"));
registerStandard(new VCFInfoHeaderLine(VCFConstants.STRAND_BIAS_KEY, 1, VCFHeaderLineType.Float, "Strand Bias"));
registerStandard(new VCFInfoHeaderLine(VCFConstants.ALLELE_FREQUENCY_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Float, "Allele Frequency, for each ALT allele, in the same order as listed"));
registerStandard(new VCFInfoHeaderLine(VCFConstants.ALLELE_COUNT_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Integer, "Allele count in genotypes, for each ALT allele, in the same order as listed"));
registerStandard(new VCFInfoHeaderLine(VCFConstants.ALLELE_NUMBER_KEY, 1, VCFHeaderLineType.Integer, "Total number of alleles in called genotypes"));
registerStandard(new VCFInfoHeaderLine(VCFConstants.MAPPING_QUALITY_ZERO_KEY, 1, VCFHeaderLineType.Integer, "Total Mapping Quality Zero Reads"));
registerStandard(new VCFInfoHeaderLine(VCFConstants.RMS_MAPPING_QUALITY_KEY, 1, VCFHeaderLineType.Float, "RMS Mapping Quality"));
registerStandard(new VCFInfoHeaderLine(VCFConstants.SOMATIC_KEY, 0, VCFHeaderLineType.Flag, "Somatic event"));
}
private static class Standards<T extends VCFCompoundHeaderLine> {
private final Map<String, T> standards = new HashMap<String, T>();
@Requires("line != null")
@Ensures({"result != null", "result.getID().equals(line.getID())"})
public T repair(final T line) {
final T standard = get(line.getID(), false);
if ( standard != null ) {
final boolean badCountType = line.getCountType() != standard.getCountType();
final boolean badCount = line.isFixedCount() && ! badCountType && line.getCount() != standard.getCount();
final boolean badType = line.getType() != standard.getType();
final boolean badDesc = ! line.getDescription().equals(standard.getDescription());
final boolean needsRepair = badCountType || badCount || badType || (REPAIR_BAD_DESCRIPTIONS && badDesc);
if ( needsRepair ) {
logger.warn("Repairing standard header line for field " + line.getID() + " because"
+ (badCountType ? " -- count types disagree; header has " + line.getCountType() + " but standard is " + standard.getCountType() : "")
+ (badType ? " -- type disagree; header has " + line.getType() + " but standard is " + standard.getType() : "")
+ (badCount ? " -- counts disagree; header has " + line.getCount() + " but standard is " + standard.getCount() : "")
+ (badDesc ? " -- descriptions disagree; header has '" + line.getDescription() + "' but standard is '" + standard.getDescription() + "'": ""));
return standard;
} else
return line;
} else
return line;
}
@Requires("headerLines != null")
@Ensures({"result != null", "result.isEmpty() || ! throwErrorForMissing", "IDs.containsAll(result)"})
public Set<String> addToHeader(final Set<VCFHeaderLine> headerLines, final Collection<String> IDs, final boolean throwErrorForMissing) {
final Set<String> missing = new HashSet<String>();
for ( final String ID : IDs ) {
final T line = get(ID, throwErrorForMissing);
if ( line == null )
missing.add(ID);
else
headerLines.add(line);
}
return missing;
}
@Requires("line != null")
@Ensures({
"standards.containsKey(line.getID())",
"old(standards.values().size()) > standards.values().size()"})
public void add(final T line) {
if ( standards.containsKey(line.getID()) )
throw new ReviewedStingException("Attempting to add multiple standard header lines for ID " + line.getID());
standards.put(line.getID(), line);
}
@Requires("ID != null")
@Ensures({"result != null || ! throwErrorForMissing"})
public T get(final String ID, final boolean throwErrorForMissing) {
final T x = standards.get(ID);
if ( throwErrorForMissing && x == null )
throw new ReviewedStingException("Couldn't find a standard VCF header line for field " + ID);
return x;
}
}
}

10
public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFUtils.java
View File

@ -247,9 +247,13 @@ public class VCFUtils {
* @param refDict the SAM formatted reference sequence dictionary
*/
public final static VCFHeader withUpdatedContigs(final VCFHeader oldHeader, final File referenceFile, final SAMSequenceDictionary refDict) {
final Set<VCFHeaderLine> lines = new LinkedHashSet<VCFHeaderLine>(oldHeader.getMetaData().size());
return new VCFHeader(withUpdatedContigsAsLines(oldHeader.getMetaData(), referenceFile, refDict), oldHeader.getGenotypeSamples());
}
for ( final VCFHeaderLine line : oldHeader.getMetaData() ) {
public final static Set<VCFHeaderLine> withUpdatedContigsAsLines(final Set<VCFHeaderLine> oldLines, final File referenceFile, final SAMSequenceDictionary refDict) {
final Set<VCFHeaderLine> lines = new LinkedHashSet<VCFHeaderLine>(oldLines.size());
for ( final VCFHeaderLine line : oldLines ) {
if ( line instanceof VCFContigHeaderLine )
continue; // skip old contig lines
if ( line.getKey().equals(VCFHeader.REFERENCE_KEY) )
@ -261,7 +265,7 @@ public class VCFUtils {
lines.add(contigLine);
lines.add(new VCFHeaderLine(VCFHeader.REFERENCE_KEY, "file://" + referenceFile.getAbsolutePath()));
return new VCFHeader(lines, oldHeader.getGenotypeSamples());
return lines;
}
/**

8
public/java/src/org/broadinstitute/sting/utils/variantcontext/Genotype.java
View File

@ -31,7 +31,7 @@ public abstract class Genotype implements Comparable<Genotype> {
VCFConstants.GENOTYPE_QUALITY_KEY,
VCFConstants.DEPTH_KEY,
VCFConstants.GENOTYPE_ALLELE_DEPTHS,
VCFConstants.PHRED_GENOTYPE_LIKELIHOODS_KEY);
VCFConstants.GENOTYPE_PL_KEY);
public final static String PHASED_ALLELE_SEPARATOR = "|";
public final static String UNPHASED_ALLELE_SEPARATOR = "/";
@ -354,7 +354,7 @@ public abstract class Genotype implements Comparable<Genotype> {
toStringIfExists(VCFConstants.GENOTYPE_QUALITY_KEY, getGQ()),
toStringIfExists(VCFConstants.DEPTH_KEY, getDP()),
toStringIfExists(VCFConstants.GENOTYPE_ALLELE_DEPTHS, getAD()),
toStringIfExists(VCFConstants.PHRED_GENOTYPE_LIKELIHOODS_KEY, getPL()),
toStringIfExists(VCFConstants.GENOTYPE_PL_KEY, getPL()),
sortedString(getExtendedAttributes()));
}
@ -502,7 +502,7 @@ public abstract class Genotype implements Comparable<Genotype> {
return getGQ();
} else if (key.equals(VCFConstants.GENOTYPE_ALLELE_DEPTHS)) {
return Arrays.asList(getAD());
} else if (key.equals(VCFConstants.PHRED_GENOTYPE_LIKELIHOODS_KEY)) {
} else if (key.equals(VCFConstants.GENOTYPE_PL_KEY)) {
return Arrays.asList(getPL());
} else if (key.equals(VCFConstants.DEPTH_KEY)) {
return getDP();
@ -518,7 +518,7 @@ public abstract class Genotype implements Comparable<Genotype> {
return hasGQ();
} else if (key.equals(VCFConstants.GENOTYPE_ALLELE_DEPTHS)) {
return hasAD();
} else if (key.equals(VCFConstants.PHRED_GENOTYPE_LIKELIHOODS_KEY)) {
} else if (key.equals(VCFConstants.GENOTYPE_PL_KEY)) {
return hasPL();
} else if (key.equals(VCFConstants.DEPTH_KEY)) {
return hasDP();

6
public/java/src/org/broadinstitute/sting/utils/variantcontext/SlowGenotype.java
View File

@ -51,7 +51,7 @@ public class SlowGenotype extends Genotype {
this.alleles = Collections.unmodifiableList(alleles);
commonInfo = new CommonInfo(sampleName, log10PError, filters, attributes);
if ( log10Likelihoods != null )
commonInfo.putAttribute(VCFConstants.PHRED_GENOTYPE_LIKELIHOODS_KEY, GenotypeLikelihoods.fromLog10Likelihoods(log10Likelihoods));
commonInfo.putAttribute(VCFConstants.GENOTYPE_PL_KEY, GenotypeLikelihoods.fromLog10Likelihoods(log10Likelihoods));
this.isPhased = isPhased;
validate();
}
@ -72,12 +72,12 @@ public class SlowGenotype extends Genotype {
// Useful methods for getting genotype likelihoods for a genotype object, if present
//
@Override public boolean hasLikelihoods() {
return (commonInfo.hasAttribute(VCFConstants.PHRED_GENOTYPE_LIKELIHOODS_KEY) && !commonInfo.getAttribute(VCFConstants.PHRED_GENOTYPE_LIKELIHOODS_KEY).equals(VCFConstants.MISSING_VALUE_v4)) ||
return (commonInfo.hasAttribute(VCFConstants.GENOTYPE_PL_KEY) && !commonInfo.getAttribute(VCFConstants.GENOTYPE_PL_KEY).equals(VCFConstants.MISSING_VALUE_v4)) ||
(commonInfo.hasAttribute(VCFConstants.GENOTYPE_LIKELIHOODS_KEY) && !commonInfo.getAttribute(VCFConstants.GENOTYPE_LIKELIHOODS_KEY).equals(VCFConstants.MISSING_VALUE_v4));
}
@Override public GenotypeLikelihoods getLikelihoods() {
GenotypeLikelihoods x = getLikelihoods(VCFConstants.PHRED_GENOTYPE_LIKELIHOODS_KEY, true);
GenotypeLikelihoods x = getLikelihoods(VCFConstants.GENOTYPE_PL_KEY, true);
if ( x != null )
return x;
else {

2
public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java
View File

@ -1398,7 +1398,7 @@ public class VariantContext implements Feature { // to enable tribble integratio
private final Object decodeValue(final String field, final Object value, final VCFCompoundHeaderLine format) {
if ( value instanceof String ) {
if ( field.equals(VCFConstants.PHRED_GENOTYPE_LIKELIHOODS_KEY) )
if ( field.equals(VCFConstants.GENOTYPE_PL_KEY) )
return GenotypeLikelihoods.fromPLField((String)value);
final String string = (String)value;

17
public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2FieldEncoder.java
View File

@ -394,9 +394,11 @@ public abstract class BCF2FieldEncoder {
} else {
// handle generic case
final List<Double> doubles = toList(Double.class, value);
for ( final double d : doubles ) {
encoder.encodeRawFloat(d);
count++;
for ( final Double d : doubles ) {
if ( d != null ) { // necessary because .,. => [null, null] in VC
encoder.encodeRawFloat(d);
count++;
}
}
}
for ( ; count < minValues; count++ ) encoder.encodeRawMissingValue(type);
@ -424,6 +426,7 @@ public abstract class BCF2FieldEncoder {
return value == null ? BCF2Type.INT8 : BCF2Utils.determineIntegerType((int[])value);
}
@Requires("value == null || ((int[])value).length <= minValues")
@Override
public void encodeValue(final BCF2Encoder encoder, final Object value, final BCF2Type type, final int minValues) throws IOException {
int count = 0;
@ -480,9 +483,11 @@ public abstract class BCF2FieldEncoder {
@Override
public void encodeValue(final BCF2Encoder encoder, final Object value, final BCF2Type type, final int minValues) throws IOException {
int count = 0;
for ( final int i : toList(Integer.class, value) ) {
encoder.encodeRawInt(i, type);
count++;
for ( final Integer i : toList(Integer.class, value) ) {
if ( i != null ) { // necessary because .,. => [null, null] in VC
encoder.encodeRawInt(i, type);
count++;
}
}
for ( ; count < minValues; count++ ) encoder.encodeRawMissingValue(type);
}

2
public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2FieldWriter.java
View File

@ -179,7 +179,7 @@ public abstract class BCF2FieldWriter {
final List<Integer> values = new ArrayList<Integer>(vc.getNSamples());
for ( final Genotype g : vc.getGenotypes() ) {
for ( final Object i : BCF2Utils.toList(g.getExtendedAttribute(getField(), null)) ) {
values.add((Integer)i); // we know they are all integers
if ( i != null ) values.add((Integer)i); // we know they are all integers
}
}

9
public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2Writer.java
View File

@ -85,6 +85,7 @@ import java.util.*;
class BCF2Writer extends IndexingVariantContextWriter {
final protected static Logger logger = Logger.getLogger(BCF2Writer.class);
final private static List<Allele> MISSING_GENOTYPE = Arrays.asList(Allele.NO_CALL, Allele.NO_CALL);
final private static boolean ALLOW_MISSING_CONTIG_LINES = false;
private final OutputStream outputStream; // Note: do not flush until completely done writing, to avoid issues with eventual BGZF support
private VCFHeader header;
@ -112,8 +113,12 @@ class BCF2Writer extends IndexingVariantContextWriter {
public void writeHeader(final VCFHeader header) {
// create the config offsets map
if ( header.getContigLines().isEmpty() ) {
logger.warn("No contig dictionary found in header, falling back to reference sequence dictionary");
createContigDictionary(VCFUtils.makeContigHeaderLines(getRefDict(), null));
if ( ALLOW_MISSING_CONTIG_LINES ) {
logger.warn("No contig dictionary found in header, falling back to reference sequence dictionary");
createContigDictionary(VCFUtils.makeContigHeaderLines(getRefDict(), null));
} else {
throw new UserException.MalformedBCF2("Cannot write BCF2 file with missing contig lines");
}
} else {
createContigDictionary(header.getContigLines());
}

2
public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/IntGenotypeFieldAccessors.java
View File

@ -44,7 +44,7 @@ class IntGenotypeFieldAccessors {
public IntGenotypeFieldAccessors() {
intGenotypeFieldEncoders.put(VCFConstants.DEPTH_KEY, new IntGenotypeFieldAccessors.DPAccessor());
intGenotypeFieldEncoders.put(VCFConstants.GENOTYPE_ALLELE_DEPTHS, new IntGenotypeFieldAccessors.ADAccessor());
intGenotypeFieldEncoders.put(VCFConstants.PHRED_GENOTYPE_LIKELIHOODS_KEY, new IntGenotypeFieldAccessors.PLAccessor());
intGenotypeFieldEncoders.put(VCFConstants.GENOTYPE_PL_KEY, new IntGenotypeFieldAccessors.PLAccessor());
intGenotypeFieldEncoders.put(VCFConstants.GENOTYPE_QUALITY_KEY, new IntGenotypeFieldAccessors.GQAccessor());
}

2
public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/VCFWriter.java
View File

@ -533,7 +533,7 @@ class VCFWriter extends IndexingVariantContextWriter {
if ( sawGoodQual ) keys.add(VCFConstants.GENOTYPE_QUALITY_KEY);
if ( sawDP ) keys.add(VCFConstants.DEPTH_KEY);
if ( sawAD ) keys.add(VCFConstants.GENOTYPE_ALLELE_DEPTHS);
if ( sawPL ) keys.add(VCFConstants.PHRED_GENOTYPE_LIKELIHOODS_KEY);
if ( sawPL ) keys.add(VCFConstants.GENOTYPE_PL_KEY);
if ( sawGenotypeFilter ) keys.add(VCFConstants.GENOTYPE_FILTER_KEY);
List<String> sortedList = ParsingUtils.sortList(new ArrayList<String>(keys));

8
public/java/test/net/sf/picard/reference/FastaSequenceIndexBuilderUnitTest.java
View File

@ -55,7 +55,7 @@ public class FastaSequenceIndexBuilderUnitTest extends BaseTest {
public void unixFileTest() {
logger.warn("Executing unixFileTest");
fastaFile = new File(testDir + "exampleFASTA.fasta");
fastaFile = new File(publicTestDir + "exampleFASTA.fasta");
builder = new FastaSequenceIndexBuilder(fastaFile, false);
FastaSequenceIndex index = builder.createIndex();
controlIndex.add(new FastaSequenceIndexEntry("chr1", 6, 100000, 60, 61,0));
@ -72,7 +72,7 @@ public class FastaSequenceIndexBuilderUnitTest extends BaseTest {
public void windowsFileTest() {
logger.warn("Executing windowsFileTest");
fastaFile = new File(testDir + "exampleFASTA-windows.fasta");
fastaFile = new File(publicTestDir + "exampleFASTA-windows.fasta");
builder = new FastaSequenceIndexBuilder(fastaFile, false);
FastaSequenceIndex index = builder.createIndex();
controlIndex.add(new FastaSequenceIndexEntry("chr2", 7, 29, 7, 9,0));
@ -88,7 +88,7 @@ public class FastaSequenceIndexBuilderUnitTest extends BaseTest {
public void combinedWindowsUnix() {
logger.warn("Executing combinedWindowsUnix");
fastaFile = new File(testDir + "exampleFASTA-combined.fasta");
fastaFile = new File(publicTestDir + "exampleFASTA-combined.fasta");
builder = new FastaSequenceIndexBuilder(fastaFile, false);
FastaSequenceIndex index = builder.createIndex();
controlIndex.add(new FastaSequenceIndexEntry("chr1", 6, 100000, 60, 61,0));
@ -105,7 +105,7 @@ public class FastaSequenceIndexBuilderUnitTest extends BaseTest {
public void threeVariableLengthContigs() {
logger.warn("Executing threeVariableLengthContigs");
fastaFile = new File(testDir + "exampleFASTA-3contigs.fasta");
fastaFile = new File(publicTestDir + "exampleFASTA-3contigs.fasta");
builder = new FastaSequenceIndexBuilder(fastaFile, false);
FastaSequenceIndex index = builder.createIndex();
controlIndex.add(new FastaSequenceIndexEntry("chr1", 6, 17, 5, 6,0));

11
public/java/test/org/broadinstitute/sting/BaseTest.java
View File

@ -87,10 +87,13 @@ public abstract class BaseTest {
private static final String networkTempDir;
private static final File networkTempDirFile;
protected static final String testDirRelative = "public/testdata/";
public static final File testDirFile = new File(testDirRelative);
public static final String testDir = testDirFile.getAbsolutePath() + "/";
protected static final String testDirRoot = testDir.replace(testDirRelative, "");
private static final String privateTestDirRelative = "private/testdata/";
public static final String privateTestDir = new File(privateTestDirRelative).getAbsolutePath() + "/";
protected static final String privateTestDirRoot = privateTestDir.replace(privateTestDirRelative, "");
private static final String publicTestDirRelative = "public/testdata/";
public static final String publicTestDir = new File(publicTestDirRelative).getAbsolutePath() + "/";
protected static final String publicTestDirRoot = publicTestDir.replace(publicTestDirRelative, "");
public static final String keysDataLocation = validationDataLocation + "keys/";
public static final String gatkKeyFile = CryptUtils.GATK_USER_KEY_DIRECTORY + "gsamembers_broadinstitute.org.key";

2
public/java/test/org/broadinstitute/sting/WalkerTest.java
View File

@ -356,7 +356,7 @@ public class WalkerTest extends BaseTest {
System.out.println(String.format("[%s] Executing test %s with GATK arguments: %s", now, name, cmdline));
// also write the command line to the HTML log for convenient follow-up
// do the replaceAll so paths become relative to the current
BaseTest.log(cmdline.replaceAll(testDirRoot, ""));
BaseTest.log(cmdline.replaceAll(publicTestDirRoot, "").replaceAll(privateTestDirRoot, ""));
CommandLineExecutable.start(instance, command);
} catch (Exception e) {
gotAnException = true;

4
public/java/test/org/broadinstitute/sting/commandline/ParsingEngineUnitTest.java
View File

@ -844,8 +844,8 @@ public class ParsingEngineUnitTest extends BaseTest {
Assert.assertEquals(argProvider.bindings.get(1).getName(), "foo2", "Name isn't set properly");
}
private final static String HISEQ_VCF = testDir + "HiSeq.10000.vcf";
private final static String TRANCHES_FILE = testDir + "tranches.6.txt";
private final static String HISEQ_VCF = privateTestDir + "HiSeq.10000.vcf";
private final static String TRANCHES_FILE = privateTestDir + "tranches.6.txt";
@Test
public void variantContextBindingTestDynamicTyping1() {

4
public/java/test/org/broadinstitute/sting/gatk/datasources/providers/ReferenceOrderedViewUnitTest.java
View File

@ -79,7 +79,7 @@ public class ReferenceOrderedViewUnitTest extends BaseTest {
*/
@Test
public void testSingleBinding() {
String fileName = testDir + "TabularDataTest.dat";
String fileName = privateTestDir + "TabularDataTest.dat";
RMDTriplet triplet = new RMDTriplet("tableTest","Table",fileName,RMDStorageType.FILE,new Tags());
ReferenceOrderedDataSource dataSource = new ReferenceOrderedDataSource(triplet,builder,seq.getSequenceDictionary(),genomeLocParser,false);
@ -101,7 +101,7 @@ public class ReferenceOrderedViewUnitTest extends BaseTest {
*/
@Test
public void testMultipleBinding() {
File file = new File(testDir + "TabularDataTest.dat");
File file = new File(privateTestDir + "TabularDataTest.dat");
RMDTriplet testTriplet1 = new RMDTriplet("tableTest1","Table",file.getAbsolutePath(),RMDStorageType.FILE,new Tags());
ReferenceOrderedDataSource dataSource1 = new ReferenceOrderedDataSource(testTriplet1,builder,seq.getSequenceDictionary(),genomeLocParser,false);

4
public/java/test/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndexUnitTest.java
View File

@ -94,13 +94,13 @@ public class GATKBAMIndexUnitTest extends BaseTest {
@Test( expectedExceptions = UserException.MalformedFile.class )
public void testDetectTruncatedBamIndexWordBoundary() {
GATKBAMIndex index = new GATKBAMIndex(new File(testDir + "truncated_at_word_boundary.bai"));
GATKBAMIndex index = new GATKBAMIndex(new File(privateTestDir + "truncated_at_word_boundary.bai"));
index.readReferenceSequence(0);
}
@Test( expectedExceptions = UserException.MalformedFile.class )
public void testDetectTruncatedBamIndexNonWordBoundary() {
GATKBAMIndex index = new GATKBAMIndex(new File(testDir + "truncated_at_non_word_boundary.bai"));
GATKBAMIndex index = new GATKBAMIndex(new File(privateTestDir + "truncated_at_non_word_boundary.bai"));
index.readReferenceSequence(0);
}

4
public/java/test/org/broadinstitute/sting/gatk/datasources/rmd/ReferenceOrderedDataPoolUnitTest.java
View File

@ -68,10 +68,10 @@ public class ReferenceOrderedDataPoolUnitTest extends BaseTest {
@BeforeMethod
public void setUp() {
String fileName = testDir + "TabularDataTest.dat";
String fileName = privateTestDir + "TabularDataTest.dat";
// check to see if we have an index, if so, delete it
File indexFileName = new File(testDir + "TabularDataTest.dat.idx");
File indexFileName = new File(privateTestDir + "TabularDataTest.dat.idx");
if (indexFileName.exists()) indexFileName.delete();
triplet = new RMDTriplet("tableTest","Table",fileName,RMDStorageType.FILE,new Tags());

2
public/java/test/org/broadinstitute/sting/gatk/datasources/rmd/ReferenceOrderedQueryDataPoolUnitTest.java
View File

@ -43,7 +43,7 @@ public class ReferenceOrderedQueryDataPoolUnitTest extends BaseTest{
@Test
public void testCloseFilePointers() throws IOException {
// Build up query parameters
File file = new File(BaseTest.testDir + "NA12878.hg19.example1.vcf");
File file = new File(BaseTest.privateTestDir + "NA12878.hg19.example1.vcf");
RMDTriplet triplet = new RMDTriplet("test", "VCF", file.getAbsolutePath(), RMDTriplet.RMDStorageType.FILE, new Tags());
IndexedFastaSequenceFile seq = new CachingIndexedFastaSequenceFile(new File(BaseTest.hg19Reference));
GenomeLocParser parser = new GenomeLocParser(seq);

5
public/java/test/org/broadinstitute/sting/gatk/filters/ReadGroupBlackListFilterUnitTest.java
View File

@ -4,7 +4,6 @@ import org.testng.Assert;
import org.broadinstitute.sting.BaseTest;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
@ -188,7 +187,7 @@ public class ReadGroupBlackListFilterUnitTest extends BaseTest {
}
List<String> filterList = new ArrayList<String>();
filterList.add(testDir + "readgroupblacklisttest.txt");
filterList.add(privateTestDir + "readgroupblacklisttest.txt");
ReadGroupBlackListFilter filter = new ReadGroupBlackListFilter(filterList);
int filtered = 0;
@ -227,7 +226,7 @@ public class ReadGroupBlackListFilterUnitTest extends BaseTest {
}
List<String> filterList = new ArrayList<String>();
filterList.add(testDir + "readgroupblacklisttestlist.txt");
filterList.add(privateTestDir + "readgroupblacklisttestlist.txt");
ReadGroupBlackListFilter filter = new ReadGroupBlackListFilter(filterList);
int filtered = 0;

10
public/java/test/org/broadinstitute/sting/gatk/refdata/tracks/FeatureManagerUnitTest.java
View File

@ -52,11 +52,11 @@ import java.util.*;
* UnitTests for RMD FeatureManager
*/
public class FeatureManagerUnitTest extends BaseTest {
private static final File RANDOM_FILE = new File(testDir + "exampleGATKReport.eval");
private static final File VCF3_FILE = new File(testDir + "vcf3.vcf");
private static final File VCF4_FILE = new File(testDir + "HiSeq.10000.vcf");
private static final File VCF4_FILE_GZ = new File(testDir + "HiSeq.10000.vcf.gz");
private static final File VCF4_FILE_BGZIP = new File(testDir + "HiSeq.10000.bgzip.vcf.gz");
private static final File RANDOM_FILE = new File(publicTestDir+ "exampleGATKReport.eval");
private static final File VCF3_FILE = new File(privateTestDir + "vcf3.vcf");
private static final File VCF4_FILE = new File(privateTestDir + "HiSeq.10000.vcf");
private static final File VCF4_FILE_GZ = new File(privateTestDir + "HiSeq.10000.vcf.gz");
private static final File VCF4_FILE_BGZIP = new File(privateTestDir + "HiSeq.10000.bgzip.vcf.gz");
private FeatureManager manager;
private GenomeLocParser genomeLocParser;

2
public/java/test/org/broadinstitute/sting/gatk/refdata/utils/FeatureToGATKFeatureIteratorUnitTest.java
View File

@ -44,7 +44,7 @@ public class FeatureToGATKFeatureIteratorUnitTest extends BaseTest {
final String chr = "20";
IndexedFastaSequenceFile seq = new CachingIndexedFastaSequenceFile(new File(BaseTest.hg19Reference));
GenomeLocParser parser = new GenomeLocParser(seq);
File file = new File(testDir + "NA12878.hg19.example1.vcf");
File file = new File(privateTestDir + "NA12878.hg19.example1.vcf");
VCFCodec codec = new VCFCodec();
TestFeatureReader reader = new TestFeatureReader(file.getAbsolutePath(), codec);
CheckableCloseableTribbleIterator<Feature> tribbleIterator = reader.query(chr, 1, 100000);

2
public/java/test/org/broadinstitute/sting/gatk/report/GATKReportUnitTest.java
View File

@ -36,7 +36,7 @@ import java.io.PrintStream;
public class GATKReportUnitTest extends BaseTest {
@Test
public void testParse() throws Exception {
String reportPath = testDir + "exampleGATKReportv2.tbl";
String reportPath = publicTestDir + "exampleGATKReportv2.tbl";
GATKReport report = new GATKReport(reportPath);
Assert.assertEquals(report.getVersion(), GATKReportVersion.V1_1);
Assert.assertEquals(report.getTables().size(), 5);

2
public/java/test/org/broadinstitute/sting/gatk/samples/SampleDBUnitTest.java
View File

@ -20,7 +20,7 @@ import java.util.*;
public class SampleDBUnitTest extends BaseTest {
private static SampleDBBuilder builder;
// all the test sample files are located here
private File testPED = new File(testDir + "ceutrio.ped");
private File testPED = new File(privateTestDir + "ceutrio.ped");
private static final Set<Sample> testPEDSamples = new HashSet<Sample>(Arrays.asList(
new Sample("kid", "fam1", "dad", "mom", Gender.MALE, Affection.AFFECTED),

2
public/java/test/org/broadinstitute/sting/gatk/walkers/CNV/SymbolicAllelesIntegrationTest.java
View File

@ -10,7 +10,7 @@ public class SymbolicAllelesIntegrationTest extends WalkerTest {
public static String baseTestString(String reference, String VCF) {
return "-T CombineVariants" +
" -R " + reference +
" --variant:vcf " + testDir + VCF +
" --variant:vcf " + privateTestDir + VCF +
" -filteredRecordsMergeType KEEP_IF_ANY_UNFILTERED" +
" -genotypeMergeOptions REQUIRE_UNIQUE" +
" -setKey null" +

8
public/java/test/org/broadinstitute/sting/gatk/walkers/ClipReadsWalkersIntegrationTest.java
View File

@ -36,7 +36,7 @@ public class ClipReadsWalkersIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
"-R " + hg18Reference +
" -T ClipReads " +
"-I " + testDir + "clippingReadsTest.withRG.bam " +
"-I " + privateTestDir + "clippingReadsTest.withRG.bam " +
"-os %s " +
"-o %s " + args,
2, // just one output file
@ -55,9 +55,9 @@ public class ClipReadsWalkersIntegrationTest extends WalkerTest {
@Test public void testClipRange2() { testClipper("clipRange2", "-CT 1-5,11-15", "be4fcad5b666a5540028b774169cbad7", "3061cf742f9e5526a61130128ae761a3"); }
@Test public void testClipSeq() { testClipper("clipSeqX", "-X CCCCC", "db199bd06561c9f2122f6ffb07941fbc", "b89459f373e40f0b835c1faff2208839"); }
@Test public void testClipSeqFile() { testClipper("clipSeqXF", "-XF " + testDir + "seqsToClip.fasta", "d011a3152b31822475afbe0281491f8d", "24e19116ef16a37a6d095ed5c22c2466"); }
@Test public void testClipSeqFile() { testClipper("clipSeqXF", "-XF " + privateTestDir + "seqsToClip.fasta", "d011a3152b31822475afbe0281491f8d", "24e19116ef16a37a6d095ed5c22c2466"); }
@Test public void testClipMulti() { testClipper("clipSeqMulti", "-QT 10 -CT 1-5 -XF " + testDir + "seqsToClip.fasta -X CCCCC", "a23187bd9bfb06557f799706d98441de", "ad8d30300cb43d5e300fcc4d2450da8e"); }
@Test public void testClipMulti() { testClipper("clipSeqMulti", "-QT 10 -CT 1-5 -XF " + privateTestDir + "seqsToClip.fasta -X CCCCC", "a23187bd9bfb06557f799706d98441de", "ad8d30300cb43d5e300fcc4d2450da8e"); }
@Test public void testClipNs() { testClipper("testClipNs", "-QT 10 -CR WRITE_NS", Q10ClipOutput, "57c05b6241db7110148a91fde2d431d0"); }
@Test public void testClipQ0s() { testClipper("testClipQs", "-QT 10 -CR WRITE_Q0S", Q10ClipOutput, "2a1a3153e0942ab355fd8a6e082b30e0"); }
@ -68,7 +68,7 @@ public class ClipReadsWalkersIntegrationTest extends WalkerTest {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-R " + hg18Reference +
" -T ClipReads" +
" -I " + testDir + "originalQuals.chr1.1-1K.bam" +
" -I " + privateTestDir + "originalQuals.chr1.1-1K.bam" +
" -L chr1:1-1,000" +
" -OQ -QT 4 -CR WRITE_Q0S" +
" -o %s -os %s",

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

@ -47,7 +47,7 @@ public class PrintReadsIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
"-T PrintReads" +
" -R " + params.reference +
" -I " + testDir + params.bam +
" -I " + privateTestDir + params.bam +
params.args +
" -o %s",
Arrays.asList(params.md5));

50
public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java
View File

@ -15,7 +15,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
@Test
public void testHasAnnotsNotAsking1() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " --variant " + testDir + "vcfexample2.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
baseTestString() + " --variant " + privateTestDir + "vcfexample2.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
Arrays.asList("bd6848e7dbf2f809ee2f690ee2cf8ef4"));
executeTest("test file has annotations, not asking for annotations, #1", spec);
}
@ -23,15 +23,15 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
@Test
public void testHasAnnotsNotAsking2() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " --variant " + testDir + "vcfexample3.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1,
Arrays.asList("9914bd19f6235c550e5182e0f4591da6"));
baseTestString() + " --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("d6f749f8dbeb2d42c9effaff9fe571d7"));
executeTest("test file has annotations, not asking for annotations, #2", spec);
}
@Test
public void testHasAnnotsAsking1() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -G Standard --variant " + testDir + "vcfexample2.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
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("9084e6c7b1cec0f3a2c6d96711844d5e"));
executeTest("test file has annotations, asking for annotations, #1", spec);
}
@ -39,15 +39,15 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
@Test
public void testHasAnnotsAsking2() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -G Standard --variant " + testDir + "vcfexample3.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1,
Arrays.asList("74d894fd31b449deffca88d0e465f01b"));
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("3dfabdcaa2648ac34380fb71860c42d3"));
executeTest("test file has annotations, asking for annotations, #2", spec);
}
@Test
public void testNoAnnotsNotAsking1() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " --variant " + testDir + "vcfexample2empty.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
baseTestString() + " --variant " + privateTestDir + "vcfexample2empty.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
Arrays.asList("b85c1ea28194484b327fbe0add1b5685"));
executeTest("test file doesn't have annotations, not asking for annotations, #1", spec);
}
@ -57,7 +57,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
// the genotype annotations in this file are actually out of order. If you don't parse the genotypes
// they don't get reordered. It's a good test of the genotype ordering system.
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " --variant " + testDir + "vcfexample3empty.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1,
baseTestString() + " --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("fe4d4e2484c4cf8b1cd50ad42cfe468e"));
executeTest("test file doesn't have annotations, not asking for annotations, #2", spec);
}
@ -65,7 +65,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
@Test
public void testNoAnnotsAsking1() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -G Standard --variant " + testDir + "vcfexample2empty.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
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("043fc6205b0633edcd3fadc9e044800c"));
executeTest("test file doesn't have annotations, asking for annotations, #1", spec);
}
@ -73,7 +73,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
@Test
public void testNoAnnotsAsking2() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -G Standard --variant " + testDir + "vcfexample3empty.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1,
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("6fafb42d374a67ba4687a23078a126af"));
executeTest("test file doesn't have annotations, asking for annotations, #2", spec);
}
@ -81,7 +81,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
@Test
public void testExcludeAnnotations() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -G Standard -XA FisherStrand -XA ReadPosRankSumTest --variant " + testDir + "vcfexample2empty.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
baseTestString() + " -G Standard -XA FisherStrand -XA ReadPosRankSumTest --variant " + privateTestDir + "vcfexample2empty.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
Arrays.asList("639462a0e0fa79e33def5f011fe55961"));
executeTest("test exclude annotations", spec);
}
@ -89,7 +89,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
@Test
public void testOverwritingHeader() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -G Standard --variant " + testDir + "vcfexample4.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,001,292", 1,
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("ebbf32f5b8b8d22f2eb247a0a3db3da0"));
executeTest("test overwriting header", spec);
}
@ -97,7 +97,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
@Test
public void testNoReads() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -G Standard --variant " + testDir + "vcfexample3empty.vcf -L " + testDir + "vcfexample3empty.vcf", 1,
baseTestString() + " -G Standard --variant " + privateTestDir + "vcfexample3empty.vcf -L " + privateTestDir + "vcfexample3empty.vcf", 1,
Arrays.asList("afe6c9d3b4b80635a541cdfcfa48db2f"));
executeTest("not passing it any reads", spec);
}
@ -105,7 +105,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
@Test
public void testDBTagWithDbsnp() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " --dbsnp " + b36dbSNP129 + " -G Standard --variant " + testDir + "vcfexample3empty.vcf -L " + testDir + "vcfexample3empty.vcf", 1,
baseTestString() + " --dbsnp " + b36dbSNP129 + " -G Standard --variant " + privateTestDir + "vcfexample3empty.vcf -L " + privateTestDir + "vcfexample3empty.vcf", 1,
Arrays.asList("21d696ea8c55d2fd4cbb4dcd5f7f7db6"));
executeTest("getting DB tag with dbSNP", spec);
}
@ -113,7 +113,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
@Test
public void testMultipleIdsWithDbsnp() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " --alwaysAppendDbsnpId --dbsnp " + b36dbSNP129 + " -G Standard --variant " + testDir + "vcfexample3withIDs.vcf -L " + testDir + "vcfexample3withIDs.vcf", 1,
baseTestString() + " --alwaysAppendDbsnpId --dbsnp " + b36dbSNP129 + " -G Standard --variant " + privateTestDir + "vcfexample3withIDs.vcf -L " + privateTestDir + "vcfexample3withIDs.vcf", 1,
Arrays.asList("ef95394c14d5c16682a322f3dfb9000c"));
executeTest("adding multiple IDs with dbSNP", spec);
}
@ -121,7 +121,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
@Test
public void testDBTagWithHapMap() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " --comp:H3 " + testDir + "fakeHM3.vcf -G Standard --variant " + testDir + "vcfexample3empty.vcf -L " + testDir + "vcfexample3empty.vcf", 1,
baseTestString() + " --comp:H3 " + privateTestDir + "fakeHM3.vcf -G Standard --variant " + privateTestDir + "vcfexample3empty.vcf -L " + privateTestDir + "vcfexample3empty.vcf", 1,
Arrays.asList("e6e276b7d517d57626c8409589cd286f"));
executeTest("getting DB tag with HM3", spec);
}
@ -129,7 +129,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
@Test
public void testNoQuals() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " --variant " + testDir + "noQual.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L " + testDir + "noQual.vcf -A QualByDepth", 1,
baseTestString() + " --variant " + privateTestDir + "noQual.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L " + privateTestDir + "noQual.vcf -A QualByDepth", 1,
Arrays.asList("a99e8315571ed1b6bce942451b3d8612"));
executeTest("test file doesn't have QUALs", spec);
}
@ -137,7 +137,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
@Test
public void testUsingExpression() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " --resource:foo " + testDir + "targetAnnotations.vcf -G Standard --variant " + testDir + "vcfexample3empty.vcf -E foo.AF -L " + testDir + "vcfexample3empty.vcf", 1,
baseTestString() + " --resource:foo " + privateTestDir + "targetAnnotations.vcf -G Standard --variant " + privateTestDir + "vcfexample3empty.vcf -E foo.AF -L " + privateTestDir + "vcfexample3empty.vcf", 1,
Arrays.asList("7d6ea3b54210620cbc7e14dad8836bcb"));
executeTest("using expression", spec);
}
@ -145,7 +145,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
@Test
public void testUsingExpressionWithID() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " --resource:foo " + testDir + "targetAnnotations.vcf -G Standard --variant " + testDir + "vcfexample3empty.vcf -E foo.ID -L " + testDir + "vcfexample3empty.vcf", 1,
baseTestString() + " --resource:foo " + privateTestDir + "targetAnnotations.vcf -G Standard --variant " + privateTestDir + "vcfexample3empty.vcf -E foo.ID -L " + privateTestDir + "vcfexample3empty.vcf", 1,
Arrays.asList("35ce4fb0288dfc5c01ec6ce8b14c6157"));
executeTest("using expression with ID", spec);
}
@ -189,8 +189,8 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
public void testTDTAnnotation() {
final String MD5 = "81f85f0ce8cc36df7c717c478e100ba1";
WalkerTestSpec spec = new WalkerTestSpec(
"-T VariantAnnotator -R " + b37KGReference + " -A TransmissionDisequilibriumTest --variant:vcf " + testDir + "ug.random50000.subset300bp.chr1.family.vcf" +
" -L " + testDir + "ug.random50000.subset300bp.chr1.family.vcf --no_cmdline_in_header -ped " + testDir + "ug.random50000.family.ped -o %s", 1,
"-T VariantAnnotator -R " + b37KGReference + " -A TransmissionDisequilibriumTest --variant:vcf " + privateTestDir + "ug.random50000.subset300bp.chr1.family.vcf" +
" -L " + privateTestDir + "ug.random50000.subset300bp.chr1.family.vcf --no_cmdline_in_header -ped " + privateTestDir + "ug.random50000.family.ped -o %s", 1,
Arrays.asList(MD5));
executeTest("Testing TDT annotation ", spec);
}
@ -200,8 +200,8 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
public void testChromosomeCountsPed() {
final String MD5 = "9830fe2247651377e68ad0b0894e9a4e";
WalkerTestSpec spec = new WalkerTestSpec(
"-T VariantAnnotator -R " + b37KGReference + " -A ChromosomeCounts --variant:vcf " + testDir + "ug.random50000.subset300bp.chr1.family.vcf" +
" -L " + testDir + "ug.random50000.subset300bp.chr1.family.vcf --no_cmdline_in_header -ped " + testDir + "ug.random50000.family.ped -o %s", 1,
"-T VariantAnnotator -R " + b37KGReference + " -A ChromosomeCounts --variant:vcf " + privateTestDir + "ug.random50000.subset300bp.chr1.family.vcf" +
" -L " + privateTestDir + "ug.random50000.subset300bp.chr1.family.vcf --no_cmdline_in_header -ped " + privateTestDir + "ug.random50000.family.ped -o %s", 1,
Arrays.asList(MD5));
executeTest("Testing ChromosomeCounts annotation with PED file", spec);
}
@ -210,8 +210,8 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
public void testInbreedingCoeffPed() {
final String MD5 = "e94d589b5691e3ecfd9cc9475a384890";
WalkerTestSpec spec = new WalkerTestSpec(
"-T VariantAnnotator -R " + b37KGReference + " -A InbreedingCoeff --variant:vcf " + testDir + "ug.random50000.subset300bp.chr1.family.vcf" +
" -L " + testDir + "ug.random50000.subset300bp.chr1.family.vcf --no_cmdline_in_header -ped " + testDir + "ug.random50000.family.ped -o %s", 1,
"-T VariantAnnotator -R " + b37KGReference + " -A InbreedingCoeff --variant:vcf " + privateTestDir + "ug.random50000.subset300bp.chr1.family.vcf" +
" -L " + privateTestDir + "ug.random50000.subset300bp.chr1.family.vcf --no_cmdline_in_header -ped " + privateTestDir + "ug.random50000.family.ped -o %s", 1,
Arrays.asList(MD5));
executeTest("Testing InbreedingCoeff annotation with PED file", spec);
}

2
public/java/test/org/broadinstitute/sting/gatk/walkers/beagle/BeagleIntegrationTest.java
View File

@ -32,7 +32,7 @@ import java.util.Arrays;
public class BeagleIntegrationTest extends WalkerTest {
private static final String beagleValidationDataLocation = testDir + "/Beagle/";
private static final String beagleValidationDataLocation = privateTestDir + "/Beagle/";
@Test
public void testBeagleOutput() {
WalkerTestSpec spec = new WalkerTestSpec(

8
public/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjectsIntegrationTest.java
View File

@ -52,10 +52,10 @@ public class DiffObjectsIntegrationTest extends WalkerTest {
@DataProvider(name = "data")
public Object[][] createData() {
new TestParams(testDir + "diffTestMaster.vcf", testDir + "diffTestTest.vcf", true, "bf7ef17436a7eccf27be41a9477904f6");
new TestParams(testDir + "exampleBAM.bam", testDir + "exampleBAM.simple.bam", true, "3f46f5a964f7c34015d972256fe49a35");
new TestParams(testDir + "diffTestMaster.vcf", testDir + "diffTestTest.vcf", false, "8ab29169cff232e670db9a4c54fc4358");
new TestParams(testDir + "exampleBAM.bam", testDir + "exampleBAM.simple.bam", false, "47bf16c27c9e2c657a7e1d13f20880c9");
new TestParams(privateTestDir + "diffTestMaster.vcf", privateTestDir + "diffTestTest.vcf", true, "aea3d5df32a2acd400da48d06b4dbc60");
new TestParams(publicTestDir + "exampleBAM.bam", publicTestDir + "exampleBAM.simple.bam", true, "3f46f5a964f7c34015d972256fe49a35");
new TestParams(privateTestDir + "diffTestMaster.vcf", privateTestDir + "diffTestTest.vcf", false, "e71e23e7ebfbe768e59527bc62f8918d");
new TestParams(publicTestDir + "exampleBAM.bam", publicTestDir + "exampleBAM.simple.bam", false, "47bf16c27c9e2c657a7e1d13f20880c9");
return TestParams.getTests(TestParams.class);
}

8
public/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffableReaderUnitTest.java
View File

@ -29,8 +29,8 @@ package org.broadinstitute.sting.gatk.walkers.diffengine;
// the imports for unit testing.
import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.BaseTest;
import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
import org.broadinstitute.sting.utils.variantcontext.Allele;
import org.testng.Assert;
import org.testng.annotations.BeforeClass;
@ -45,8 +45,8 @@ import java.util.*;
public class DiffableReaderUnitTest extends BaseTest {
DiffEngine engine;
File vcfFile = new File(testDir + "diffTestMaster.vcf");
File bamFile = new File(testDir + "exampleBAM.bam");
File vcfFile = new File(privateTestDir + "diffTestMaster.vcf");
File bamFile = new File(publicTestDir + "exampleBAM.bam");
@BeforeClass(enabled = true)
public void createDiffEngine() {
@ -97,7 +97,7 @@ public class DiffableReaderUnitTest extends BaseTest {
testLeaf(rec1, "REF", Allele.create("G", true));
testLeaf(rec1, "ALT", Arrays.asList(Allele.create("A")));
testLeaf(rec1, "QUAL", 0.15);
testLeaf(rec1, "FILTER", Collections.<Object>emptySet());
testLeaf(rec1, "FILTER", VCFConstants.PASSES_FILTERS_v4);
testLeaf(rec1, "AC", "2");
testLeaf(rec1, "AF", "1.00");
testLeaf(rec1, "AN", "2");

22
public/java/test/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationIntegrationTest.java
View File

@ -15,7 +15,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
@Test
public void testNoAction() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " --variant " + testDir + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
baseTestString() + " --variant " + privateTestDir + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
Arrays.asList("49471b44ac165929d3ff81f98ce19063"));
executeTest("test no action", spec);
}
@ -23,7 +23,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
@Test
public void testClusteredSnps() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -window 10 --variant " + testDir + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
baseTestString() + " -window 10 --variant " + privateTestDir + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
Arrays.asList("8b45895d7ae1f36b70e7fd26aa9451d3"));
executeTest("test clustered SNPs", spec);
}
@ -31,7 +31,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
@Test
public void testMask1() {
WalkerTestSpec spec1 = new WalkerTestSpec(
baseTestString() + " -maskName foo --mask " + testDir + "vcfexample2.vcf --variant " + testDir + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
baseTestString() + " -maskName foo --mask " + privateTestDir + "vcfexample2.vcf --variant " + privateTestDir + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
Arrays.asList("06307029f5da87ae4edd9804063a98f9"));
executeTest("test mask all", spec1);
}
@ -39,7 +39,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
@Test
public void testMask2() {
WalkerTestSpec spec2 = new WalkerTestSpec(
baseTestString() + " -maskName foo --mask:VCF " + testDir + "vcfMask.vcf --variant " + testDir + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
baseTestString() + " -maskName foo --mask:VCF " + privateTestDir + "vcfMask.vcf --variant " + privateTestDir + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
Arrays.asList("1fd06f6b2642685093ed36342f002b58"));
executeTest("test mask some", spec2);
}
@ -47,7 +47,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
@Test
public void testMask3() {
WalkerTestSpec spec3 = new WalkerTestSpec(
baseTestString() + " -maskName foo -maskExtend 10 --mask:VCF " + testDir + "vcfMask.vcf --variant " + testDir + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
baseTestString() + " -maskName foo -maskExtend 10 --mask:VCF " + privateTestDir + "vcfMask.vcf --variant " + privateTestDir + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
Arrays.asList("d8c5206d5d13477a5929fb1ae5a6bfc4"));
executeTest("test mask extend", spec3);
}
@ -55,7 +55,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
@Test
public void testFilter1() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -filter 'DoC < 20 || FisherStrand > 20.0' -filterName foo --variant " + testDir + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
baseTestString() + " -filter 'DoC < 20 || FisherStrand > 20.0' -filterName foo --variant " + privateTestDir + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
Arrays.asList("a3be095e8aa75d9ef4235b9487527307"));
executeTest("test filter #1", spec);
}
@ -63,7 +63,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
@Test
public void testFilter2() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -filter 'AlleleBalance < 70.0 && FisherStrand == 1.4' -filterName bar --variant " + testDir + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
baseTestString() + " -filter 'AlleleBalance < 70.0 && FisherStrand == 1.4' -filterName bar --variant " + privateTestDir + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
Arrays.asList("bd1361ddc52d73b8cd7adeb9e5c47200"));
executeTest("test filter #2", spec);
}
@ -71,7 +71,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
@Test
public void testFilterWithSeparateNames() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " --filterName ABF -filter 'AlleleBalance < 0.7' --filterName FSF -filter 'FisherStrand == 1.4' --variant " + testDir + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
baseTestString() + " --filterName ABF -filter 'AlleleBalance < 0.7' --filterName FSF -filter 'FisherStrand == 1.4' --variant " + privateTestDir + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
Arrays.asList("4a43ec0285433df426ab482f88cf7ca6"));
executeTest("test filter with separate names #2", spec);
}
@ -79,7 +79,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
@Test
public void testGenotypeFilters1() {
WalkerTestSpec spec1 = new WalkerTestSpec(
baseTestString() + " -G_filter 'GQ == 0.60' -G_filterName foo --variant " + testDir + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
baseTestString() + " -G_filter 'GQ == 0.60' -G_filterName foo --variant " + privateTestDir + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
Arrays.asList("5ee4485a022e163645c08b9691384f67"));
executeTest("test genotype filter #1", spec1);
}
@ -87,7 +87,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
@Test
public void testGenotypeFilters2() {
WalkerTestSpec spec2 = new WalkerTestSpec(
baseTestString() + " -G_filter 'AF == 0.04 && isHomVar == 1' -G_filterName foo --variant " + testDir + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
baseTestString() + " -G_filter 'AF == 0.04 && isHomVar == 1' -G_filterName foo --variant " + privateTestDir + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
Arrays.asList("d0a068c8cfb0758d2a8d471383f39b68"));
executeTest("test genotype filter #2", spec2);
}
@ -95,7 +95,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
@Test
public void testDeletions() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " --filterExpression 'QUAL < 100' --filterName foo --variant:VCF " + testDir + "twoDeletions.vcf", 1,
baseTestString() + " --filterExpression 'QUAL < 100' --filterName foo --variant:VCF " + privateTestDir + "twoDeletions.vcf", 1,
Arrays.asList("a1c02a5a90f1262e9eb3d2cad1fd08f2"));
executeTest("test deletions", spec);
}

79
public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
View File

@ -8,7 +8,6 @@ import org.testng.annotations.Test;
import java.io.File;
import java.util.Arrays;
import java.util.List;
import java.util.Map;
// ********************************************************************************** //
// Note that this class also serves as an integration test for the VariantAnnotator! //
@ -29,23 +28,23 @@ 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("a4c520b56f85513423c1c0204cabb5e1"));
Arrays.asList("f98c38defc8d619609399b4a3ba874e8"));
executeTest("test MultiSample Pilot1", spec);
}
@Test
public void testWithAllelesPassedIn1() {
WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
baseCommand + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + testDir + "allelesForUG.vcf -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,025,000", 1,
Arrays.asList("26ec9db9c7ad4b9a2ef25a8b1cb0d45c"));
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("6f0c49b76225e2099c74015b6f79c96d"));
executeTest("test MultiSample Pilot2 with alleles passed in", spec1);
}
@Test
public void testWithAllelesPassedIn2() {
WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
baseCommand + " --output_mode EMIT_ALL_SITES --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + testDir + "allelesForUG.vcf -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,025,000", 1,
Arrays.asList("f2624782525929384d9f2c59f3c65529"));
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("42c4e37e0f130dc796231003638a197c"));
executeTest("test MultiSample Pilot2 with alleles passed in and emitting all sites", spec2);
}
@ -53,23 +52,23 @@ 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("a71d4abbad9c31e66aeb21b1fe2cfe9a"));
Arrays.asList("736607ee529b5624a3ab5521ab9e1b35"));
executeTest("test SingleSample Pilot2", spec);
}
@Test
public void testMultipleSNPAlleles() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T UnifiedGenotyper -R " + b37KGReference + " -nosl --no_cmdline_in_header -glm BOTH --dbsnp " + b37dbSNP129 + " -I " + testDir + "multiallelic.snps.bam -o %s -L " + testDir + "multiallelic.snps.intervals", 1,
Arrays.asList("2429c0f24da57ab1a1313e807e53e48e"));
"-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("f33507add5d5c30448948906467dd3f3"));
executeTest("test Multiple SNP alleles", spec);
}
@Test
public void testBadRead() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T UnifiedGenotyper -R " + b37KGReference + " -nosl --no_cmdline_in_header -glm BOTH -I " + testDir + "badRead.test.bam -o %s -L 1:22753424-22753464", 1,
Arrays.asList("995c8f57d1f211e004ce81d356a80d16"));
"-T UnifiedGenotyper -R " + b37KGReference + " -nosl --no_cmdline_in_header -glm BOTH -I " + privateTestDir + "badRead.test.bam -o %s -L 1:22753424-22753464", 1,
Arrays.asList("d915535c1458733f09f82670092fcab6"));
executeTest("test bad read", spec);
}
@ -77,7 +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("53f60fe15ebffdf85183426b93d48b10"));
Arrays.asList("0d724551e00129730b95fd4d70faaa58"));
executeTest("test reverse trim", spec);
}
@ -87,7 +86,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
//
// --------------------------------------------------------------------------------------------------------------
private final static String COMPRESSED_OUTPUT_MD5 = "65846f5a8591d591ffbd1f85afadd9d5";
private final static String COMPRESSED_OUTPUT_MD5 = "fe3429b736c50bb770e40c0320d498ed";
@Test
public void testCompressedOutput() {
@ -108,7 +107,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
// Note that we need to turn off any randomization for this to work, so no downsampling and no annotations
String md5 = "36e6c8b0f30b159915eedaa5926ebbad";
String md5 = "306943dd63111e2e64388cd2e2de6c01";
WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
baseCommand + " -dt NONE -G none -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,075,000", 1,
@ -140,7 +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("efc4882c1150b246be163e08d81f428f"));
Arrays.asList("b341b87742848a3224115fe94e73f244"));
executeTest("test min_base_quality_score 26", spec);
}
@ -148,7 +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("b47b08b514acf5e96fb4994754e0e9ce"));
Arrays.asList("acb5332a267927d78edd51d93685111c"));
executeTest("test SLOD", spec);
}
@ -156,7 +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("08db1413ed6a04fcb03d58e3ece9f366"));
Arrays.asList("74779b59730962bdf36a7a8ef84ac24d"));
executeTest("test NDA", spec);
}
@ -164,23 +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("d78f95c225db2a4b21c99a688330df52"));
Arrays.asList("036edf58a4ed6c626f53bd2ab34b9f97"));
executeTest("test using comp track", spec);
}
@Test
public void testOutputParameterSitesOnly() {
testOutputParameters("-sites_only", "1e4a98213ec00479cc090f53620317e4");
testOutputParameters("-sites_only", "52b8336f347d182c158e8384b78f5a6d");
}
@Test
public void testOutputParameterAllConfident() {
testOutputParameters("--output_mode EMIT_ALL_CONFIDENT_SITES", "5580e3e7c2b358ed416bc03409c54c1d");
testOutputParameters("--output_mode EMIT_ALL_CONFIDENT_SITES", "281363e6afb3260143bfdb22710e3d0e");
}
@Test
public void testOutputParameterAllSites() {
testOutputParameters("--output_mode EMIT_ALL_SITES", "23ab7f15a01dd6dbf9f09a7560a2055b");
testOutputParameters("--output_mode EMIT_ALL_SITES", "a802b672850b6fbc2764611d3ad071d9");
}
private void testOutputParameters(final String args, final String md5) {
@ -194,7 +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("87c55fece67a562d208c538868307d7b"));
Arrays.asList("99ef7ba1747c7289ce1f963130539e18"));
executeTest("test confidence 1", spec1);
}
@ -202,7 +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("87c55fece67a562d208c538868307d7b"));
Arrays.asList("99ef7ba1747c7289ce1f963130539e18"));
executeTest("test confidence 2", spec2);
}
@ -213,12 +212,12 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
// --------------------------------------------------------------------------------------------------------------
@Test
public void testHeterozyosity1() {
testHeterozosity( 0.01, "481b17c5541f758a49f84263e5b0f795" );
testHeterozosity( 0.01, "7e1681b9052e357ca4a065fa76c8afb6" );
}
@Test
public void testHeterozyosity2() {
testHeterozosity( 1.0 / 1850, "70ad4b50a22de917eb91a95ca191eb17" );
testHeterozosity( 1.0 / 1850, "68a12f3eccac6cf4b27b6424f23628ee" );
}
private void testHeterozosity(final double arg, final String md5) {
@ -242,7 +241,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
" -o %s" +
" -L 1:10,000,000-10,100,000",
1,
Arrays.asList("3d20dbf7912e49cdfa929eb04840d351"));
Arrays.asList("b098a7744a448cf91a50886e4cc7d268"));
executeTest(String.format("test multiple technologies"), spec);
}
@ -261,7 +260,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
" -L 1:10,000,000-10,100,000" +
" -baq CALCULATE_AS_NECESSARY",
1,
Arrays.asList("0b141419428831b598813272cb7af055"));
Arrays.asList("2f008169b82d542ec9cc94908c395a0f"));
executeTest(String.format("test calling with BAQ"), spec);
}
@ -280,7 +279,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
" -o %s" +
" -L 1:10,000,000-10,500,000",
1,
Arrays.asList("9a54f9f820efa74e5a719e5ca44bc04d"));
Arrays.asList("0d4177d7f963f4b4e8568613e7a468f0"));
executeTest(String.format("test indel caller in SLX"), spec);
}
@ -295,7 +294,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
" -minIndelCnt 1" +
" -L 1:10,000,000-10,100,000",
1,
Arrays.asList("7f6c4e55b8e77c19199e8ad8b3594280"));
Arrays.asList("1268bde77842e6bb6a4f337c1d589f4d"));
executeTest(String.format("test indel caller in SLX with low min allele count"), spec);
}
@ -308,7 +307,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
" -o %s" +
" -L 1:10,000,000-10,500,000",
1,
Arrays.asList("7ef98a593945f0269ac2d29982a2a72b"));
Arrays.asList("181c4ed8dd084b83f8de92123bb85c41"));
executeTest(String.format("test indel calling, multiple technologies"), spec);
}
@ -316,9 +315,9 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
@Test
public void testWithIndelAllelesPassedIn1() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
baseCommandIndels + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + testDir + "indelAllelesForUG.vcf -I " + validationDataLocation +
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("656185ebade2db034441c787d6a363c1"));
Arrays.asList("5250cefb1fff262a6a3985dee29c154d"));
executeTest("test MultiSample Pilot2 indels with alleles passed in", spec);
}
@ -326,9 +325,9 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testWithIndelAllelesPassedIn2() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
baseCommandIndels + " --output_mode EMIT_ALL_SITES --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles "
+ testDir + "indelAllelesForUG.vcf -I " + validationDataLocation +
+ privateTestDir + "indelAllelesForUG.vcf -I " + validationDataLocation +
"pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,100,000", 1,
Arrays.asList("eb9624642e814a0b8962acc89422be23"));
Arrays.asList("c9b468fe75e7215a6d6d5a050af07918"));
executeTest("test MultiSample Pilot2 indels with alleles passed in and emitting all sites", spec);
}
@ -336,7 +335,7 @@ 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("e7b471d2a0eada2c7f37f120f2f1fa88"));
Arrays.asList("01fd223deb4f88fb7d9ee9736b664d8a"));
List<File> result = executeTest("test MultiSample Pilot1 CEU indels", spec1).getFirst();
WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
@ -350,9 +349,9 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testGGAwithNoEvidenceInReads() {
final String vcf = "small.indel.test.vcf";
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
baseCommandIndelsb37 + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles " + testDir + vcf + " -I " + validationDataLocation +
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("e362dc0488c8ee3013fa636d929db688"));
Arrays.asList("db0f91abb901e097714d8755058e1319"));
executeTest("test GENOTYPE_GIVEN_ALLELES with no evidence in reads", spec);
}
@ -385,7 +384,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testMinIndelFraction0() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
assessMinIndelFraction + " -minIndelFrac 0.0", 1,
Arrays.asList("3c9786453eb59013c70d99ee74f957a9"));
Arrays.asList("25465c6dd3c4845f61b0f8e383388824"));
executeTest("test minIndelFraction 0.0", spec);
}
@ -393,7 +392,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testMinIndelFraction25() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
assessMinIndelFraction + " -minIndelFrac 0.25", 1,
Arrays.asList("72b82f04dd7f9b9318ef7f8604f8085a"));
Arrays.asList("aa58dc9f77132c30363562bcdc321f6e"));
executeTest("test minIndelFraction 0.25", spec);
}
@ -401,7 +400,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testMinIndelFraction100() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
assessMinIndelFraction + " -minIndelFrac 1", 1,
Arrays.asList("0e9f485edabbed613e50c699cfa8822f"));
Arrays.asList("3f07efb768e08650a7ce333edd4f9a52"));
executeTest("test minIndelFraction 1.0", spec);
}
}

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

@ -44,7 +44,7 @@ public class RealignerTargetCreatorIntegrationTest extends WalkerTest {
@Test
public void testKnownsOnly() {
WalkerTest.WalkerTestSpec spec3 = new WalkerTest.WalkerTestSpec(
"-T RealignerTargetCreator -R " + b36KGReference + " --known " + testDir + "NA12878.chr1_10mb_11mb.slx.indels.vcf4 -L " + testDir + "NA12878.chr1_10mb_11mb.slx.indels.vcf4 -o %s",
"-T RealignerTargetCreator -R " + b36KGReference + " --known " + privateTestDir + "NA12878.chr1_10mb_11mb.slx.indels.vcf4 -L " + privateTestDir + "NA12878.chr1_10mb_11mb.slx.indels.vcf4 -o %s",
1,
Arrays.asList("5206cee6c01b299417bf2feeb8b3dc96"));
executeTest("test rods only", spec3);

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

@ -6,7 +6,7 @@ import org.testng.annotations.Test;
import java.util.Arrays;
public class PhaseByTransmissionIntegrationTest extends WalkerTest {
private static String phaseByTransmissionTestDataRoot = testDir + "PhaseByTransmission/";
private static String phaseByTransmissionTestDataRoot = privateTestDir + "PhaseByTransmission/";
private static String goodFamilyFile = phaseByTransmissionTestDataRoot + "PhaseByTransmission.IntegrationTest.goodFamilies.ped";
private static String TNTest = phaseByTransmissionTestDataRoot + "PhaseByTransmission.IntegrationTest.TN.vcf";
private static String TPTest = phaseByTransmissionTestDataRoot + "PhaseByTransmission.IntegrationTest.TP.vcf";

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 +
" --variant " + ( VCF.contains("phasing_test") ? testDir : validationDataLocation) + VCF +
" --variant " + ( VCF.contains("phasing_test") ? privateTestDir : validationDataLocation) + VCF +
" --cacheWindowSize " + cacheWindowSize +
" --maxPhaseSites " + maxPhaseSites +
" --phaseQualityThresh " + phaseQualityThresh +

2
public/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java
View File

@ -271,7 +271,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-R " + b36KGReference +
" -knownSites:anyNameABCD,VCF " + testDir + "vcfexample3.vcf" +
" -knownSites:anyNameABCD,VCF " + privateTestDir + "vcfexample3.vcf" +
" -T CountCovariates" +
" -I " + bam +
" -knownSites " + b36dbSNP129 +

16
public/java/test/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmpliconsIntegrationTest.java
View File

@ -17,8 +17,8 @@ public class ValidationAmpliconsIntegrationTest extends WalkerTest {
@Test(enabled=true)
public void testWikiExample() {
String siteVCF = validationDataLocation + "sites_to_validate.vcf";
String maskVCF = testDir + "amplicon_mask_sites.vcf";
String intervalTable = testDir + "amplicon_interval_table1.table";
String maskVCF = privateTestDir + "amplicon_mask_sites.vcf";
String intervalTable = privateTestDir + "amplicon_interval_table1.table";
String testArgs = "-R " + b37KGReference + " -T ValidationAmplicons --ValidateAlleles:VCF "+siteVCF+" -o %s";
testArgs += " --ProbeIntervals:table "+intervalTable+" -L:table "+intervalTable+" --MaskAlleles:VCF "+maskVCF;
testArgs += " --virtualPrimerSize 30";
@ -29,9 +29,9 @@ public class ValidationAmpliconsIntegrationTest extends WalkerTest {
@Test(enabled=true)
public void testWikiExampleNoBWA() {
String siteVCF = testDir + "sites_to_validate.vcf";
String maskVCF = testDir + "amplicon_mask_sites.vcf";
String intervalTable = testDir + "amplicon_interval_table1.table";
String siteVCF = privateTestDir + "sites_to_validate.vcf";
String maskVCF = privateTestDir + "amplicon_mask_sites.vcf";
String intervalTable = privateTestDir + "amplicon_interval_table1.table";
String testArgs = "-R " + b37KGReference + " -T ValidationAmplicons --ValidateAlleles:VCF "+siteVCF+" -o %s";
testArgs += " --ProbeIntervals:table "+intervalTable+" -L:table "+intervalTable+" --MaskAlleles:VCF "+maskVCF;
testArgs += " --virtualPrimerSize 30 --doNotUseBWA";
@ -42,9 +42,9 @@ public class ValidationAmpliconsIntegrationTest extends WalkerTest {
@Test(enabled=true)
public void testWikiExampleMonoFilter() {
String siteVCF = testDir + "sites_to_validate.vcf";
String maskVCF = testDir + "amplicon_mask_sites.vcf";
String intervalTable = testDir + "amplicon_interval_table1.table";
String siteVCF = privateTestDir + "sites_to_validate.vcf";
String maskVCF = privateTestDir + "amplicon_mask_sites.vcf";
String intervalTable = privateTestDir + "amplicon_interval_table1.table";
String testArgs = "-R " + b37KGReference + " -T ValidationAmplicons --ValidateAlleles:VCF "+siteVCF+" -o %s";
testArgs += " --ProbeIntervals:table "+intervalTable+" -L:table "+intervalTable+" --MaskAlleles:VCF "+maskVCF;
testArgs += " --virtualPrimerSize 30 --filterMonomorphic";

10
public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java
View File

@ -303,7 +303,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
String tests = cmdRoot +
" --dbsnp " + b36dbSNP129 +
" --eval " + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf" +
" --comp:comp_genotypes " + testDir + "yri.trio.gatk.ug.head.vcf";
" --comp:comp_genotypes " + privateTestDir + "yri.trio.gatk.ug.head.vcf";
WalkerTestSpec spec = new WalkerTestSpec(withSelect(tests, "DP < 50", "DP50") + " " + extraArgs + " -ST CpG -o %s",
1, Arrays.asList("4b9dcbce0717285e3c0c736c1bed744c"));
executeTestParallel("testSelect1", spec);
@ -343,7 +343,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
@Test(enabled = false) // no longer supported in the GATK
public void testTranches() {
String extraArgs = "-T VariantEval -R "+ hg18Reference +" --eval " + validationDataLocation + "GA2.WEx.cleaned.ug.snpfiltered.indelfiltered.optimized.vcf -o %s -EV TiTvVariantEvaluator -L chr1 -noEV -ST CpG -tf " + testDir + "tranches.6.txt";
String extraArgs = "-T VariantEval -R "+ hg18Reference +" --eval " + validationDataLocation + "GA2.WEx.cleaned.ug.snpfiltered.indelfiltered.optimized.vcf -o %s -EV TiTvVariantEvaluator -L chr1 -noEV -ST CpG -tf " + privateTestDir + "tranches.6.txt";
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("6af2b9959aa1778a5b712536de453952"));
executeTestParallel("testTranches",spec);
}
@ -530,11 +530,11 @@ public class VariantEvalIntegrationTest extends WalkerTest {
buildCommandLine(
"-T VariantEval",
"-R " + b37KGReference,
"-eval " + testDir + "/withSymbolic.b37.vcf",
"-eval " + privateTestDir + "/withSymbolic.b37.vcf",
"-noEV",
"-EV CountVariants",
"-noST",
"-stratIntervals " + testDir + "/overlapTest.bed",
"-stratIntervals " + privateTestDir + "/overlapTest.bed",
"-ST IntervalStratification",
"-L 20",
"-o %s"
@ -602,7 +602,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
buildCommandLine(
"-T VariantEval",
"-R " + b37KGReference,
"-eval " + testDir + "/ac0.vcf",
"-eval " + privateTestDir + "/ac0.vcf",
"-L 20:81006 -noST -noEV -EV VariantSummary -o %s" + (includeAC0 ? " -keepAC0" : "")
),
1,

6
public/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantGaussianMixtureModelUnitTest.java
View File

@ -45,10 +45,10 @@ public final class VariantGaussianMixtureModelUnitTest extends BaseTest {
private static int N_VARIANTS = 100;
VariantDatum[] variantData1 = new VariantDatum[N_VARIANTS];
private final File QUAL_DATA = new File(testDir + "tranches.raw.dat");
private final File QUAL_DATA = new File(privateTestDir + "tranches.raw.dat");
private final double[] TRUTH_SENSITIVITY_CUTS = new double[]{99.9, 99.0, 97.0, 95.0};
private final File EXPECTED_TRANCHES_NEW = new File(testDir + "tranches.6.txt");
private final File EXPECTED_TRANCHES_OLD = new File(testDir + "tranches.4.txt");
private final File EXPECTED_TRANCHES_NEW = new File(privateTestDir + "tranches.6.txt");
private final File EXPECTED_TRANCHES_OLD = new File(privateTestDir + "tranches.4.txt");
private ArrayList<VariantDatum> readData() {
ArrayList<VariantDatum> vd = new ArrayList<VariantDatum>();

7
public/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java
View File

@ -1,6 +1,5 @@
package org.broadinstitute.sting.gatk.walkers.variantrecalibration;
import org.broadinstitute.sting.MD5DB;
import org.broadinstitute.sting.WalkerTest;
import org.testng.annotations.Test;
import org.testng.annotations.DataProvider;
@ -129,10 +128,10 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
" -L 20:1000100-1000500" +
" -mode BOTH" +
" --no_cmdline_in_header" +
" -input " + testDir + "VQSR.mixedTest.input" +
" -input " + privateTestDir + "VQSR.mixedTest.input" +
" -o %s" +
" -tranchesFile " + testDir + "VQSR.mixedTest.tranches" +
" -recalFile " + testDir + "VQSR.mixedTest.recal",
" -tranchesFile " + privateTestDir + "VQSR.mixedTest.tranches" +
" -recalFile " + privateTestDir + "VQSR.mixedTest.recal",
Arrays.asList("beadf841bbf39c3f0d0bc7fb55462b37"));
executeTest("testApplyRecalibrationSnpAndIndelTogether", spec);
}

49
public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java
View File

@ -34,8 +34,23 @@ import java.util.Arrays;
* Tests CombineVariants
*/
public class CombineVariantsIntegrationTest extends WalkerTest {
public static String baseTestString(String args) {
return "-T CombineVariants --no_cmdline_in_header -L 1:1-50,000,000 -o %s -R " + b36KGReference + args;
//
// TODO TODO TODO TODO TODO TODO TODO TODO
// TODO TODO TODO TODO TODO TODO TODO TODO
//
// TODO WHEN THE HC EMITS VALID VCF HEADERS ENABLE BCF AND REMOVE allowMissingVCFHeaders ARGUMENTS
//
// TODO TODO TODO TODO TODO TODO TODO TODO
// TODO TODO TODO TODO TODO TODO TODO TODO
// TODO TODO TODO TODO TODO TODO TODO TODO
//
private static String baseTestString(String args) {
return "-T CombineVariants --no_cmdline_in_header -L 1:1-50,000,000 -o %s --allowMissingVCFHeaders -R " + b36KGReference + args;
}
private void cvExecuteTest(final String name, final WalkerTestSpec spec) {
spec.disableShadowBCF();
executeTest(name, spec);
}
public void test1InOut(String file, String md5) {
@ -47,7 +62,7 @@ public class CombineVariantsIntegrationTest extends WalkerTest {
baseTestString(" -priority v1 -V:v1 " + validationDataLocation + file + args),
1,
Arrays.asList(md5));
executeTest("testInOut1--" + file, spec);
cvExecuteTest("testInOut1--" + file, spec);
}
public void combine2(String file1, String file2, String args, String md5) {
@ -55,7 +70,7 @@ public class CombineVariantsIntegrationTest extends WalkerTest {
baseTestString(" -priority v1,v2 -V:v1 " + validationDataLocation + file1 + " -V:v2 "+ validationDataLocation + file2 + args),
1,
Arrays.asList(md5));
executeTest("combine2 1:" + new File(file1).getName() + " 2:" + new File(file2).getName(), spec);
cvExecuteTest("combine2 1:" + new File(file1).getName() + " 2:" + new File(file2).getName(), spec);
}
public void combineSites(String args, String md5) {
@ -67,15 +82,15 @@ public class CombineVariantsIntegrationTest extends WalkerTest {
+ " -V:hm3 " + validationDataLocation + file2 + args,
1,
Arrays.asList(md5));
executeTest("combineSites 1:" + new File(file1).getName() + " 2:" + new File(file2).getName() + " args = " + args, spec);
cvExecuteTest("combineSites 1:" + new File(file1).getName() + " 2:" + new File(file2).getName() + " args = " + args, spec);
}
public void combinePLs(String file1, String file2, String md5) {
WalkerTestSpec spec = new WalkerTestSpec(
"-T CombineVariants --no_cmdline_in_header -o %s -R " + b36KGReference + " -priority v1,v2 -V:v1 " + testDir + file1 + " -V:v2 " + testDir + file2,
"-T CombineVariants --no_cmdline_in_header -o %s -R " + b36KGReference + " -priority v1,v2 -V:v1 " + privateTestDir + file1 + " -V:v2 " + privateTestDir + file2,
1,
Arrays.asList(md5));
executeTest("combine PLs 1:" + new File(file1).getName() + " 2:" + new File(file2).getName(), spec);
cvExecuteTest("combine PLs 1:" + new File(file1).getName() + " 2:" + new File(file2).getName(), spec);
}
@Test public void test1SNP() { test1InOut("pilot2.snps.vcf4.genotypes.vcf", "6469fce8a5cd5a0f77e5ac5d9e9e192b"); }
@ -86,7 +101,7 @@ public class CombineVariantsIntegrationTest extends WalkerTest {
@Test public void test1Indel1() { test1InOut("CEU.dindel.vcf4.trio.2010_06.indel.genotypes.vcf", "ef2d249ea4b25311966e038aac05c661"); }
@Test public void test1Indel2() { test1InOut("CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "cdb448aaa92ca5a9e393d875b42581b3"); }
@Test public void combineWithPLs() { combinePLs("combine.3.vcf", "combine.4.vcf", "284083f60792c5f817899445dfa63a42"); }
@Test public void combineWithPLs() { combinePLs("combine.3.vcf", "combine.4.vcf", "f0ce3fb83d4ad9ba402d7cb11cd000c3"); }
@Test public void combineTrioCalls() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "YRI.trio.2010_03.genotypes.vcf.gz", "", "4efdf983918db822e4ac13d911509576"); } // official project VCF files in tabix format
@Test public void combineTrioCallsMin() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "YRI.trio.2010_03.genotypes.vcf.gz", " -minimalVCF", "848d4408ee953053d2307cefebc6bd6d"); } // official project VCF files in tabix format
@ -111,7 +126,7 @@ public class CombineVariantsIntegrationTest extends WalkerTest {
" -genotypeMergeOptions UNIQUIFY -L 1"),
1,
Arrays.asList("c0d4d601aa5d2b29927c535868448d2a"));
executeTest("threeWayWithRefs", spec);
cvExecuteTest("threeWayWithRefs", spec);
}
// complex examples with filtering, indels, and multiple alleles
@ -120,17 +135,17 @@ public class CombineVariantsIntegrationTest extends WalkerTest {
String file2 = "combine.2.vcf";
WalkerTestSpec spec = new WalkerTestSpec(
"-T CombineVariants --no_cmdline_in_header -o %s -R " + b37KGReference
+ " -V:one " + testDir + file1
+ " -V:two " + testDir + file2 + args,
+ " -V:one " + privateTestDir + file1
+ " -V:two " + privateTestDir + file2 + args,
1,
Arrays.asList(md5));
executeTest("combineComplexSites 1:" + new File(file1).getName() + " 2:" + new File(file2).getName() + " args = " + args, spec);
cvExecuteTest("combineComplexSites 1:" + new File(file1).getName() + " 2:" + new File(file2).getName() + " args = " + args, spec);
}
@Test public void complexTestFull() { combineComplexSites("", "7d587bf49bbc9f8239476bab84bf9708"); }
@Test public void complexTestMinimal() { combineComplexSites(" -minimalVCF", "4d1e0c12d95f50e472493fc14af3cc06"); }
@Test public void complexTestSitesOnly() { combineComplexSites(" -sites_only", "9a98b01b9b2a28ae6af3125edc131dea"); }
@Test public void complexTestSitesOnlyMinimal() { combineComplexSites(" -sites_only -minimalVCF", "9a98b01b9b2a28ae6af3125edc131dea"); }
@Test public void complexTestFull() { combineComplexSites("", "8b19b54516b59de40992f0c4b328258a"); }
@Test public void complexTestMinimal() { combineComplexSites(" -minimalVCF", "a38dd097adc37420fe36ef8be14cfded"); }
@Test public void complexTestSitesOnly() { combineComplexSites(" -sites_only", "a3957dac9a617f50ce2668607e3baef0"); }
@Test public void complexTestSitesOnlyMinimal() { combineComplexSites(" -sites_only -minimalVCF", "a3957dac9a617f50ce2668607e3baef0"); }
@Test
public void combineDBSNPDuplicateSites() {
@ -138,6 +153,6 @@ public class CombineVariantsIntegrationTest extends WalkerTest {
"-T CombineVariants --no_cmdline_in_header -L 1:902000-903000 -o %s -R " + b37KGReference + " -V:v1 " + b37dbSNP132,
1,
Arrays.asList("3d2a5a43db86e3f6217ed2a63251285b"));
executeTest("combineDBSNPDuplicateSites:", spec);
cvExecuteTest("combineDBSNPDuplicateSites:", spec);
}
}

2
public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariantsIntegrationTest.java
View File

@ -38,7 +38,7 @@ public class LeftAlignVariantsIntegrationTest extends WalkerTest {
@Test
public void testLeftAlignment() {
WalkerTestSpec spec = new WalkerTestSpec(
"-T LeftAlignVariants -o %s -R " + b37KGReference + " --variant:vcf " + testDir + "forLeftAlignVariantsTest.vcf --no_cmdline_in_header",
"-T LeftAlignVariants -o %s -R " + b37KGReference + " --variant:vcf " + privateTestDir + "forLeftAlignVariantsTest.vcf --no_cmdline_in_header",
1,
Arrays.asList("bcf05f56adbb32a47b6d6b27b327d5c2"));
executeTest("test left alignment", spec);

8
public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariantsIntegrationTest.java
View File

@ -38,7 +38,7 @@ public class LiftoverVariantsIntegrationTest extends WalkerTest {
@Test
public void testb36Tohg19() {
WalkerTestSpec spec = new WalkerTestSpec(
"-T LiftoverVariants -o %s -R " + b36KGReference + " --variant " + testDir + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.500.noheader.vcf -chain " + validationDataLocation + "b36ToHg19.broad.over.chain -dict /seq/references/Homo_sapiens_assembly19/v0/Homo_sapiens_assembly19.dict",
"-T LiftoverVariants -o %s -R " + b36KGReference + " --variant " + privateTestDir + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.500.noheader.vcf -chain " + validationDataLocation + "b36ToHg19.broad.over.chain -dict /seq/references/Homo_sapiens_assembly19/v0/Homo_sapiens_assembly19.dict",
1,
Arrays.asList("b8f4171b0c39954b283dfed4afed87d7"));
executeTest("test b36 to hg19", spec);
@ -47,16 +47,16 @@ public class LiftoverVariantsIntegrationTest extends WalkerTest {
@Test
public void testb36Tohg19UnsortedSamples() {
WalkerTestSpec spec = new WalkerTestSpec(
"-T LiftoverVariants -o %s -R " + b36KGReference + " --variant " + testDir + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.500.noheader.unsortedSamples.vcf -chain " + validationDataLocation + "b36ToHg19.broad.over.chain -dict /seq/references/Homo_sapiens_assembly19/v0/Homo_sapiens_assembly19.dict",
"-T LiftoverVariants -o %s -R " + b36KGReference + " --variant " + privateTestDir + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.500.noheader.unsortedSamples.vcf -chain " + validationDataLocation + "b36ToHg19.broad.over.chain -dict /seq/references/Homo_sapiens_assembly19/v0/Homo_sapiens_assembly19.dict",
1,
Arrays.asList("07d1bf52125d1f9a25e260e13ec7b010"));
Arrays.asList("2fd072a88006e3d7cfea4cac5d7b0d98"));
executeTest("test b36 to hg19, unsorted samples", spec);
}
@Test
public void testhg18Tohg19Unsorted() {
WalkerTestSpec spec = new WalkerTestSpec(
"-T LiftoverVariants -o %s -R " + hg18Reference + " --variant:vcf " + testDir + "liftover_test.vcf -chain " + validationDataLocation + "hg18ToHg19.broad.over.chain -dict /seq/references/Homo_sapiens_assembly19/v0/Homo_sapiens_assembly19.dict",
"-T LiftoverVariants -o %s -R " + hg18Reference + " --variant:vcf " + privateTestDir + "liftover_test.vcf -chain " + validationDataLocation + "hg18ToHg19.broad.over.chain -dict /seq/references/Homo_sapiens_assembly19/v0/Homo_sapiens_assembly19.dict",
1,
Arrays.asList("e0b813ff873185ab51995a151f80ec98"));
executeTest("test hg18 to hg19, unsorted", spec);

26
public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java
View File

@ -13,7 +13,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
@Test
public void testDiscordanceNoSampleSpecified() {
String testFile = testDir + "NA12878.hg19.example1.vcf";
String testFile = privateTestDir + "NA12878.hg19.example1.vcf";
WalkerTestSpec spec = new WalkerTestSpec(
"-T SelectVariants -R " + hg19Reference + " -L 20:1012700-1020000 --variant "
@ -29,7 +29,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
@Test
public void testRepeatedLineSelection() {
String testfile = testDir + "test.dup.vcf";
String testfile = privateTestDir + "test.dup.vcf";
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString(" -sn A -sn B -sn C --variant " + testfile),
@ -42,7 +42,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
@Test
public void testDiscordance() {
String testFile = testDir + "NA12878.hg19.example1.vcf";
String testFile = privateTestDir + "NA12878.hg19.example1.vcf";
WalkerTestSpec spec = new WalkerTestSpec(
"-T SelectVariants -R " + hg19Reference + " -sn NA12878 -L 20:1012700-1020000 --variant "
@ -88,14 +88,14 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
@Test
public void testConcordance() {
String testFile = testDir + "NA12878.hg19.example1.vcf";
String testFile = privateTestDir + "NA12878.hg19.example1.vcf";
WalkerTestSpec spec = new WalkerTestSpec(
"-T SelectVariants -R " + hg19Reference + " -sn NA12878 -L 20:1012700-1020000 -conc "
+ b37hapmapGenotypes + " --variant " + testFile
+ " -o %s --no_cmdline_in_header --allowMissingVCFHeaders",
1,
Arrays.asList("7d2c7deeacf307d140a85a34629c6539")
Arrays.asList("25b3a8fd7b62b035c9d7c090db3c682d")
);
spec.disableShadowBCF();
@ -104,7 +104,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
@Test
public void testVariantTypeSelection() {
String testFile = testDir + "complexExample1.vcf";
String testFile = privateTestDir + "complexExample1.vcf";
WalkerTestSpec spec = new WalkerTestSpec(
"-T SelectVariants -R " + b36KGReference + " -restrictAllelesTo MULTIALLELIC -selectType MIXED --variant " + testFile + " -o %s --no_cmdline_in_header",
@ -117,7 +117,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
@Test
public void testUsingDbsnpName() {
String testFile = testDir + "combine.3.vcf";
String testFile = privateTestDir + "combine.3.vcf";
WalkerTestSpec spec = new WalkerTestSpec(
"-T SelectVariants -R " + b36KGReference + " -sn NA12892 --variant:dbsnp " + testFile + " -o %s --no_cmdline_in_header",
@ -130,7 +130,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
@Test
public void testRegenotype() {
String testFile = testDir + "combine.3.vcf";
String testFile = privateTestDir + "combine.3.vcf";
WalkerTestSpec spec = new WalkerTestSpec(
"-T SelectVariants -R " + b36KGReference + " -regenotype -sn NA12892 --variant " + testFile + " -o %s --no_cmdline_in_header",
@ -143,7 +143,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
@Test
public void testMultipleRecordsAtOnePosition() {
String testFile = testDir + "selectVariants.onePosition.vcf";
String testFile = privateTestDir + "selectVariants.onePosition.vcf";
WalkerTestSpec spec = new WalkerTestSpec(
"-T SelectVariants -R " + b36KGReference + " -select 'KG_FREQ < 0.5' --variant " + testFile + " -o %s --no_cmdline_in_header",
@ -156,7 +156,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
@Test
public void testNoGTs() {
String testFile = testDir + "vcf4.1.example.vcf";
String testFile = privateTestDir + "vcf4.1.example.vcf";
WalkerTestSpec spec = new WalkerTestSpec(
"-T SelectVariants -R " + b37KGReference + " --variant " + testFile + " -o %s --no_cmdline_in_header",
@ -199,8 +199,8 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
@Test
public void testSelectFromMultiAllelic() {
String testfile = testDir + "multi-allelic.bi-allelicInGIH.vcf";
String samplesFile = testDir + "GIH.samples.list";
String testfile = privateTestDir + "multi-allelic.bi-allelicInGIH.vcf";
String samplesFile = privateTestDir + "GIH.samples.list";
WalkerTestSpec spec = new WalkerTestSpec(
"-T SelectVariants -R " + b37KGReference + " -o %s --no_cmdline_in_header -sf " + samplesFile + " --excludeNonVariants --variant " + testfile,
1,
@ -220,7 +220,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
}
private void testFileWithoutInfoLineInHeader(final String name, final Class expectedException) {
final String testFile = testDir + "missingHeaderLine.vcf";
final String testFile = privateTestDir + "missingHeaderLine.vcf";
final String cmd = "-T SelectVariants -R " + b36KGReference + " -sn NA12892 --variant:dbsnp "
+ testFile + " -o %s --no_cmdline_in_header"
+ (expectedException == null ? " -allowMissingVCFHeaders" : "");

4
public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VCFStreamingIntegrationTest.java
View File

@ -46,7 +46,7 @@ public class VCFStreamingIntegrationTest extends WalkerTest {
// Copy VCF data from the test file into the FIFO.
String testFile = testDir + "yri.trio.gatk.ug.head.vcf";
String testFile = privateTestDir + "yri.trio.gatk.ug.head.vcf";
FileInputStream inputStream = new FileInputStream(testFile);
FileOutputStream outputStream = new FileOutputStream(tmpFifo);
outputStream.getChannel().transferFrom(inputStream.getChannel(),0,inputStream.getChannel().size());
@ -74,7 +74,7 @@ public class VCFStreamingIntegrationTest extends WalkerTest {
File tmpFifo = File.createTempFile("vcfstreaming","");
Runtime.getRuntime().exec(new String[] {"mkfifo",tmpFifo.getAbsolutePath()});
String testFile = testDir + "yri.trio.gatk.ug.head.vcf";
String testFile = privateTestDir + "yri.trio.gatk.ug.head.vcf";
// Output select to FIFO
WalkerTestSpec selectTestSpec = new WalkerTestSpec(

2
public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariantsIntegrationTest.java
View File

@ -34,7 +34,7 @@ import java.util.Arrays;
public class ValidateVariantsIntegrationTest extends WalkerTest {
public static String baseTestString(String file, String type) {
return "-T ValidateVariants -R " + b36KGReference + " -L 1:10001292-10001303 --variant:vcf " + testDir + file + " --validationType " + type;
return "-T ValidateVariants -R " + b36KGReference + " -L 1:10001292-10001303 --variant:vcf " + privateTestDir + file + " --validationType " + type;
}
@Test

14
public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTableIntegrationTest.java
View File

@ -33,7 +33,7 @@ import java.util.*;
public class VariantsToTableIntegrationTest extends WalkerTest {
private String variantsToTableCmd(String moreArgs) {
return "-R " + hg18Reference +
" --variant:vcf " + testDir + "soap_gatk_annotated.vcf" +
" --variant:vcf " + privateTestDir + "soap_gatk_annotated.vcf" +
" -T VariantsToTable" +
" -F CHROM -F POS -F ID -F REF -F ALT -F QUAL -F FILTER -F TRANSITION -F DP -F SB -F set -F RankSumP -F refseq.functionalClass*" +
" -L chr1 -o %s" + moreArgs;
@ -41,7 +41,7 @@ public class VariantsToTableIntegrationTest extends WalkerTest {
private String variantsToTableMultiAllelicCmd(String moreArgs) {
return "-R " + b37KGReference +
" --variant " + testDir + "multiallelic.vcf" +
" --variant " + privateTestDir + "multiallelic.vcf" +
" -T VariantsToTable" +
" -F CHROM -F POS -F ID -F REF -F ALT -F QUAL -F MULTI-ALLELIC -F AC -F AF" +
" -o %s" + moreArgs;
@ -78,7 +78,7 @@ public class VariantsToTableIntegrationTest extends WalkerTest {
public void testGenotypeFields() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-R " + b36KGReference +
" --variant " + testDir + "vcfexample2.vcf" +
" --variant " + privateTestDir + "vcfexample2.vcf" +
" -T VariantsToTable" +
" -GF RD" +
" -o %s",
@ -91,7 +91,7 @@ public class VariantsToTableIntegrationTest extends WalkerTest {
public void testGenotypeFieldsWithInline() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-R " + b36KGReference +
" --variant " + testDir + "vcfexample2.vcf" +
" --variant " + privateTestDir + "vcfexample2.vcf" +
" -T VariantsToTable" +
" -GF RD -GF GT -GF GQ" +
" -o %s",
@ -104,7 +104,7 @@ public class VariantsToTableIntegrationTest extends WalkerTest {
public void testMoltenOutput() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-R " + b36KGReference +
" --variant " + testDir + "vcfexample2.vcf" +
" --variant " + privateTestDir + "vcfexample2.vcf" +
" -T VariantsToTable" +
" -F CHROM -F POS -F ID -F REF -F ALT -F QUAL -F FILTER" +
" --moltenize" +
@ -118,7 +118,7 @@ public class VariantsToTableIntegrationTest extends WalkerTest {
public void testMoltenOutputWithGenotypeFields() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-R " + b36KGReference +
" --variant " + testDir + "vcfexample2.vcf" +
" --variant " + privateTestDir + "vcfexample2.vcf" +
" -T VariantsToTable" +
" -GF RD" +
" --moltenize" +
@ -132,7 +132,7 @@ public class VariantsToTableIntegrationTest extends WalkerTest {
public void testMoltenOutputWithMultipleAlleles() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-R " + b37KGReference +
" --variant " + testDir + "multiallelic.vcf" +
" --variant " + privateTestDir + "multiallelic.vcf" +
" -T VariantsToTable" +
" -F CHROM -F POS -F ID -F REF -F ALT -F QUAL -F MULTI-ALLELIC -F AC -F AF" +
" --moltenize -SMA" +

12
public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCFIntegrationTest.java
View File

@ -19,7 +19,7 @@ public class VariantsToVCFIntegrationTest extends WalkerTest {
@Test
public void testVariantsToVCFUsingDbsnpInput() {
List<String> md5 = new ArrayList<String>();
md5.add("268c116f825c2a4b5200a416ca587adc");
md5.add("72e6ce7aff7dec7ca9e7580be7ddd435");
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-R " + b36KGReference +
@ -36,7 +36,7 @@ public class VariantsToVCFIntegrationTest extends WalkerTest {
@Test
public void testVariantsToVCFUsingGeliInput() {
List<String> md5 = new ArrayList<String>();
md5.add("82ca5ecef2df5d64dee9ef5a4b14ef2f");
md5.add("22373883afa2221b5a4f75a50f30f26b");
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-R " + b36KGReference +
@ -54,7 +54,7 @@ public class VariantsToVCFIntegrationTest extends WalkerTest {
@Test
public void testGenotypesToVCFUsingGeliInput() {
List<String> md5 = new ArrayList<String>();
md5.add("90bc2e21d633fa6c3c47c6bd86c134a0");
md5.add("738eb66dbc400dcd1786cd9e49902e8c");
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-R " + b36KGReference +
@ -72,7 +72,7 @@ public class VariantsToVCFIntegrationTest extends WalkerTest {
@Test
public void testGenotypesToVCFUsingHapMapInput() {
List<String> md5 = new ArrayList<String>();
md5.add("bb71dabd072a679cc85fe8d3e130fb2b");
md5.add("67656672acc264156f5a3e01e5cac61a");
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-R " + b36KGReference +
@ -89,11 +89,11 @@ public class VariantsToVCFIntegrationTest extends WalkerTest {
@Test
public void testGenotypesToVCFUsingVCFInput() {
List<String> md5 = new ArrayList<String>();
md5.add("ae39e2249bc20fcd0a668a7fe5fb84b0");
md5.add("95898aad8c9f9515c0e668e2fb65a024");
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-R " + b36KGReference +
" --variant:VCF " + testDir + "complexExample.vcf4" +
" --variant:VCF " + privateTestDir + "complexExample.vcf4" +
" -T VariantsToVCF" +
" -o %s" +
" --no_cmdline_in_header",

19
public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFIntegrationTest.java
View File

@ -13,7 +13,7 @@ public class VCFIntegrationTest extends WalkerTest {
public void testReadingAndWritingWitHNoChanges() {
String md5ofInputVCF = "babf02baabcfa7f72a2c6f7da5fdc996";
String testVCF = testDir + "vcf4.1.example.vcf";
String testVCF = privateTestDir + "vcf4.1.example.vcf";
String baseCommand = "-R " + b37KGReference + " --no_cmdline_in_header -o %s ";
@ -26,10 +26,10 @@ public class VCFIntegrationTest extends WalkerTest {
executeTest("Test Variants To VCF from new output", spec2);
}
@Test
@Test(enabled = false)
// See https://getsatisfaction.com/gsa/topics/support_vcf_4_1_structural_variation_breakend_alleles?utm_content=topic_link&utm_medium=email&utm_source=new_topic
public void testReadingAndWritingBreakpointAlleles() {
String testVCF = testDir + "breakpoint-example.vcf";
String testVCF = privateTestDir + "breakpoint-example.vcf";
//String testVCF = validationDataLocation + "multiallelic.vcf";
String baseCommand = "-R " + b37KGReference + " --no_cmdline_in_header -o %s ";
@ -41,12 +41,21 @@ public class VCFIntegrationTest extends WalkerTest {
@Test
public void testReadingAndWritingSamtools() {
String testVCF = testDir + "samtools.vcf";
String testVCF = privateTestDir + "samtools.vcf";
String baseCommand = "-R " + b37KGReference + " --no_cmdline_in_header -o %s ";
String test1 = baseCommand + "-T SelectVariants -V " + testVCF;
WalkerTestSpec spec1 = new WalkerTestSpec(test1, 1, Arrays.asList("0807ff11bebba81b87a273ad6bee01a8"));
WalkerTestSpec spec1 = new WalkerTestSpec(test1, 1, Arrays.asList("cf3f09ef63feba6958d32f95d587af80"));
executeTest("Test reading and writing samtools vcf", spec1);
}
@Test
public void testReadingAndWritingSamtoolsWExBCFExample() {
String testVCF = privateTestDir + "ex2.vcf";
String baseCommand = "-R " + b36KGReference + " --no_cmdline_in_header -o %s ";
String test1 = baseCommand + "-T SelectVariants -V " + testVCF;
WalkerTestSpec spec1 = new WalkerTestSpec(test1, 1, Arrays.asList("5839ed4972e2ccf3a7b190752ede6596"));
executeTest("Test reading and writing samtools WEx vcf/BCF example", spec1);
}
}

148
public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFStandardHeaderLinesUnitTest.java 100644
View File

@ -0,0 +1,148 @@
/*
* Copyright (c) 2012, The Broad Institute
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.utils.codecs.vcf;
import org.broadinstitute.sting.BaseTest;
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;
import org.testng.Assert;
import java.util.ArrayList;
import java.util.Collections;
import java.util.List;
/**
* Created by IntelliJ IDEA.
* User: aaron
* Date: Jun 30, 2010
* Time: 3:32:08 PM
* To change this template use File | Settings | File Templates.
*/
public class VCFStandardHeaderLinesUnitTest extends BaseTest {
@DataProvider(name = "getStandardLines")
public Object[][] makeGetStandardLines() {
List<Object[]> tests = new ArrayList<Object[]>();
// info
tests.add(new Object[]{"AC", "info", true});
tests.add(new Object[]{"AN", "info", true});
tests.add(new Object[]{"AF", "info", true});
tests.add(new Object[]{"DP", "info", true});
tests.add(new Object[]{"DB", "info", true});
tests.add(new Object[]{"END", "info", true});
// format
tests.add(new Object[]{"GT", "format", true});
tests.add(new Object[]{"GQ", "format", true});
tests.add(new Object[]{"DP", "format", true});
tests.add(new Object[]{"AD", "format", true});
tests.add(new Object[]{"PL", "format", true});
tests.add(new Object[]{"NOT_STANDARD", "info", false});
tests.add(new Object[]{"NOT_STANDARD", "format", false});
return tests.toArray(new Object[][]{});
}
@Test(dataProvider = "getStandardLines")
public void getStandardLines(final String key, final String type, final boolean expectedToBeStandard) {
VCFCompoundHeaderLine line = null;
if ( type.equals("info") )
line = VCFStandardHeaderLines.getInfoLine(key, false);
else if ( type.equals("format") )
line = VCFStandardHeaderLines.getFormatLine(key, false);
else
throw new IllegalArgumentException("Unexpected type in getStandardLines " + type);
if ( expectedToBeStandard ) {
Assert.assertNotNull(line);
Assert.assertEquals(line.getID(), key);
} else
Assert.assertNull(line);
}
private class RepairHeaderTest extends TestDataProvider {
final VCFCompoundHeaderLine original, expectedResult;
private RepairHeaderTest(final VCFCompoundHeaderLine original) {
this(original, original);
}
private RepairHeaderTest(final VCFCompoundHeaderLine original, final VCFCompoundHeaderLine expectedResult) {
super(RepairHeaderTest.class);
this.original = original;
this.expectedResult = expectedResult;
}
}
@DataProvider(name = "RepairHeaderTest")
public Object[][] makeRepairHeaderTest() {
final VCFInfoHeaderLine standardAC = VCFStandardHeaderLines.getInfoLine("AC");
final VCFInfoHeaderLine goodAC = new VCFInfoHeaderLine("AC", VCFHeaderLineCount.A, VCFHeaderLineType.Integer, "x");
final VCFFormatHeaderLine standardGT = VCFStandardHeaderLines.getFormatLine("GT");
final VCFFormatHeaderLine goodGT = new VCFFormatHeaderLine("GT", 1, VCFHeaderLineType.String, "x");
new RepairHeaderTest( standardGT, standardGT);
new RepairHeaderTest( goodGT, goodGT );
new RepairHeaderTest( new VCFFormatHeaderLine("GT", 2, VCFHeaderLineType.String, "x"), standardGT);
new RepairHeaderTest( new VCFFormatHeaderLine("GT", 1, VCFHeaderLineType.Integer, "x"), standardGT);
new RepairHeaderTest( new VCFFormatHeaderLine("GT", 1, VCFHeaderLineType.Float, "x"), standardGT);
new RepairHeaderTest( new VCFFormatHeaderLine("GT", VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.Float, "x"), standardGT);
new RepairHeaderTest( new VCFFormatHeaderLine("GT", VCFHeaderLineCount.G, VCFHeaderLineType.String, "x"), standardGT);
new RepairHeaderTest( new VCFFormatHeaderLine("GT", VCFHeaderLineCount.A, VCFHeaderLineType.String, "x"), standardGT);
new RepairHeaderTest( standardAC, standardAC);
new RepairHeaderTest( goodAC, goodAC );
new RepairHeaderTest( new VCFInfoHeaderLine("AC", 1, VCFHeaderLineType.Integer, "x"), standardAC);
new RepairHeaderTest( new VCFInfoHeaderLine("AC", VCFHeaderLineCount.G, VCFHeaderLineType.Integer, "x"), standardAC);
new RepairHeaderTest( new VCFInfoHeaderLine("AC", VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.Integer, "x"), standardAC);
new RepairHeaderTest( new VCFInfoHeaderLine("AC", 1, VCFHeaderLineType.Float, "x"), standardAC);
new RepairHeaderTest( new VCFInfoHeaderLine("AC", 1, VCFHeaderLineType.String, "x"), standardAC);
new RepairHeaderTest( new VCFInfoHeaderLine("AC", 0, VCFHeaderLineType.Flag, "x"), standardAC);
new RepairHeaderTest( new VCFInfoHeaderLine("NON_STANDARD_INFO", 1, VCFHeaderLineType.String, "x"));
new RepairHeaderTest( new VCFFormatHeaderLine("NON_STANDARD_FORMAT", 1, VCFHeaderLineType.String, "x"));
return RepairHeaderTest.getTests(RepairHeaderTest.class);
}
@Test(dataProvider = "RepairHeaderTest")
public void testRepairHeaderTest(RepairHeaderTest cfg) {
final VCFHeader toRepair = new VCFHeader(Collections.singleton((VCFHeaderLine)cfg.original));
final VCFHeader repaired = VCFStandardHeaderLines.repairStandardHeaderLines(toRepair);
VCFCompoundHeaderLine repairedLine = (VCFCompoundHeaderLine)repaired.getFormatHeaderLine(cfg.original.getID());
if ( repairedLine == null ) repairedLine = (VCFCompoundHeaderLine)repaired.getInfoHeaderLine(cfg.original.getID());
Assert.assertNotNull(repairedLine, "Repaired header didn't contain the expected line");
Assert.assertEquals(repairedLine.getID(), cfg.expectedResult.getID());
Assert.assertEquals(repairedLine.getType(), cfg.expectedResult.getType());
Assert.assertEquals(repairedLine.getCountType(), cfg.expectedResult.getCountType());
if ( repairedLine.getCountType() == VCFHeaderLineCount.INTEGER )
Assert.assertEquals(repairedLine.getCount(), cfg.expectedResult.getCount());
}
}

4
public/java/test/org/broadinstitute/sting/utils/crypt/GATKKeyIntegrationTest.java
View File

@ -35,8 +35,8 @@ import java.util.Arrays;
public class GATKKeyIntegrationTest extends WalkerTest {
public static final String BASE_COMMAND = String.format("-T PrintReads -R %s -I %s -o %%s",
testDir + "exampleFASTA.fasta",
testDir + "exampleBAM.bam");
publicTestDir + "exampleFASTA.fasta",
publicTestDir + "exampleBAM.bam");
public static final String MD5_UPON_SUCCESSFUL_RUN = "b9dc5bf6753ca2819e70b056eaf61258";

4
public/java/test/org/broadinstitute/sting/utils/fasta/CachingIndexedFastaSequenceFileUnitTest.java
View File

@ -9,8 +9,6 @@ import org.broadinstitute.sting.utils.exceptions.UserException;
import org.testng.Assert;
import org.testng.annotations.Test;
import org.testng.annotations.DataProvider;
import org.testng.annotations.BeforeTest;
import org.testng.annotations.BeforeMethod;
import org.broadinstitute.sting.BaseTest;
import java.io.File;
@ -27,7 +25,7 @@ import net.sf.samtools.SAMSequenceRecord;
* Basic unit test for GenomeLoc
*/
public class CachingIndexedFastaSequenceFileUnitTest extends BaseTest {
private File simpleFasta = new File(testDir + "/exampleFASTA.fasta");
private File simpleFasta = new File(privateTestDir + "/exampleFASTA.fasta");
private static final int STEP_SIZE = 1;
//private static final List<Integer> QUERY_SIZES = Arrays.asList(1);

2
public/java/test/org/broadinstitute/sting/utils/interval/IntervalIntegrationTest.java
View File

@ -279,7 +279,7 @@ public class IntervalIntegrationTest extends WalkerTest {
" -I " + validationDataLocation + "NA12878.chrom1.SLX.SRP000032.2009_06.bam" +
" -R " + b36KGReference +
" -o %s" +
" -L " + testDir + "symbolic_alleles_1.vcf",
" -L " + privateTestDir + "symbolic_alleles_1.vcf",
1, // just one output file
Arrays.asList(md5));
executeTest("testSymbolicAlleles", spec);

8
public/java/test/org/broadinstitute/sting/utils/interval/IntervalUtilsUnitTest.java
View File

@ -357,8 +357,8 @@ public class IntervalUtilsUnitTest extends BaseTest {
@Test
public void testIsIntervalFile() {
Assert.assertTrue(IntervalUtils.isIntervalFile(BaseTest.testDir + "empty_intervals.list"));
Assert.assertTrue(IntervalUtils.isIntervalFile(BaseTest.testDir + "empty_intervals.list", true));
Assert.assertTrue(IntervalUtils.isIntervalFile(BaseTest.privateTestDir + "empty_intervals.list"));
Assert.assertTrue(IntervalUtils.isIntervalFile(BaseTest.privateTestDir + "empty_intervals.list", true));
List<String> extensions = Arrays.asList("bed", "interval_list", "intervals", "list", "picard");
for (String extension: extensions) {
@ -368,7 +368,7 @@ public class IntervalUtilsUnitTest extends BaseTest {
@Test(expectedExceptions = UserException.CouldNotReadInputFile.class)
public void testMissingIntervalFile() {
IntervalUtils.isIntervalFile(BaseTest.testDir + "no_such_intervals.list");
IntervalUtils.isIntervalFile(BaseTest.privateTestDir + "no_such_intervals.list");
}
@Test
@ -758,7 +758,7 @@ public class IntervalUtilsUnitTest extends BaseTest {
@Test(dataProvider="unmergedIntervals")
public void testUnmergedIntervals(String unmergedIntervals) {
List<GenomeLoc> locs = IntervalUtils.parseIntervalArguments(hg18GenomeLocParser, Collections.singletonList(testDir + unmergedIntervals));
List<GenomeLoc> locs = IntervalUtils.parseIntervalArguments(hg18GenomeLocParser, Collections.singletonList(privateTestDir + unmergedIntervals));
Assert.assertEquals(locs.size(), 2);
List<GenomeLoc> merged = IntervalUtils.mergeIntervalLocations(locs, IntervalMergingRule.ALL);

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

@ -62,8 +62,8 @@ public class VariantContextTestProvider {
private static VariantContext ROOT;
private final static List<File> testSourceVCFs = Arrays.asList(
new File(BaseTest.testDir + "ILLUMINA.wex.broad_phase2_baseline.20111114.both.exome.genotypes.1000.vcf"),
new File(BaseTest.testDir + "dbsnp_135.b37.1000.vcf")
new File(BaseTest.privateTestDir + "ILLUMINA.wex.broad_phase2_baseline.20111114.both.exome.genotypes.1000.vcf"),
new File(BaseTest.privateTestDir + "dbsnp_135.b37.1000.vcf")
);
public abstract static class VariantContextIOTest {

12
public/scala/test/org/broadinstitute/sting/queue/pipeline/DataProcessingPipelineTest.scala
View File

@ -36,9 +36,9 @@ class DataProcessingPipelineTest {
spec.name = "DataProcessingPipeline"
spec.args = Array(
" -S public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala",
" -R " + BaseTest.testDir + "exampleFASTA.fasta",
" -i " + BaseTest.testDir + "exampleBAM.bam",
" -D " + BaseTest.testDir + "exampleDBSNP.vcf",
" -R " + BaseTest.publicTestDir + "exampleFASTA.fasta",
" -i " + BaseTest.publicTestDir + "exampleBAM.bam",
" -D " + BaseTest.publicTestDir + "exampleDBSNP.vcf",
" -nv ",
" -test ",
" -p " + projectName).mkString
@ -54,9 +54,9 @@ class DataProcessingPipelineTest {
spec.name = "DataProcessingPipeline"
spec.args = Array(
" -S public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala",
" -R " + BaseTest.testDir + "exampleFASTA.fasta",
" -i " + BaseTest.testDir + "exampleBAM.bam",
" -D " + BaseTest.testDir + "exampleDBSNP.vcf",
" -R " + BaseTest.publicTestDir + "exampleFASTA.fasta",
" -i " + BaseTest.publicTestDir + "exampleBAM.bam",
" -D " + BaseTest.publicTestDir + "exampleDBSNP.vcf",
" -nv ",
" -test ",
" -bwa /home/unix/carneiro/bin/bwa",

6
public/scala/test/org/broadinstitute/sting/queue/pipeline/PacbioProcessingPipelineTest.scala
View File

@ -35,11 +35,11 @@ class PacbioProcessingPipelineTest {
spec.name = "pacbioProcessingPipeline"
spec.args = Array(
" -S public/scala/qscript/org/broadinstitute/sting/queue/qscripts/PacbioProcessingPipeline.scala",
" -R " + BaseTest.testDir + "exampleFASTA.fasta",
" -i " + BaseTest.testDir + "exampleBAM.bam",
" -R " + BaseTest.publicTestDir + "exampleFASTA.fasta",
" -i " + BaseTest.publicTestDir + "exampleBAM.bam",
" -blasr ",
" -test ",
" -D " + BaseTest.testDir + "exampleDBSNP.vcf").mkString
" -D " + BaseTest.publicTestDir + "exampleDBSNP.vcf").mkString
spec.fileMD5s += testOut -> "cf147e7f56806598371f8d5d6794b852"
PipelineTest.executeTest(spec)
}

4
public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/DevNullOutputPipelineTest.scala
View File

@ -59,8 +59,8 @@ class DevNullOutputPipelineTest {
spec.name = "devnulloutput"
spec.args = Array(
" -S public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/DevNullOutput.scala",
" -R " + BaseTest.testDir + "exampleFASTA.fasta",
" -I " + BaseTest.testDir + "exampleBAM.bam").mkString
" -R " + BaseTest.publicTestDir + "exampleFASTA.fasta",
" -I " + BaseTest.publicTestDir + "exampleBAM.bam").mkString
spec.jobRunners = PipelineTest.allJobRunners
PipelineTest.executeTest(spec)
}

4
public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/ExampleCountLociPipelineTest.scala
View File

@ -36,8 +36,8 @@ class ExampleCountLociPipelineTest {
spec.name = "countloci"
spec.args = Array(
" -S public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleCountLoci.scala",
" -R " + BaseTest.testDir + "exampleFASTA.fasta",
" -I " + BaseTest.testDir + "exampleBAM.bam",
" -R " + BaseTest.publicTestDir + "exampleFASTA.fasta",
" -I " + BaseTest.publicTestDir + "exampleBAM.bam",
" -o " + testOut).mkString
spec.fileMD5s += testOut -> "ade93df31a6150321c1067e749cae9be"
PipelineTest.executeTest(spec)

4
public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/ExampleCountReadsPipelineTest.scala
View File

@ -35,8 +35,8 @@ class ExampleCountReadsPipelineTest {
spec.name = "countreads"
spec.args = Array(
" -S public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleCountReads.scala",
" -R " + BaseTest.testDir + "exampleFASTA.fasta",
" -I " + BaseTest.testDir + "exampleBAM.bam").mkString
" -R " + BaseTest.publicTestDir + "exampleFASTA.fasta",
" -I " + BaseTest.publicTestDir + "exampleBAM.bam").mkString
PipelineTest.executeTest(spec)
}
}

4
public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/ExampleReadFilterPipelineTest.scala
View File

@ -83,8 +83,8 @@ class ExampleReadFilterPipelineTest {
spec.name = "examplereadfilter"
spec.args = Array(
" -S public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleReadFilter.scala",
" -R " + BaseTest.testDir + "exampleFASTA.fasta",
" -I " + BaseTest.testDir + "exampleBAM.bam").mkString
" -R " + BaseTest.publicTestDir + "exampleFASTA.fasta",
" -I " + BaseTest.publicTestDir + "exampleBAM.bam").mkString
PipelineTest.executeTest(spec)
}
}

4
public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/ExampleUnifiedGenotyperPipelineTest.scala
View File

@ -35,8 +35,8 @@ class ExampleUnifiedGenotyperPipelineTest {
spec.name = "unifiedgenotyper"
spec.args = Array(
" -S public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleUnifiedGenotyper.scala",
" -R " + BaseTest.testDir + "exampleFASTA.fasta",
" -I " + BaseTest.testDir + "exampleBAM.bam",
" -R " + BaseTest.publicTestDir + "exampleFASTA.fasta",
" -I " + BaseTest.publicTestDir + "exampleBAM.bam",
" -filter QD",
" -filterExpression 'QD < 2.0'").mkString
spec.jobRunners = PipelineTest.allJobRunners