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Move BaseUtils back to the GATK by request, along with associated utility methods

This commit is contained in:
David Roazen 2013-01-30 12:54:57 -05:00
parent 51a322fb54
commit 9985f82a7a
66 changed files with 153 additions and 155 deletions
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2
protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GCContent.java
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@ -54,7 +54,7 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompa
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.variant.vcf.VCFHeaderLineType;
import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;

2
protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java
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@ -55,7 +55,7 @@ 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.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.QualityUtils;
import org.broadinstitute.variant.vcf.VCFHeaderLineType;

2
protected/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java
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@ -60,7 +60,7 @@ import org.broadinstitute.sting.gatk.iterators.ReadTransformer;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.baq.BAQ;
import org.broadinstitute.sting.utils.clipping.ReadClipper;
import org.broadinstitute.sting.utils.collections.Pair;

2
protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidSNPGenotypeLikelihoods.java
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@ -47,7 +47,7 @@
package org.broadinstitute.sting.gatk.walkers.genotyper;
import net.sf.samtools.SAMUtils;
import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.QualityUtils;
import org.broadinstitute.sting.utils.exceptions.UserException;

3
protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidySNPGenotypeLikelihoods.java
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@ -49,9 +49,8 @@ package org.broadinstitute.sting.gatk.walkers.genotyper;
import net.sf.samtools.SAMUtils;
import org.broadinstitute.sting.gatk.walkers.genotyper.afcalc.ExactACset;
import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.baq.BAQ;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.pileup.PileupElement;

2
protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidySNPGenotypeLikelihoodsCalculationModel.java
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@ -77,7 +77,7 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.utils.*;
import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.variant.variantcontext.*;
import java.util.*;

2
protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java
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@ -51,7 +51,7 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.pileup.PileupElement;

2
protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java
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@ -52,7 +52,7 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.indels.PairHMMIndelErrorModel;
import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.Haplotype;

2
protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java
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@ -51,7 +51,7 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.MathUtils;

2
protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
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@ -62,7 +62,7 @@ import org.broadinstitute.sting.utils.*;
import org.broadinstitute.sting.utils.baq.BAQ;
import org.broadinstitute.sting.utils.classloader.PluginManager;
import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.variant.vcf.VCFConstants;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.pileup.PileupElement;

2
protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngine.java
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@ -58,7 +58,7 @@ import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.variant.variantcontext.*;
import java.io.PrintStream;

2
protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
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@ -75,7 +75,7 @@ import org.broadinstitute.sting.utils.sam.NWaySAMFileWriter;
import org.broadinstitute.sting.utils.sam.ReadUtils;
import org.broadinstitute.sting.utils.text.TextFormattingUtils;
import org.broadinstitute.sting.utils.text.XReadLines;
import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.variant.variantcontext.VariantContext;
import java.io.File;

2
protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/BaseArray.java
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@ -46,7 +46,7 @@
package org.broadinstitute.sting.gatk.walkers.phasing;
import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.BaseUtils;
import java.util.Arrays;
import java.util.LinkedList;

2
protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhasingRead.java
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@ -46,7 +46,7 @@
package org.broadinstitute.sting.gatk.walkers.phasing;
import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.QualityUtils;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;

2
protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasing.java
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@ -59,7 +59,7 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.HasGenomeLocation;
import org.broadinstitute.sting.utils.SampleUtils;

2
protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/SNPallelePair.java
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@ -46,7 +46,7 @@
package org.broadinstitute.sting.gatk.walkers.phasing;
import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.variant.variantcontext.Allele;
import org.broadinstitute.variant.variantcontext.Genotype;

4
protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
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@ -59,6 +59,7 @@ 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.variant.GATKVariantContextUtils;
import org.broadinstitute.variant.vcf.VCFHeader;
import org.broadinstitute.variant.vcf.VCFHeaderLine;
import org.broadinstitute.sting.utils.collections.ExpandingArrayList;
@ -66,7 +67,6 @@ import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.sting.utils.io.Resource;
import org.broadinstitute.variant.variantcontext.VariantContext;
import org.broadinstitute.variant.variantcontext.VariantContextUtils;
import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter;
import java.io.File;
@ -274,7 +274,7 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
datum.loc = getToolkit().getGenomeLocParser().createGenomeLoc(vc);
datum.originalQual = vc.getPhredScaledQual();
datum.isSNP = vc.isSNP() && vc.isBiallelic();
datum.isTransition = datum.isSNP && VariantContextUtils.isTransition(vc);
datum.isTransition = datum.isSNP && GATKVariantContextUtils.isTransition(vc);
// Loop through the training data sets and if they overlap this loci then update the prior and training status appropriately
dataManager.parseTrainingSets( tracker, context.getLocation(), vc, datum, TRUST_ALL_POLYMORPHIC );

2
protected/java/src/org/broadinstitute/sting/utils/recalibration/RecalUtils.java
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@ -52,7 +52,7 @@ import org.broadinstitute.sting.gatk.report.GATKReportTable;
import org.broadinstitute.sting.gatk.walkers.bqsr.RecalibrationArgumentCollection;
import org.broadinstitute.sting.utils.classloader.JVMUtils;
import org.broadinstitute.sting.utils.recalibration.covariates.*;
import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.R.RScriptExecutor;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.classloader.PluginManager;

2
protected/java/src/org/broadinstitute/sting/utils/recalibration/covariates/ContextCovariate.java
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@ -48,7 +48,7 @@ package org.broadinstitute.sting.utils.recalibration.covariates;
import org.apache.log4j.Logger;
import org.broadinstitute.sting.gatk.walkers.bqsr.RecalibrationArgumentCollection;
import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.clipping.ClippingRepresentation;
import org.broadinstitute.sting.utils.clipping.ReadClipper;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;

2
protected/java/src/org/broadinstitute/sting/utils/recalibration/covariates/CycleCovariate.java
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@ -48,7 +48,7 @@ package org.broadinstitute.sting.utils.recalibration.covariates;
import org.broadinstitute.sting.utils.recalibration.ReadCovariates;
import org.broadinstitute.sting.gatk.walkers.bqsr.RecalibrationArgumentCollection;
import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.NGSPlatform;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;

2
protected/java/src/org/broadinstitute/sting/utils/recalibration/covariates/RepeatCovariate.java
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@ -52,7 +52,7 @@ import org.broadinstitute.sting.gatk.walkers.bqsr.RecalibrationArgumentCollectio
import org.broadinstitute.sting.utils.recalibration.ReadCovariates;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.collections.Pair;
import java.util.Arrays;

2
protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/ArtificialReadPileupTestProvider.java
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@ -52,7 +52,7 @@ import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.utils.locusiterator.LocusIteratorByState;
import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.QualityUtils;

2
protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyGenotypeLikelihoodsUnitTest.java
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@ -50,7 +50,7 @@ import net.sf.samtools.SAMUtils;
import org.apache.log4j.Logger;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.walkers.Walker;
import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;

2
protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/ConcordanceMetricsUnitTest.java
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@ -51,7 +51,7 @@ import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.variant.variantcontext.Allele;
import org.broadinstitute.variant.variantcontext.Genotype;
import org.broadinstitute.variant.variantcontext.GenotypeBuilder;

2
protected/java/test/org/broadinstitute/sting/utils/pairhmm/PairHMMUnitTest.java
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@ -50,7 +50,7 @@ package org.broadinstitute.sting.utils.pairhmm;
// the imports for unit testing.
import org.broadinstitute.sting.BaseTest;
import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.Utils;
import org.testng.Assert;
import org.testng.annotations.DataProvider;

2
protected/java/test/org/broadinstitute/sting/utils/recalibration/RepeatCovariatesUnitTest.java
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@ -52,7 +52,7 @@ import org.broadinstitute.sting.utils.recalibration.covariates.*;
import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.collections.Pair;
import org.testng.Assert;
import org.testng.annotations.BeforeClass;

2
public/java/src/org/broadinstitute/sting/alignment/Alignment.java
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@ -26,7 +26,7 @@
package org.broadinstitute.sting.alignment;
import net.sf.samtools.*;
import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;

2
public/java/src/org/broadinstitute/sting/alignment/AlignmentValidation.java
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@ -33,7 +33,7 @@ import org.broadinstitute.sting.gatk.CommandLineGATK;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.ReadWalker;
import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;

2
public/java/src/org/broadinstitute/sting/alignment/bwa/java/AlignerTestHarness.java
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@ -29,7 +29,7 @@ import net.sf.picard.reference.IndexedFastaSequenceFile;
import net.sf.samtools.*;
import org.broadinstitute.sting.alignment.Aligner;
import org.broadinstitute.sting.alignment.Alignment;
import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import java.io.File;

2
public/java/src/org/broadinstitute/sting/alignment/bwa/java/BWAJavaAligner.java
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@ -31,7 +31,7 @@ import org.broadinstitute.sting.alignment.Alignment;
import org.broadinstitute.sting.alignment.bwa.BWAAligner;
import org.broadinstitute.sting.alignment.bwa.BWAConfiguration;
import org.broadinstitute.sting.alignment.reference.bwt.*;
import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.Utils;
import java.io.File;

2
public/java/src/org/broadinstitute/sting/gatk/contexts/ReferenceContext.java
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@ -27,7 +27,7 @@ package org.broadinstitute.sting.gatk.contexts;
import com.google.java.contract.Ensures;
import com.google.java.contract.Requires;
import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser;

2
public/java/src/org/broadinstitute/sting/gatk/downsampling/AlleleBiasedDownsamplingUtils.java
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@ -29,7 +29,7 @@ import net.sf.samtools.SAMReadGroupRecord;
import org.broadinstitute.sting.utils.*;
import org.broadinstitute.sting.utils.pileup.*;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.variant.variantcontext.Allele;
import java.io.PrintStream;

2
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseCounts.java
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@ -31,7 +31,7 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.variant.vcf.VCFHeaderLineType;
import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.variant.variantcontext.VariantContext;

2
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/NBaseCount.java
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@ -31,7 +31,7 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.variant.vcf.VCFHeaderLineType;
import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.pileup.PileupElement;

2
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
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@ -36,7 +36,7 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.*;
import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.classloader.PluginManager;
import org.broadinstitute.variant.vcf.*;

2
public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLoci.java
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@ -39,7 +39,7 @@ import org.broadinstitute.sting.utils.*;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.BaseUtils;
import java.io.File;
import java.io.FileNotFoundException;

2
public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CoverageUtils.java
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@ -28,7 +28,7 @@ package org.broadinstitute.sting.gatk.walkers.coverage;
import net.sf.samtools.SAMReadGroupRecord;
import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.fragments.FragmentCollection;

2
public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverage.java
View File

@ -41,7 +41,7 @@ import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
import org.broadinstitute.sting.gatk.refdata.utils.LocationAwareSeekableRODIterator;
import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList;
import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.codecs.refseq.RefSeqCodec;

2
public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageStats.java
View File

@ -25,7 +25,7 @@
package org.broadinstitute.sting.gatk.walkers.coverage;
import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.exceptions.UserException;
import java.util.HashMap;

2
public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/GCContentByInterval.java
View File

@ -31,7 +31,7 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;

2
public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ErrorRatePerCycle.java
View File

@ -34,7 +34,7 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.report.GATKReport;
import org.broadinstitute.sting.gatk.report.GATKReportTable;
import org.broadinstitute.sting.gatk.walkers.LocusWalker;
import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.QualityUtils;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.sting.utils.pileup.PileupElement;

2
public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaStats.java
View File

@ -31,7 +31,7 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.RefWalker;
import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import java.io.PrintStream;

2
public/java/src/org/broadinstitute/sting/gatk/walkers/qc/QCRef.java
View File

@ -33,7 +33,7 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.RefWalker;
import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.exceptions.StingException;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;

2
public/java/src/org/broadinstitute/sting/gatk/walkers/readutils/ClipReads.java
View File

@ -40,7 +40,7 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.DataSource;
import org.broadinstitute.sting.gatk.walkers.ReadWalker;
import org.broadinstitute.sting.gatk.walkers.Requires;
import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.clipping.ClippingOp;
import org.broadinstitute.sting.utils.clipping.ClippingRepresentation;

2
public/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java
View File

@ -41,7 +41,7 @@ import org.broadinstitute.sting.utils.codecs.table.TableFeature;
import org.broadinstitute.sting.gatk.walkers.DataSource;
import org.broadinstitute.sting.gatk.walkers.Requires;
import org.broadinstitute.sting.gatk.walkers.RodWalker;
import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;

4
public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MultiallelicSummary.java
View File

@ -32,9 +32,9 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
import org.broadinstitute.variant.variantcontext.Allele;
import org.broadinstitute.variant.variantcontext.VariantContext;
import org.broadinstitute.variant.variantcontext.VariantContextUtils;
@Analysis(description = "Evaluation summary for multi-allelic variants")
public class MultiallelicSummary extends VariantEvaluator implements StandardEval {
@ -122,7 +122,7 @@ public class MultiallelicSummary extends VariantEvaluator implements StandardEva
private void calculatePairwiseTiTv(VariantContext vc) {
for ( Allele alt : vc.getAlternateAlleles() ) {
if ( VariantContextUtils.isTransition(vc.getReference(), alt) )
if ( GATKVariantContextUtils.isTransition(vc.getReference(), alt) )
nTi++;
else
nTv++;

6
public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/TiTvVariantEvaluator.java
View File

@ -30,9 +30,9 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
import org.broadinstitute.variant.variantcontext.VariantContext;
import org.broadinstitute.variant.variantcontext.VariantContextUtils;
@Analysis(description = "Ti/Tv Variant Evaluator")
public class TiTvVariantEvaluator extends VariantEvaluator implements StandardEval {
@ -61,7 +61,7 @@ public class TiTvVariantEvaluator extends VariantEvaluator implements StandardEv
public void updateTiTv(VariantContext vc, boolean updateStandard) {
if (vc != null && vc.isSNP() && vc.isBiallelic() && vc.isPolymorphicInSamples()) {
if (VariantContextUtils.isTransition(vc)) {
if ( GATKVariantContextUtils.isTransition(vc)) {
if (updateStandard) nTiInComp++;
else nTi++;
} else {

4
public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantSummary.java
View File

@ -35,11 +35,11 @@ import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
import org.broadinstitute.variant.vcf.VCFConstants;
import org.broadinstitute.sting.utils.interval.IntervalUtils;
import org.broadinstitute.variant.variantcontext.Genotype;
import org.broadinstitute.variant.variantcontext.VariantContext;
import org.broadinstitute.variant.variantcontext.VariantContextUtils;
import java.util.*;
@ -226,7 +226,7 @@ public class VariantSummary extends VariantEvaluator implements StandardEval {
// type specific calculations
if ( type == Type.SNP && eval.isBiallelic() ) {
titvTable = VariantContextUtils.isTransition(eval) ? transitionsPerSample : transversionsPerSample;
titvTable = GATKVariantContextUtils.isTransition(eval) ? transitionsPerSample : transversionsPerSample;
titvTable.inc(type, ALL);
}

6
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java
View File

@ -40,12 +40,12 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.RodWalker;
import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
import org.broadinstitute.variant.vcf.*;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.variant.variantcontext.VariantContext;
import org.broadinstitute.variant.variantcontext.VariantContextBuilder;
import org.broadinstitute.variant.variantcontext.VariantContextUtils;
import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter;
import org.broadinstitute.variant.variantcontext.writer.VariantContextWriterFactory;
@ -122,7 +122,7 @@ public class LiftoverVariants extends RodWalker<Integer, Integer> {
if ( toInterval != null ) {
// check whether the strand flips, and if so reverse complement everything
if ( fromInterval.isPositiveStrand() != toInterval.isPositiveStrand() && vc.isPointEvent() ) {
vc = VariantContextUtils.reverseComplement(vc);
vc = GATKVariantContextUtils.reverseComplement(vc);
}
vc = new VariantContextBuilder(vc).loc(toInterval.getSequence(), toInterval.getStart(), toInterval.getStart() + length).make();
@ -133,7 +133,7 @@ public class LiftoverVariants extends RodWalker<Integer, Integer> {
.attribute("OriginalStart", fromInterval.getStart()).make();
}
if ( originalVC.isSNP() && originalVC.isBiallelic() && VariantContextUtils.getSNPSubstitutionType(originalVC) != VariantContextUtils.getSNPSubstitutionType(vc) ) {
if ( originalVC.isSNP() && originalVC.isBiallelic() && GATKVariantContextUtils.getSNPSubstitutionType(originalVC) != GATKVariantContextUtils.getSNPSubstitutionType(vc) ) {
logger.warn(String.format("VCF at %s / %d => %s / %d is switching substitution type %s/%s to %s/%s",
originalVC.getChr(), originalVC.getStart(), vc.getChr(), vc.getStart(),
originalVC.getReference(), originalVC.getAlternateAllele(0), vc.getReference(), vc.getAlternateAllele(0)));

3
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java
View File

@ -41,7 +41,6 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.RodWalker;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.variant.variantcontext.VariantContextUtils;
import java.io.PrintStream;
import java.lang.reflect.Array;
@ -432,7 +431,7 @@ public class VariantsToTable extends RodWalker<Integer, Integer> {
getters.put("QUAL", new Getter() { public String get(VariantContext vc) { return Double.toString(vc.getPhredScaledQual()); } });
getters.put("TRANSITION", new Getter() { public String get(VariantContext vc) {
if ( vc.isSNP() && vc.isBiallelic() )
return VariantContextUtils.isTransition(vc) ? "1" : "0";
return GATKVariantContextUtils.isTransition(vc) ? "1" : "0";
else
return "-1";
}});

2
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java
View File

@ -39,7 +39,7 @@ import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
import org.broadinstitute.sting.gatk.walkers.Reference;
import org.broadinstitute.sting.gatk.walkers.RodWalker;
import org.broadinstitute.sting.gatk.walkers.Window;
import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.codecs.hapmap.RawHapMapFeature;

17
public/java/src/org/broadinstitute/variant/utils/BaseUtils.java → public/java/src/org/broadinstitute/sting/utils/BaseUtils.java
View File

@ -23,12 +23,14 @@
* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.variant.utils;
package org.broadinstitute.sting.utils;
import net.sf.samtools.util.StringUtil;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.UserException;
import java.util.Arrays;
import java.util.Random;
/**
* BaseUtils contains some basic utilities for manipulating nucleotides.
@ -95,9 +97,6 @@ public class BaseUtils {
baseIndexWithIupacMap['v'] = Base.N.ordinal();
}
// Use a fixed random seed to allow for deterministic results when using random bases
private static final Random randomNumberGen = new Random(47382911L);
/// In genetics, a transition is a mutation changing a purine to another purine nucleotide (A <-> G) or
// a pyrimidine to another pyrimidine nucleotide (C <-> T).
// Approximately two out of every three single nucleotide polymorphisms (SNPs) are transitions.
@ -174,7 +173,7 @@ public class BaseUtils {
if ( baseIndex == Base.N.ordinal() ) {
bases[i] = 'N';
} else if ( errorOnBadReferenceBase && baseIndex == -1 ) {
throw new IllegalStateException("We encountered a non-standard non-IUPAC base in the provided reference: '" + bases[i] + "'");
throw new UserException.BadInput("We encountered a non-standard non-IUPAC base in the provided reference: '" + bases[i] + "'");
}
}
return bases;
@ -251,7 +250,7 @@ public class BaseUtils {
*/
static public int simpleBaseToBaseIndex(final byte base) {
if ( base < 0 || base >= 256 )
throw new IllegalArgumentException("Non-standard bases were encountered in either the input reference or BAM file(s)");
throw new UserException.BadInput("Non-standard bases were encountered in either the input reference or BAM file(s)");
return baseIndexMap[base];
}
@ -491,7 +490,7 @@ public class BaseUtils {
int randomBaseIndex = excludeBaseIndex;
while (randomBaseIndex == excludeBaseIndex) {
randomBaseIndex = randomNumberGen.nextInt(4);
randomBaseIndex = GenomeAnalysisEngine.getRandomGenerator().nextInt(4);
}
return randomBaseIndex;
@ -515,7 +514,7 @@ public class BaseUtils {
case 'N':
return 'N';
default:
throw new IllegalArgumentException("base must be A, C, G or T. " + (char) base + " is not a valid base.");
throw new ReviewedStingException("base must be A, C, G or T. " + (char) base + " is not a valid base.");
}
}
}

2
public/java/src/org/broadinstitute/sting/utils/duplicates/DupUtils.java
View File

@ -25,7 +25,7 @@
package org.broadinstitute.sting.utils.duplicates;
import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.QualityUtils;

2
public/java/src/org/broadinstitute/sting/utils/fasta/CachingIndexedFastaSequenceFile.java
View File

@ -33,7 +33,7 @@ import net.sf.samtools.SAMSequenceRecord;
import net.sf.samtools.util.StringUtil;
import org.apache.log4j.Priority;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.BaseUtils;
import java.io.File;
import java.io.FileNotFoundException;

2
public/java/src/org/broadinstitute/sting/utils/genotyper/DiploidGenotype.java
View File

@ -25,7 +25,7 @@
package org.broadinstitute.sting.utils.genotyper;
import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.BaseUtils;
public enum DiploidGenotype {
AA ('A', 'A'),

2
public/java/src/org/broadinstitute/sting/utils/pileup/PileupElement.java
View File

@ -29,7 +29,7 @@ import com.google.java.contract.Ensures;
import com.google.java.contract.Requires;
import net.sf.samtools.CigarElement;
import net.sf.samtools.CigarOperator;
import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;

2
public/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedPileupImpl.java
View File

@ -32,7 +32,7 @@ import org.broadinstitute.sting.utils.fragments.FragmentCollection;
import org.broadinstitute.sting.utils.fragments.FragmentUtils;
import org.broadinstitute.sting.utils.locusiterator.LocusIteratorByState;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.BaseUtils;
import java.util.*;

2
public/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java
View File

@ -30,7 +30,7 @@ import net.sf.samtools.CigarElement;
import net.sf.samtools.CigarOperator;
import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;

2
public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java
View File

@ -34,7 +34,7 @@ import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.NGSPlatform;
import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.BaseUtils;
import java.io.File;
import java.util.*;

67
public/java/src/org/broadinstitute/sting/utils/variant/GATKVariantContextUtils.java
View File

@ -30,10 +30,7 @@ import org.apache.commons.lang.ArrayUtils;
import org.apache.log4j.Logger;
import org.broad.tribble.TribbleException;
import org.broad.tribble.util.popgen.HardyWeinbergCalculation;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.*;
import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.variant.variantcontext.*;
import org.broadinstitute.variant.vcf.VCFConstants;
@ -108,6 +105,68 @@ public class GATKVariantContextUtils {
return genomeLocParser.createGenomeLoc(vc.getChr(), vc.getStart(), vc.getEnd(), true);
}
public static BaseUtils.BaseSubstitutionType getSNPSubstitutionType(VariantContext context) {
if (!context.isSNP() || !context.isBiallelic())
throw new IllegalStateException("Requested SNP substitution type for bialleic non-SNP " + context);
return BaseUtils.SNPSubstitutionType(context.getReference().getBases()[0], context.getAlternateAllele(0).getBases()[0]);
}
/**
* If this is a BiAlleic SNP, is it a transition?
*/
public static boolean isTransition(VariantContext context) {
return getSNPSubstitutionType(context) == BaseUtils.BaseSubstitutionType.TRANSITION;
}
/**
* If this is a BiAlleic SNP, is it a transversion?
*/
public static boolean isTransversion(VariantContext context) {
return getSNPSubstitutionType(context) == BaseUtils.BaseSubstitutionType.TRANSVERSION;
}
public static boolean isTransition(Allele ref, Allele alt) {
return BaseUtils.SNPSubstitutionType(ref.getBases()[0], alt.getBases()[0]) == BaseUtils.BaseSubstitutionType.TRANSITION;
}
public static boolean isTransversion(Allele ref, Allele alt) {
return BaseUtils.SNPSubstitutionType(ref.getBases()[0], alt.getBases()[0]) == BaseUtils.BaseSubstitutionType.TRANSVERSION;
}
/**
* Returns a context identical to this with the REF and ALT alleles reverse complemented.
*
* @param vc variant context
* @return new vc
*/
public static VariantContext reverseComplement(VariantContext vc) {
// create a mapping from original allele to reverse complemented allele
HashMap<Allele, Allele> alleleMap = new HashMap<Allele, Allele>(vc.getAlleles().size());
for ( Allele originalAllele : vc.getAlleles() ) {
Allele newAllele;
if ( originalAllele.isNoCall() )
newAllele = originalAllele;
else
newAllele = Allele.create(BaseUtils.simpleReverseComplement(originalAllele.getBases()), originalAllele.isReference());
alleleMap.put(originalAllele, newAllele);
}
// create new Genotype objects
GenotypesContext newGenotypes = GenotypesContext.create(vc.getNSamples());
for ( final Genotype genotype : vc.getGenotypes() ) {
List<Allele> newAlleles = new ArrayList<Allele>();
for ( Allele allele : genotype.getAlleles() ) {
Allele newAllele = alleleMap.get(allele);
if ( newAllele == null )
newAllele = Allele.NO_CALL;
newAlleles.add(newAllele);
}
newGenotypes.add(new GenotypeBuilder(genotype).alleles(newAlleles).make());
}
return new VariantContextBuilder(vc).alleles(alleleMap.values()).genotypes(newGenotypes).make();
}
/**
* Returns true iff VC is an non-complex indel where every allele represents an expansion or
* contraction of a series of identical bases in the reference.

4
public/java/src/org/broadinstitute/variant/variantcontext/Allele.java
View File

@ -25,7 +25,7 @@
package org.broadinstitute.variant.variantcontext;
import org.broadinstitute.variant.utils.BaseUtils;
import net.sf.samtools.util.StringUtil;
import java.util.Arrays;
import java.util.Collection;
@ -130,7 +130,7 @@ public class Allele implements Comparable<Allele> {
if ( isRef ) throw new IllegalArgumentException("Cannot tag a symbolic allele as the reference allele");
}
else {
BaseUtils.convertToUpperCase(bases);
StringUtil.toUpperCase(bases);
}
this.isRef = isRef;

63
public/java/src/org/broadinstitute/variant/variantcontext/VariantContextUtils.java
View File

@ -30,7 +30,6 @@ import com.google.java.contract.Requires;
import org.apache.commons.jexl2.Expression;
import org.apache.commons.jexl2.JexlEngine;
import org.broad.tribble.TribbleException;
import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.variant.utils.GeneralUtils;
import org.broadinstitute.variant.vcf.*;
@ -432,40 +431,6 @@ public class VariantContextUtils {
// }
/**
* Returns a context identical to this with the REF and ALT alleles reverse complemented.
*
* @param vc variant context
* @return new vc
*/
public static VariantContext reverseComplement(VariantContext vc) {
// create a mapping from original allele to reverse complemented allele
HashMap<Allele, Allele> alleleMap = new HashMap<Allele, Allele>(vc.getAlleles().size());
for ( Allele originalAllele : vc.getAlleles() ) {
Allele newAllele;
if ( originalAllele.isNoCall() )
newAllele = originalAllele;
else
newAllele = Allele.create(BaseUtils.simpleReverseComplement(originalAllele.getBases()), originalAllele.isReference());
alleleMap.put(originalAllele, newAllele);
}
// create new Genotype objects
GenotypesContext newGenotypes = GenotypesContext.create(vc.getNSamples());
for ( final Genotype genotype : vc.getGenotypes() ) {
List<Allele> newAlleles = new ArrayList<Allele>();
for ( Allele allele : genotype.getAlleles() ) {
Allele newAllele = alleleMap.get(allele);
if ( newAllele == null )
newAllele = Allele.NO_CALL;
newAlleles.add(newAllele);
}
newGenotypes.add(new GenotypeBuilder(genotype).alleles(newAlleles).make());
}
return new VariantContextBuilder(vc).alleles(alleleMap.values()).genotypes(newGenotypes).make();
}
public static VariantContext purgeUnallowedGenotypeAttributes(VariantContext vc, Set<String> allowedAttributes) {
if ( allowedAttributes == null )
return vc;
@ -483,34 +448,6 @@ public class VariantContextUtils {
return new VariantContextBuilder(vc).genotypes(newGenotypes).make();
}
public static BaseUtils.BaseSubstitutionType getSNPSubstitutionType(VariantContext context) {
if (!context.isSNP() || !context.isBiallelic())
throw new IllegalStateException("Requested SNP substitution type for bialleic non-SNP " + context);
return BaseUtils.SNPSubstitutionType(context.getReference().getBases()[0], context.getAlternateAllele(0).getBases()[0]);
}
/**
* If this is a BiAlleic SNP, is it a transition?
*/
public static boolean isTransition(VariantContext context) {
return getSNPSubstitutionType(context) == BaseUtils.BaseSubstitutionType.TRANSITION;
}
/**
* If this is a BiAlleic SNP, is it a transversion?
*/
public static boolean isTransversion(VariantContext context) {
return getSNPSubstitutionType(context) == BaseUtils.BaseSubstitutionType.TRANSVERSION;
}
public static boolean isTransition(Allele ref, Allele alt) {
return BaseUtils.SNPSubstitutionType(ref.getBases()[0], alt.getBases()[0]) == BaseUtils.BaseSubstitutionType.TRANSITION;
}
public static boolean isTransversion(Allele ref, Allele alt) {
return BaseUtils.SNPSubstitutionType(ref.getBases()[0], alt.getBases()[0]) == BaseUtils.BaseSubstitutionType.TRANSVERSION;
}
public static int getSize( VariantContext vc ) {
return vc.getEnd() - vc.getStart() + 1;
}

14
public/java/test/org/broadinstitute/variant/utils/BaseUtilsUnitTest.java → public/java/test/org/broadinstitute/sting/utils/BaseUtilsUnitTest.java
View File

@ -23,20 +23,22 @@
* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.variant.utils;
package org.broadinstitute.sting.utils;
import org.broadinstitute.variant.VariantBaseTest;
import org.broadinstitute.sting.BaseTest;
import org.testng.Assert;
import org.testng.annotations.Test;
import org.testng.annotations.BeforeClass;
public class BaseUtilsUnitTest extends VariantBaseTest {
public class BaseUtilsUnitTest extends BaseTest {
@BeforeClass
public void init() { }
@Test
public void testMostFrequentBaseFraction() {
logger.warn("Executing testMostFrequentBaseFraction");
compareFrequentBaseFractionToExpected("AAAAA", 1.0);
compareFrequentBaseFractionToExpected("ACCG", 0.5);
compareFrequentBaseFractionToExpected("ACCCCTTTTG", 4.0/10.0);
@ -44,7 +46,7 @@ public class BaseUtilsUnitTest extends VariantBaseTest {
private void compareFrequentBaseFractionToExpected(String sequence, double expected) {
double fraction = BaseUtils.mostFrequentBaseFraction(sequence.getBytes());
Assert.assertTrue(GeneralUtils.compareDoubles(fraction, expected) == 0);
Assert.assertTrue(MathUtils.compareDoubles(fraction, expected) == 0);
}
@Test
@ -64,6 +66,8 @@ public class BaseUtilsUnitTest extends VariantBaseTest {
@Test
public void testTransitionTransversion() {
logger.warn("Executing testTransitionTransversion");
Assert.assertTrue( BaseUtils.SNPSubstitutionType( (byte)'A', (byte)'T' ) == BaseUtils.BaseSubstitutionType.TRANSVERSION );
Assert.assertTrue( BaseUtils.SNPSubstitutionType( (byte)'A', (byte)'C' ) == BaseUtils.BaseSubstitutionType.TRANSVERSION );
Assert.assertTrue( BaseUtils.SNPSubstitutionType( (byte)'A', (byte)'G' ) == BaseUtils.BaseSubstitutionType.TRANSITION );
@ -89,6 +93,8 @@ public class BaseUtilsUnitTest extends VariantBaseTest {
@Test
public void testReverseComplementString() {
logger.warn("Executing testReverseComplementString");
compareRCStringToExpected("ACGGT", "ACCGT");
compareRCStringToExpected("TCGTATATCTCGCTATATATATATAGCTCTAGTATA", "TATACTAGAGCTATATATATATAGCGAGATATACGA");
compareRCStringToExpected("AAAN", "NTTT");

2
public/java/test/org/broadinstitute/sting/utils/fasta/CachingIndexedFastaSequenceFileUnitTest.java
View File

@ -252,7 +252,7 @@ public class CachingIndexedFastaSequenceFileUnitTest extends BaseTest {
Assert.assertEquals(changingNs, preservingNs + 4);
}
@Test(enabled = true, expectedExceptions = {IllegalStateException.class})
@Test(enabled = true, expectedExceptions = {UserException.class})
public void testFailOnBadBase() throws FileNotFoundException, InterruptedException {
final String testFasta = privateTestDir + "problematicFASTA.fasta";
final CachingIndexedFastaSequenceFile fasta = new CachingIndexedFastaSequenceFile(new File(testFasta));

2
public/java/test/org/broadinstitute/sting/utils/sam/ReadUtilsUnitTest.java
View File

@ -27,7 +27,7 @@ package org.broadinstitute.sting.utils.sam;
import org.broadinstitute.sting.BaseTest;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.BaseUtils;
import org.testng.Assert;
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;

7
public/java/test/org/broadinstitute/variant/variantcontext/GenotypeLikelihoodsUnitTest.java
View File

@ -31,7 +31,6 @@ package org.broadinstitute.variant.variantcontext;
import org.broad.tribble.TribbleException;
import org.broadinstitute.variant.VariantBaseTest;
import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.variant.utils.GeneralUtils;
import org.testng.Assert;
import org.testng.annotations.Test;
@ -154,9 +153,9 @@ public class GenotypeLikelihoodsUnitTest extends VariantBaseTest {
public void testGetQualFromLikelihoodsMultiAllelic() {
GenotypeLikelihoods gl = GenotypeLikelihoods.fromLog10Likelihoods(triAllelic);
Allele ref = Allele.create(BaseUtils.Base.A.base,true);
Allele alt1 = Allele.create(BaseUtils.Base.C.base);
Allele alt2 = Allele.create(BaseUtils.Base.T.base);
Allele ref = Allele.create((byte)'A',true);
Allele alt1 = Allele.create((byte)'C');
Allele alt2 = Allele.create((byte)'T');
List<Allele> allAlleles = Arrays.asList(ref,alt1,alt2);
List<Allele> gtAlleles = Arrays.asList(alt1,alt2);
GenotypeBuilder gtBuilder = new GenotypeBuilder();