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Moving around classes in VCF and BCF2 

-- Refactored VCF writers into vcf.writers package
-- Moved BCF2Writer to bcf2.writer
-- Updates to all of the walkers using VCFWriter to reflect new packages
-- A large number of files had their headers cleaned up because of this as well
This commit is contained in:
Mark DePristo 2012-05-12 12:24:56 -04:00
parent 679ffdd333
commit c3b8048e2e
48 changed files with 223 additions and 194 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

4
public/java/src/org/broadinstitute/sting/gatk/io/storage/VCFWriterStorage.java
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@ -4,10 +4,10 @@ import net.sf.samtools.util.BlockCompressedOutputStream;
import org.apache.log4j.Logger;
import org.broad.tribble.AbstractFeatureReader;
import org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub;
import org.broadinstitute.sting.utils.codecs.vcf.StandardVCFWriter;
import org.broadinstitute.sting.utils.codecs.vcf.writer.StandardVCFWriter;
import org.broadinstitute.sting.utils.codecs.vcf.VCFCodec;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter;
import org.broadinstitute.sting.utils.codecs.vcf.writer.VCFWriter;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;

2
public/java/src/org/broadinstitute/sting/gatk/io/stubs/VCFWriterArgumentTypeDescriptor.java
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@ -27,7 +27,7 @@ package org.broadinstitute.sting.gatk.io.stubs;
import org.broadinstitute.sting.commandline.*;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter;
import org.broadinstitute.sting.utils.codecs.vcf.writer.VCFWriter;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import java.io.File;

2
public/java/src/org/broadinstitute/sting/gatk/io/stubs/VCFWriterStub.java
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@ -32,7 +32,7 @@ import org.broadinstitute.sting.utils.classloader.JVMUtils;
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.VCFWriter;
import org.broadinstitute.sting.utils.codecs.vcf.writer.VCFWriter;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import java.io.File;

1
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
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@ -38,6 +38,7 @@ import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.classloader.PluginManager;
import org.broadinstitute.sting.utils.codecs.vcf.*;
import org.broadinstitute.sting.utils.codecs.vcf.writer.VCFWriter;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import java.util.*;

1
public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCFWalker.java
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@ -36,6 +36,7 @@ import org.broadinstitute.sting.gatk.walkers.RodWalker;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.codecs.vcf.*;
import org.broadinstitute.sting.utils.codecs.vcf.writer.VCFWriter;
import org.broadinstitute.sting.utils.variantcontext.*;
import java.util.*;

1
public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInputWalker.java
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@ -38,6 +38,7 @@ import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.codecs.vcf.*;
import org.broadinstitute.sting.utils.codecs.vcf.writer.VCFWriter;
import org.broadinstitute.sting.utils.exceptions.StingException;
import org.broadinstitute.sting.utils.variantcontext.*;

2
public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/VariantsToBeagleUnphasedWalker.java
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@ -38,7 +38,7 @@ 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.VCFWriter;
import org.broadinstitute.sting.utils.codecs.vcf.writer.VCFWriter;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.variantcontext.Allele;
import org.broadinstitute.sting.utils.variantcontext.Genotype;

1
public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/DiagnoseTargets.java
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@ -35,6 +35,7 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompa
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.codecs.vcf.*;
import org.broadinstitute.sting.utils.codecs.vcf.writer.VCFWriter;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.variantcontext.Allele;
import org.broadinstitute.sting.utils.variantcontext.Genotype;

1
public/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java
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@ -35,6 +35,7 @@ import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.codecs.vcf.*;
import org.broadinstitute.sting.utils.codecs.vcf.writer.VCFWriter;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.variantcontext.*;

1
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
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@ -39,6 +39,7 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompa
import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.baq.BAQ;
import org.broadinstitute.sting.utils.codecs.vcf.*;
import org.broadinstitute.sting.utils.codecs.vcf.writer.VCFWriter;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.variantcontext.GenotypeLikelihoods;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;

1
public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetectorWalker.java
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@ -53,6 +53,7 @@ import org.broadinstitute.sting.utils.codecs.refseq.RefSeqCodec;
import org.broadinstitute.sting.utils.codecs.refseq.RefSeqFeature;
import org.broadinstitute.sting.utils.codecs.refseq.Transcript;
import org.broadinstitute.sting.utils.codecs.vcf.*;
import org.broadinstitute.sting.utils.codecs.vcf.writer.VCFWriter;
import org.broadinstitute.sting.utils.collections.CircularArray;
import org.broadinstitute.sting.utils.collections.PrimitivePair;
import org.broadinstitute.sting.utils.exceptions.StingException;

2
public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesVCFWriter.java
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@ -29,7 +29,7 @@ import org.apache.log4j.Logger;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter;
import org.broadinstitute.sting.utils.codecs.vcf.writer.VCFWriter;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;

1
public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java
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@ -12,6 +12,7 @@ import org.broadinstitute.sting.gatk.walkers.RodWalker;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.codecs.vcf.*;
import org.broadinstitute.sting.utils.codecs.vcf.writer.VCFWriter;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.variantcontext.*;

2
public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java
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@ -38,6 +38,8 @@ import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.HasGenomeLocation;
import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.codecs.vcf.*;
import org.broadinstitute.sting.utils.codecs.vcf.writer.SortingVCFWriter;
import org.broadinstitute.sting.utils.codecs.vcf.writer.VCFWriter;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.pileup.PileupElement;

2
public/java/src/org/broadinstitute/sting/gatk/walkers/qc/DocumentationTest.java
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@ -32,7 +32,7 @@ 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.RodWalker;
import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter;
import org.broadinstitute.sting.utils.codecs.vcf.writer.VCFWriter;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import java.util.*;

2
public/java/src/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidateWalker.java
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@ -38,7 +38,7 @@ 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.VCFWriter;
import org.broadinstitute.sting.utils.codecs.vcf.writer.VCFWriter;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.sting.utils.variantcontext.VariantContextBuilder;
import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;

1
public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/ValidationSiteSelectorWalker.java
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@ -31,6 +31,7 @@ import org.broadinstitute.sting.gatk.walkers.RodWalker;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.codecs.vcf.*;
import org.broadinstitute.sting.utils.codecs.vcf.writer.VCFWriter;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;

1
public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java
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@ -38,6 +38,7 @@ 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.*;
import org.broadinstitute.sting.utils.codecs.vcf.writer.VCFWriter;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.sting.utils.variantcontext.VariantContextBuilder;

3
public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java
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@ -31,8 +31,7 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter;
import org.broadinstitute.sting.utils.codecs.vcf.writer.VCFWriter;
import org.broadinstitute.sting.utils.collections.ExpandingArrayList;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.variantcontext.Allele;

2
public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
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@ -37,7 +37,7 @@ 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.codecs.vcf.StandardVCFWriter;
import org.broadinstitute.sting.utils.codecs.vcf.writer.StandardVCFWriter;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
import org.broadinstitute.sting.utils.collections.ExpandingArrayList;
import org.broadinstitute.sting.utils.exceptions.UserException;

1
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java
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@ -37,6 +37,7 @@ import org.broadinstitute.sting.gatk.walkers.annotator.ChromosomeCounts;
import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.codecs.vcf.*;
import org.broadinstitute.sting.utils.codecs.vcf.writer.VCFWriter;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.sting.utils.variantcontext.VariantContextBuilder;

2
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java
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@ -34,7 +34,7 @@ import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter;
import org.broadinstitute.sting.utils.codecs.vcf.writer.VCFWriter;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import java.util.Arrays;

2
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java
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@ -37,6 +37,8 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.codecs.vcf.*;
import org.broadinstitute.sting.utils.codecs.vcf.writer.SortingVCFWriter;
import org.broadinstitute.sting.utils.codecs.vcf.writer.VCFWriter;
import org.broadinstitute.sting.utils.sam.AlignmentUtils;
import org.broadinstitute.sting.utils.variantcontext.*;

1
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java
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@ -36,6 +36,7 @@ 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.codecs.vcf.*;
import org.broadinstitute.sting.utils.codecs.vcf.writer.StandardVCFWriter;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.sting.utils.variantcontext.VariantContextBuilder;

2
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/RandomlySplitVariants.java
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@ -33,6 +33,8 @@ 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.codecs.vcf.*;
import org.broadinstitute.sting.utils.codecs.vcf.writer.StandardVCFWriter;
import org.broadinstitute.sting.utils.codecs.vcf.writer.VCFWriter;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;

2
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectHeaders.java
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@ -37,7 +37,7 @@ 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.VCFWriter;
import org.broadinstitute.sting.utils.codecs.vcf.writer.VCFWriter;
import org.broadinstitute.sting.utils.text.ListFileUtils;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;

1
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
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@ -39,6 +39,7 @@ import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine;
import org.broadinstitute.sting.utils.MendelianViolation;
import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.codecs.vcf.*;
import org.broadinstitute.sting.utils.codecs.vcf.writer.VCFWriter;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.text.XReadLines;
import org.broadinstitute.sting.utils.variantcontext.*;

1
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantValidationAssessor.java
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@ -34,6 +34,7 @@ import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.utils.QualityUtils;
import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.codecs.vcf.*;
import org.broadinstitute.sting.utils.codecs.vcf.writer.VCFWriter;
import org.broadinstitute.sting.utils.variantcontext.Allele;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.sting.utils.variantcontext.VariantContextBuilder;

2
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java
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@ -41,6 +41,8 @@ import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.codecs.hapmap.RawHapMapFeature;
import org.broadinstitute.sting.utils.codecs.vcf.*;
import org.broadinstitute.sting.utils.codecs.vcf.writer.SortingVCFWriter;
import org.broadinstitute.sting.utils.codecs.vcf.writer.VCFWriter;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.variantcontext.*;

2
public/java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentDefinitionField.java
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@ -29,7 +29,7 @@ import net.sf.samtools.SAMFileWriter;
import org.broad.tribble.Tribble;
import org.broadinstitute.sting.commandline.*;
import org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterArgumentTypeDescriptor;
import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter;
import org.broadinstitute.sting.utils.codecs.vcf.writer.VCFWriter;
import java.io.File;
import java.lang.annotation.Annotation;

2
public/java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentField.java
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@ -29,7 +29,7 @@ import net.sf.samtools.SAMFileWriter;
import org.apache.commons.lang.StringEscapeUtils;
import org.apache.commons.lang.StringUtils;
import org.broadinstitute.sting.gatk.filters.PlatformUnitFilterHelper;
import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter;
import org.broadinstitute.sting.utils.codecs.vcf.writer.VCFWriter;
import java.io.File;
import java.io.InputStream;

14
public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Codec.java
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@ -186,22 +186,22 @@ public class BCF2Codec implements FeatureCodec<VariantContext> {
// --------------------------------------------------------------------------------
private final SitesInfoForDecoding decodeSitesBlock(final VariantContextBuilder builder) {
final int contigOffset = decoder.decodeInt(BCFType.INT32.getSizeInBytes());
final int contigOffset = decoder.decodeInt(BCF2Type.INT32.getSizeInBytes());
final String contig = lookupContigName(contigOffset);
builder.chr(contig);
final int pos = decoder.decodeInt(BCFType.INT32.getSizeInBytes());
final int refLength = decoder.decodeInt(BCFType.INT32.getSizeInBytes());
final int pos = decoder.decodeInt(BCF2Type.INT32.getSizeInBytes());
final int refLength = decoder.decodeInt(BCF2Type.INT32.getSizeInBytes());
builder.start((long)pos);
builder.stop((long)(pos + refLength - 1)); // minus one because of our open intervals
final Object qual = decoder.decodeSingleValue(BCFType.FLOAT);
final Object qual = decoder.decodeSingleValue(BCF2Type.FLOAT);
if ( qual != null ) {
builder.log10PError(((Double)qual) / -10.0);
}
final int nAlleleInfo = decoder.decodeInt(BCFType.INT32.getSizeInBytes());
final int nFormatSamples = decoder.decodeInt(BCFType.INT32.getSizeInBytes());
final int nAlleleInfo = decoder.decodeInt(BCF2Type.INT32.getSizeInBytes());
final int nFormatSamples = decoder.decodeInt(BCF2Type.INT32.getSizeInBytes());
final int nAlleles = nAlleleInfo >> 16;
final int nInfo = nAlleleInfo & 0x00FF;
final int nFormatFields = nFormatSamples >> 24;
@ -326,7 +326,7 @@ public class BCF2Codec implements FeatureCodec<VariantContext> {
alleles = decodeGenotypeAlleles(siteInfo.alleles, (List<Integer>)values.get(i));
} else if ( field.equals(VCFConstants.GENOTYPE_QUALITY_KEY) ) {
final Integer value = (Integer)values.get(i);
if ( value != BCFType.INT8.getMissingJavaValue() )
if ( value != BCF2Type.INT8.getMissingJavaValue() )
log10PError = value / -10.0;
} else if ( field.equals(VCFConstants.GENOTYPE_FILTER_KEY) ) {
throw new ReviewedStingException("Genotype filters not implemented in GATK BCF2");

2
public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Constants.java
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@ -34,8 +34,6 @@ public class BCF2Constants {
public static final String DICTIONARY_LINE_TAG = "dictionary";
public static final String DICTIONARY_LINE_ENTRY_SEPARATOR = ",";
public static final Charset BCF2_TEXT_CHARSET = Charset.forName("US-ASCII"); // TODO: enforce this!
// Note that these values are prefixed by FFFFFF for convenience
public static final int INT8_MISSING_VALUE = 0xFFFFFF80;
public static final int INT16_MISSING_VALUE = 0xFFFF8000;

10
public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Decoder.java
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@ -130,13 +130,13 @@ public class BCF2Decoder {
public final Object decodeTypedValue(final byte typeDescriptor) {
final int size = TypeDescriptor.sizeIsOverflow(typeDescriptor) ? decodeVectorSize() : TypeDescriptor.decodeSize(typeDescriptor);
final BCFType type = TypeDescriptor.decodeType(typeDescriptor);
final BCF2Type type = TypeDescriptor.decodeType(typeDescriptor);
assert size >= 0;
if ( size == 0 ) {
return null;
} else if ( type == BCFType.CHAR ) { // special case string decoding for efficiency
} else if ( type == BCF2Type.CHAR ) { // special case string decoding for efficiency
return decodeLiteralString(size);
} else if ( size == 1 ) {
return decodeSingleValue(type);
@ -149,7 +149,7 @@ public class BCF2Decoder {
}
}
public final Object decodeSingleValue(final BCFType type) {
public final Object decodeSingleValue(final BCF2Type type) {
// TODO -- decodeTypedValue should integrate this routine
final int value = readInt(type.getSizeInBytes(), recordStream);
@ -187,10 +187,10 @@ public class BCF2Decoder {
private final int decodeVectorSize() {
final byte typeDescriptor = readTypeDescriptor();
final int size = TypeDescriptor.decodeSize(typeDescriptor);
final BCFType type = TypeDescriptor.decodeType(typeDescriptor);
final BCF2Type type = TypeDescriptor.decodeType(typeDescriptor);
assert size == 1;
assert type == BCFType.INT8 || type == BCFType.INT16 || type == BCFType.INT32;
assert type == BCF2Type.INT8 || type == BCF2Type.INT16 || type == BCF2Type.INT32;
return decodeInt(type.getSizeInBytes());
}

58
public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Encoder.java
View File

@ -69,17 +69,17 @@ public class BCF2Encoder {
* @param o
* @return
*/
public final BCFType encode(final Object o) throws IOException {
public final BCF2Type encode(final Object o) throws IOException {
if ( o == null ) throw new ReviewedStingException("Generic encode cannot deal with null values");
if ( o instanceof String ) {
return encodeString((String)o);
} else if ( o instanceof List ) {
final BCFType type = determinePrimitiveType(((List) o).get(0));
final BCF2Type type = determinePrimitiveType(((List) o).get(0));
encodeTypedVector((List) o, type);
return type;
} else {
final BCFType type = determinePrimitiveType(o);
final BCF2Type type = determinePrimitiveType(o);
encodeTypedSingleton(o, type);
return type;
}
@ -91,31 +91,31 @@ public class BCF2Encoder {
//
// --------------------------------------------------------------------------------
public final void encodeTypedMissing(final BCFType type) throws IOException {
public final void encodeTypedMissing(final BCF2Type type) throws IOException {
encodeTypedVector(Collections.emptyList(), type);
}
// todo -- should be specialized for each object type for efficiency
public final void encodeTypedSingleton(final Object v, final BCFType type) throws IOException {
public final void encodeTypedSingleton(final Object v, final BCF2Type type) throws IOException {
encodeTypedVector(Collections.singleton(v), type);
}
public final BCFType encodeString(final String v) throws IOException {
public final BCF2Type encodeString(final String v) throws IOException {
// TODO -- this needs to be optimized
final byte[] bytes = v.getBytes();
final List<Byte> l = new ArrayList<Byte>(bytes.length);
for ( int i = 0; i < bytes.length; i++) l.add(bytes[i]);
encodeTypedVector(l, BCFType.CHAR);
return BCFType.CHAR;
encodeTypedVector(l, BCF2Type.CHAR);
return BCF2Type.CHAR;
}
public final <T extends Object> void encodeTypedVector(final Collection<T> v, final BCFType type) throws IOException {
public final <T extends Object> void encodeTypedVector(final Collection<T> v, final BCF2Type type) throws IOException {
encodeType(v.size(), type);
encodeRawValues(v, type);
}
public final BCFType encodeTypedIntOfBestSize(final int value) throws IOException {
final BCFType type = determineIntegerType(value);
public final BCF2Type encodeTypedIntOfBestSize(final int value) throws IOException {
final BCF2Type type = determineIntegerType(value);
encodeTypedSingleton(value, type);
return type;
}
@ -126,13 +126,13 @@ public class BCF2Encoder {
//
// --------------------------------------------------------------------------------
public final <T extends Object> void encodeRawValues(final Collection<T> v, final BCFType type) throws IOException {
public final <T extends Object> void encodeRawValues(final Collection<T> v, final BCF2Type type) throws IOException {
for ( final T v1 : v ) {
encodeRawValue(v1, type);
}
}
public final <T extends Object> void encodeRawValue(final T value, final BCFType type) throws IOException {
public final <T extends Object> void encodeRawValue(final T value, final BCF2Type type) throws IOException {
if ( value == type.getMissingJavaValue() )
encodeRawMissingValue(type);
else {
@ -147,11 +147,11 @@ public class BCF2Encoder {
}
}
public final void encodeRawMissingValue(final BCFType type) throws IOException {
public final void encodeRawMissingValue(final BCF2Type type) throws IOException {
encodePrimitive(type.getMissingBytes(), type);
}
public final void encodeRawMissingValues(final int size, final BCFType type) throws IOException {
public final void encodeRawMissingValues(final int size, final BCF2Type type) throws IOException {
for ( int i = 0; i < size; i++ )
encodeRawMissingValue(type);
}
@ -166,22 +166,22 @@ public class BCF2Encoder {
encodeStream.write(c);
}
public final void encodeRawFloat(final float value, final BCFType type) throws IOException {
public final void encodeRawFloat(final float value, final BCF2Type type) throws IOException {
encodePrimitive(Float.floatToIntBits(value), type);
}
public final void encodeType(final int size, final BCFType type) throws IOException {
public final void encodeType(final int size, final BCF2Type type) throws IOException {
final byte typeByte = TypeDescriptor.encodeTypeDescriptor(size, type);
encodeStream.write(typeByte);
if ( TypeDescriptor.willOverflow(size) )
encodeTypedIntOfBestSize(size);
}
public final void encodeRawInt(final int value, final BCFType type) throws IOException {
public final void encodeRawInt(final int value, final BCF2Type type) throws IOException {
encodePrimitive(value, type, encodeStream);
}
public final void encodePrimitive(final int value, final BCFType type) throws IOException {
public final void encodePrimitive(final int value, final BCF2Type type) throws IOException {
encodePrimitive(value, type, encodeStream);
}
@ -191,22 +191,22 @@ public class BCF2Encoder {
//
// --------------------------------------------------------------------------------
public final BCFType determineIntegerType(final List<Integer> values) {
BCFType maxType = BCFType.INT8;
public final BCF2Type determineIntegerType(final List<Integer> values) {
BCF2Type maxType = BCF2Type.INT8;
for ( final int value : values ) {
final BCFType type1 = determineIntegerType(value);
final BCF2Type type1 = determineIntegerType(value);
switch ( type1 ) {
case INT8: break;
case INT16: maxType = BCFType.INT16; break;
case INT32: return BCFType.INT32; // fast path for largest possible value
case INT16: maxType = BCF2Type.INT16; break;
case INT32: return BCF2Type.INT32; // fast path for largest possible value
default: throw new ReviewedStingException("Unexpected integer type " + type1 );
}
}
return maxType;
}
public final BCFType determineIntegerType(final int value) {
for ( final BCFType potentialType : TypeDescriptor.INTEGER_TYPES_BY_SIZE ) {
public final BCF2Type determineIntegerType(final int value) {
for ( final BCF2Type potentialType : TypeDescriptor.INTEGER_TYPES_BY_SIZE ) {
if ( potentialType.withinRange(value) )
return potentialType;
}
@ -214,16 +214,16 @@ public class BCF2Encoder {
throw new ReviewedStingException("Integer cannot be encoded in allowable range of even INT32: " + value);
}
private final BCFType determinePrimitiveType(final Object v) {
private final BCF2Type determinePrimitiveType(final Object v) {
if ( v instanceof Integer )
return determineIntegerType((Integer)v);
else if ( v instanceof Float )
return BCFType.FLOAT;
return BCF2Type.FLOAT;
else
throw new ReviewedStingException("No native encoding for Object of type " + v.getClass().getSimpleName());
}
public final static void encodePrimitive(final int value, final BCFType type, final OutputStream encodeStream) throws IOException {
public final static void encodePrimitive(final int value, final BCF2Type type, final OutputStream encodeStream) throws IOException {
for ( int i = type.getSizeInBytes() - 1; i >= 0; i-- ) {
final int shift = i * 8;
int mask = 0xFF << shift;

1
public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2TestWalker.java
View File

@ -31,6 +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.RodWalker;
import org.broadinstitute.sting.utils.codecs.bcf2.writer.BCF2Writer;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
import org.broadinstitute.sting.utils.exceptions.UserException;

8
public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCFType.java → public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Type.java
View File

@ -30,7 +30,7 @@ package org.broadinstitute.sting.utils.codecs.bcf2;
* @author depristo
* @since 05/12
*/
public enum BCFType {
public enum BCF2Type {
RESERVED_0,
INT8(1, BCF2Constants.INT8_MISSING_VALUE, -127, 127), // todo -- confirm range
INT16(2, BCF2Constants.INT16_MISSING_VALUE, -32767, 32767),
@ -45,15 +45,15 @@ public enum BCFType {
private final int sizeInBytes;
private final long minValue, maxValue;
BCFType() {
BCF2Type() {
this(-1, 0, 0, 0);
}
BCFType(final int sizeInBytes, final int missingBytes) {
BCF2Type(final int sizeInBytes, final int missingBytes) {
this(sizeInBytes, missingBytes, 0, 0);
}
BCFType(final int sizeInBytes, final int missingBytes, final long minValue, final long maxValue) {
BCF2Type(final int sizeInBytes, final int missingBytes, final long minValue, final long maxValue) {
this.sizeInBytes = sizeInBytes;
this.missingJavaValue = null;
this.missingBytes = missingBytes;

22
public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/TypeDescriptor.java
View File

@ -25,25 +25,25 @@
package org.broadinstitute.sting.utils.codecs.bcf2;
/**
* Simple BCF decoder
* Convenience methods for encoding, decoding BCF2 type descriptors (size + type)
* @author Mark DePristo
* @since 5/3/12
*/
public class TypeDescriptor {
class TypeDescriptor {
public static final int OVERFLOW_ELEMENT_MARKER = 15;
public static final int MAX_INLINE_ELEMENTS = 14;
public final static BCFType[] INTEGER_TYPES_BY_SIZE = new BCFType[3];
public final static BCFType[] DICTIONARY_TYPES_BY_SIZE = INTEGER_TYPES_BY_SIZE;
private final static BCFType[] lookup = BCFType.values();
public final static BCF2Type[] INTEGER_TYPES_BY_SIZE = new BCF2Type[3];
public final static BCF2Type[] DICTIONARY_TYPES_BY_SIZE = INTEGER_TYPES_BY_SIZE;
private final static BCF2Type[] LOOKUP = BCF2Type.values();
static {
INTEGER_TYPES_BY_SIZE[0] = BCFType.INT8;
INTEGER_TYPES_BY_SIZE[1] = BCFType.INT16;
INTEGER_TYPES_BY_SIZE[2] = BCFType.INT32;
INTEGER_TYPES_BY_SIZE[0] = BCF2Type.INT8;
INTEGER_TYPES_BY_SIZE[1] = BCF2Type.INT16;
INTEGER_TYPES_BY_SIZE[2] = BCF2Type.INT32;
}
public final static byte encodeTypeDescriptor(final int nElements, final BCFType type ) {
public final static byte encodeTypeDescriptor(final int nElements, final BCF2Type type ) {
int encodeSize = Math.min(nElements, OVERFLOW_ELEMENT_MARKER);
byte typeByte = (byte)((0x0F & encodeSize) << 4 | (type.getID() & 0x0F));
return typeByte;
@ -57,8 +57,8 @@ public class TypeDescriptor {
return typeDescriptor & 0x0F;
}
public final static BCFType decodeType(final byte typeDescriptor) {
return lookup[decodeTypeID(typeDescriptor)];
public final static BCF2Type decodeType(final byte typeDescriptor) {
return LOOKUP[decodeTypeID(typeDescriptor)];
}
public final static boolean sizeIsOverflow(final byte typeDescriptor) {

77
public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Writer.java → public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/writer/BCF2Writer.java
View File

@ -22,12 +22,17 @@
* OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.utils.codecs.bcf2;
package org.broadinstitute.sting.utils.codecs.bcf2.writer;
import net.sf.samtools.SAMSequenceDictionary;
import org.apache.log4j.Logger;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.codecs.bcf2.BCF2Constants;
import org.broadinstitute.sting.utils.codecs.bcf2.BCF2Encoder;
import org.broadinstitute.sting.utils.codecs.bcf2.BCF2Type;
import org.broadinstitute.sting.utils.codecs.vcf.*;
import org.broadinstitute.sting.utils.codecs.vcf.writer.IndexingVCFWriter;
import org.broadinstitute.sting.utils.codecs.vcf.writer.StandardVCFWriter;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.variantcontext.Allele;
@ -135,19 +140,19 @@ public class BCF2Writer extends IndexingVCFWriter {
throw new UserException(String.format("Contig %s not found in sequence dictionary from reference", vc.getChr()));
// note use of encodeRawValue to not insert the typing byte
encoder.encodeRawValue(contigIndex, BCFType.INT32);
encoder.encodeRawValue(contigIndex, BCF2Type.INT32);
// pos
encoder.encodeRawValue(vc.getStart(), BCFType.INT32);
encoder.encodeRawValue(vc.getStart(), BCF2Type.INT32);
// ref length
encoder.encodeRawValue(vc.getEnd() - vc.getStart() + 1, BCFType.INT32);
encoder.encodeRawValue(vc.getEnd() - vc.getStart() + 1, BCF2Type.INT32);
// qual
if ( vc.hasLog10PError() )
encoder.encodeRawFloat((float) vc.getPhredScaledQual(), BCFType.FLOAT);
encoder.encodeRawFloat((float) vc.getPhredScaledQual(), BCF2Type.FLOAT);
else
encoder.encodeRawMissingValue(BCFType.FLOAT);
encoder.encodeRawMissingValue(BCF2Type.FLOAT);
// info fields
final int nAlleles = vc.getNAlleles();
@ -155,8 +160,8 @@ public class BCF2Writer extends IndexingVCFWriter {
final int nGenotypeFormatFields = StandardVCFWriter.calcVCFGenotypeKeys(vc).size();
final int nSamples = vc.getNSamples();
encoder.encodeRawInt((nAlleles << 16) | (nInfo & 0x00FF), BCFType.INT32);
encoder.encodeRawInt((nGenotypeFormatFields << 24) | (nSamples & 0x0FFF), BCFType.INT32);
encoder.encodeRawInt((nAlleles << 16) | (nInfo & 0x00FF), BCF2Type.INT32);
encoder.encodeRawInt((nGenotypeFormatFields << 24) | (nSamples & 0x0FFF), BCF2Type.INT32);
buildID(vc);
buildAlleles(vc);
@ -181,7 +186,7 @@ public class BCF2Writer extends IndexingVCFWriter {
if ( vc.isFiltered() ) {
encodeStringsByRef(vc.getFilters());
} else {
encoder.encodeTypedMissing(BCFType.INT32);
encoder.encodeTypedMissing(BCF2Type.INT32);
}
}
@ -196,11 +201,11 @@ public class BCF2Writer extends IndexingVCFWriter {
encodeStringByRef(key);
if ( value instanceof List ) // NOTE: ONLY WORKS WITH LISTS
encoder.encodeTypedVector((List) value, typeEquiv.bcfType);
encoder.encodeTypedVector((List) value, typeEquiv.BCF2Type);
else if ( value instanceof String )
encoder.encodeString((String)value);
else
encoder.encodeTypedSingleton(value, typeEquiv.bcfType);
encoder.encodeTypedSingleton(value, typeEquiv.BCF2Type);
}
}
@ -256,25 +261,25 @@ public class BCF2Writer extends IndexingVCFWriter {
final int numInFormatField = getNGenotypeFieldValues(field, vc);
final VCFToBCFType type = getBCF2TypeFromHeader(field, null);
startGenotypeField(field, numInFormatField, type.bcfType);
startGenotypeField(field, numInFormatField, type.BCF2Type);
for ( final Genotype g : vc.getGenotypes() ) {
if ( ! g.hasAttribute(field) ) {
encoder.encodeRawMissingValues(numInFormatField, type.bcfType);
encoder.encodeRawMissingValues(numInFormatField, type.BCF2Type);
} else {
final Object val = g.getAttribute(field);
final Collection<Object> vals = numInFormatField == 1 ? Collections.singleton(val) : (Collection)val;
encoder.encodeRawValues(vals, type.bcfType);
encoder.encodeRawValues(vals, type.BCF2Type);
}
}
}
private final class VCFToBCFType {
VCFHeaderLineType vcfType;
BCFType bcfType;
BCF2Type BCF2Type;
private VCFToBCFType(final VCFHeaderLineType vcfType, final BCFType bcfType) {
private VCFToBCFType(final VCFHeaderLineType vcfType, final BCF2Type BCF2Type) {
this.vcfType = vcfType;
this.bcfType = bcfType;
this.BCF2Type = BCF2Type;
}
}
@ -285,11 +290,11 @@ public class BCF2Writer extends IndexingVCFWriter {
// TODO -- no sense in allocating these over and over
switch ( metaData.getType() ) {
case Character: return new VCFToBCFType(metaData.getType(), BCFType.CHAR);
case Flag: return new VCFToBCFType(metaData.getType(), BCFType.INT8);
case String: return new VCFToBCFType(metaData.getType(), BCFType.CHAR);
case Integer: return new VCFToBCFType(metaData.getType(), maybeIntValue != null ? encoder.determineIntegerType((Integer)maybeIntValue) : BCFType.INT32);
case Float: return new VCFToBCFType(metaData.getType(), BCFType.FLOAT);
case Character: return new VCFToBCFType(metaData.getType(), BCF2Type.CHAR);
case Flag: return new VCFToBCFType(metaData.getType(), BCF2Type.INT8);
case String: return new VCFToBCFType(metaData.getType(), BCF2Type.CHAR);
case Integer: return new VCFToBCFType(metaData.getType(), maybeIntValue != null ? encoder.determineIntegerType((Integer)maybeIntValue) : BCF2Type.INT32);
case Float: return new VCFToBCFType(metaData.getType(), BCF2Type.FLOAT);
default: throw new ReviewedStingException("Unexpected type for field " + field);
}
}
@ -308,14 +313,14 @@ public class BCF2Writer extends IndexingVCFWriter {
}
private final void addGQ(final VariantContext vc) throws IOException {
startGenotypeField(VCFConstants.GENOTYPE_QUALITY_KEY, 1, BCFType.INT8);
startGenotypeField(VCFConstants.GENOTYPE_QUALITY_KEY, 1, BCF2Type.INT8);
for ( final Genotype g : vc.getGenotypes() ) {
if ( g.hasLog10PError() ) {
final int GQ = (int)Math.round(Math.min(g.getPhredScaledQual(), VCFConstants.MAX_GENOTYPE_QUAL));
if ( GQ > VCFConstants.MAX_GENOTYPE_QUAL ) throw new ReviewedStingException("Unexpectedly large GQ " + GQ + " at " + vc);
encoder.encodeRawValue(GQ, BCFType.INT8);
encoder.encodeRawValue(GQ, BCF2Type.INT8);
} else {
encoder.encodeRawMissingValues(1, BCFType.INT8);
encoder.encodeRawMissingValues(1, BCF2Type.INT8);
}
}
}
@ -328,7 +333,7 @@ public class BCF2Writer extends IndexingVCFWriter {
final Map<Allele, String> alleleMap = StandardVCFWriter.buildAlleleMap(vc);
final int requiredPloidy = 2; // TODO -- handle ploidy, will need padding / depadding
startGenotypeField(VCFConstants.GENOTYPE_KEY, requiredPloidy, BCFType.INT8);
startGenotypeField(VCFConstants.GENOTYPE_KEY, requiredPloidy, BCF2Type.INT8);
for ( final Genotype g : vc.getGenotypes() ) {
if ( g.getPloidy() != requiredPloidy ) throw new ReviewedStingException("Cannot currently handle non-diploid calls!");
final List<Integer> encoding = new ArrayList<Integer>(requiredPloidy);
@ -336,7 +341,7 @@ public class BCF2Writer extends IndexingVCFWriter {
final int offset = a.isNoCall() ? -1 : Integer.valueOf(alleleMap.get(a));
encoding.add(((offset+1) << 1) | (g.isPhased() ? 0x01 : 0x00));
}
encoder.encodeRawValues(encoding, BCFType.INT8);
encoder.encodeRawValues(encoding, BCF2Type.INT8);
}
}
@ -348,29 +353,29 @@ public class BCF2Writer extends IndexingVCFWriter {
* @throws IOException
*/
private void writeBlock(final byte[] infoBlock, final byte[] genotypesBlock) throws IOException {
BCF2Encoder.encodePrimitive(infoBlock.length, BCFType.INT32, outputStream);
BCF2Encoder.encodePrimitive(genotypesBlock.length, BCFType.INT32, outputStream);
BCF2Encoder.encodePrimitive(infoBlock.length, BCF2Type.INT32, outputStream);
BCF2Encoder.encodePrimitive(genotypesBlock.length, BCF2Type.INT32, outputStream);
outputStream.write(infoBlock);
outputStream.write(genotypesBlock);
}
public final BCFType encodeStringByRef(final String string) throws IOException {
public final BCF2Type encodeStringByRef(final String string) throws IOException {
return encodeStringsByRef(Collections.singleton(string));
}
public final BCFType encodeStringsByRef(final Collection<String> strings) throws IOException {
public final BCF2Type encodeStringsByRef(final Collection<String> strings) throws IOException {
final List<Integer> offsets = new ArrayList<Integer>(strings.size());
BCFType maxType = BCFType.INT8; // start with the smallest size
BCF2Type maxType = BCF2Type.INT8; // start with the smallest size
// iterate over strings until we find one that needs 16 bits, and break
for ( final String string : strings ) {
final int offset = stringDictionary.get(string);
offsets.add(offset);
final BCFType type1 = encoder.determineIntegerType(offset);
final BCF2Type type1 = encoder.determineIntegerType(offset);
switch ( type1 ) {
case INT8: break;
case INT16: if ( maxType == BCFType.INT8 ) maxType = BCFType.INT16; break;
case INT32: maxType = BCFType.INT32; break;
case INT16: if ( maxType == BCF2Type.INT8 ) maxType = BCF2Type.INT16; break;
case INT32: maxType = BCF2Type.INT32; break;
default: throw new ReviewedStingException("Unexpected type " + type1);
}
}
@ -380,7 +385,7 @@ public class BCF2Writer extends IndexingVCFWriter {
return maxType;
}
public final void startGenotypeField(final String key, final int size, final BCFType valueType) throws IOException {
public final void startGenotypeField(final String key, final int size, final BCF2Type valueType) throws IOException {
encodeStringByRef(key);
encoder.encodeType(size, valueType);
}

3
public/java/src/org/broadinstitute/sting/utils/codecs/vcf/IndexingVCFWriter.java → public/java/src/org/broadinstitute/sting/utils/codecs/vcf/writer/IndexingVCFWriter.java
View File

@ -22,7 +22,7 @@
* OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.utils.codecs.vcf;
package org.broadinstitute.sting.utils.codecs.vcf.writer;
import com.google.java.contract.Ensures;
import com.google.java.contract.Requires;
@ -33,6 +33,7 @@ import org.broad.tribble.index.Index;
import org.broad.tribble.index.IndexFactory;
import org.broad.tribble.util.LittleEndianOutputStream;
import org.broadinstitute.sting.gatk.refdata.tracks.IndexDictionaryUtils;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;

2
public/java/src/org/broadinstitute/sting/utils/codecs/vcf/ManualSortingVCFWriter.java → public/java/src/org/broadinstitute/sting/utils/codecs/vcf/writer/ManualSortingVCFWriter.java
View File

@ -23,7 +23,7 @@
* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.utils.codecs.vcf;
package org.broadinstitute.sting.utils.codecs.vcf.writer;
/**
* this class writes VCF files, allowing records to be passed in unsorted.

2
public/java/src/org/broadinstitute/sting/utils/codecs/vcf/SortingVCFWriter.java → public/java/src/org/broadinstitute/sting/utils/codecs/vcf/writer/SortingVCFWriter.java
View File

@ -23,7 +23,7 @@
* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.utils.codecs.vcf;
package org.broadinstitute.sting.utils.codecs.vcf.writer;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;

3
public/java/src/org/broadinstitute/sting/utils/codecs/vcf/SortingVCFWriterBase.java → public/java/src/org/broadinstitute/sting/utils/codecs/vcf/writer/SortingVCFWriterBase.java
View File

@ -23,8 +23,9 @@
* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.utils.codecs.vcf;
package org.broadinstitute.sting.utils.codecs.vcf.writer;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import java.util.*;

3
public/java/src/org/broadinstitute/sting/utils/codecs/vcf/StandardVCFWriter.java → public/java/src/org/broadinstitute/sting/utils/codecs/vcf/writer/StandardVCFWriter.java
View File

@ -22,11 +22,12 @@
* OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.utils.codecs.vcf;
package org.broadinstitute.sting.utils.codecs.vcf.writer;
import net.sf.samtools.SAMSequenceDictionary;
import org.broad.tribble.TribbleException;
import org.broad.tribble.util.ParsingUtils;
import org.broadinstitute.sting.utils.codecs.vcf.*;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.variantcontext.*;

3
public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFWriter.java → public/java/src/org/broadinstitute/sting/utils/codecs/vcf/writer/VCFWriter.java
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@ -1,5 +1,6 @@
package org.broadinstitute.sting.utils.codecs.vcf;
package org.broadinstitute.sting.utils.codecs.vcf.writer;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
/**

150
public/java/test/org/broadinstitute/sting/utils/codecs/bcf2/EncoderDecoderUnitTest.java
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@ -50,91 +50,91 @@ public class EncoderDecoderUnitTest extends BaseTest {
@BeforeSuite
public void before() {
basicTypes.add(new BCF2TypedValue(1, BCFType.INT8));
basicTypes.add(new BCF2TypedValue(1000, BCFType.INT16));
basicTypes.add(new BCF2TypedValue(1000000, BCFType.INT32));
basicTypes.add(new BCF2TypedValue(1.2345e6, BCFType.FLOAT));
basicTypes.add(new BCF2TypedValue(new Byte((byte)'A'), BCFType.CHAR));
basicTypes.add(new BCF2TypedValue(1, BCF2Type.INT8));
basicTypes.add(new BCF2TypedValue(1000, BCF2Type.INT16));
basicTypes.add(new BCF2TypedValue(1000000, BCF2Type.INT32));
basicTypes.add(new BCF2TypedValue(1.2345e6, BCF2Type.FLOAT));
basicTypes.add(new BCF2TypedValue(new Byte((byte)'A'), BCF2Type.CHAR));
// small ints
primitives.add(new BCF2TypedValue(0, BCFType.INT8));
primitives.add(new BCF2TypedValue(10, BCFType.INT8));
primitives.add(new BCF2TypedValue(-1, BCFType.INT8));
primitives.add(new BCF2TypedValue(100, BCFType.INT8));
primitives.add(new BCF2TypedValue(-100, BCFType.INT8));
primitives.add(new BCF2TypedValue(-127, BCFType.INT8)); // last value in range
primitives.add(new BCF2TypedValue( 127, BCFType.INT8)); // last value in range
primitives.add(new BCF2TypedValue(0, BCF2Type.INT8));
primitives.add(new BCF2TypedValue(10, BCF2Type.INT8));
primitives.add(new BCF2TypedValue(-1, BCF2Type.INT8));
primitives.add(new BCF2TypedValue(100, BCF2Type.INT8));
primitives.add(new BCF2TypedValue(-100, BCF2Type.INT8));
primitives.add(new BCF2TypedValue(-127, BCF2Type.INT8)); // last value in range
primitives.add(new BCF2TypedValue( 127, BCF2Type.INT8)); // last value in range
// medium ints
primitives.add(new BCF2TypedValue(-1000, BCFType.INT16));
primitives.add(new BCF2TypedValue(1000, BCFType.INT16));
primitives.add(new BCF2TypedValue(-128, BCFType.INT16)); // first value in range
primitives.add(new BCF2TypedValue( 128, BCFType.INT16)); // first value in range
primitives.add(new BCF2TypedValue(-32767, BCFType.INT16)); // last value in range
primitives.add(new BCF2TypedValue( 32767, BCFType.INT16)); // last value in range
primitives.add(new BCF2TypedValue(-1000, BCF2Type.INT16));
primitives.add(new BCF2TypedValue(1000, BCF2Type.INT16));
primitives.add(new BCF2TypedValue(-128, BCF2Type.INT16)); // first value in range
primitives.add(new BCF2TypedValue( 128, BCF2Type.INT16)); // first value in range
primitives.add(new BCF2TypedValue(-32767, BCF2Type.INT16)); // last value in range
primitives.add(new BCF2TypedValue( 32767, BCF2Type.INT16)); // last value in range
// larger ints
primitives.add(new BCF2TypedValue(-32768, BCFType.INT32)); // first value in range
primitives.add(new BCF2TypedValue( 32768, BCFType.INT32)); // first value in range
primitives.add(new BCF2TypedValue(-100000, BCFType.INT32));
primitives.add(new BCF2TypedValue(100000, BCFType.INT32));
primitives.add(new BCF2TypedValue(-2147483647, BCFType.INT32));
primitives.add(new BCF2TypedValue(2147483647, BCFType.INT32));
primitives.add(new BCF2TypedValue(-32768, BCF2Type.INT32)); // first value in range
primitives.add(new BCF2TypedValue( 32768, BCF2Type.INT32)); // first value in range
primitives.add(new BCF2TypedValue(-100000, BCF2Type.INT32));
primitives.add(new BCF2TypedValue(100000, BCF2Type.INT32));
primitives.add(new BCF2TypedValue(-2147483647, BCF2Type.INT32));
primitives.add(new BCF2TypedValue(2147483647, BCF2Type.INT32));
// floats
primitives.add(new BCF2TypedValue(0.0, BCFType.FLOAT));
primitives.add(new BCF2TypedValue(-0.0, BCFType.FLOAT));
primitives.add(new BCF2TypedValue(1.0, BCFType.FLOAT));
primitives.add(new BCF2TypedValue(-1.0, BCFType.FLOAT));
primitives.add(new BCF2TypedValue(1.1, BCFType.FLOAT));
primitives.add(new BCF2TypedValue(-1.1, BCFType.FLOAT));
primitives.add(new BCF2TypedValue(5.0 / 3.0, BCFType.FLOAT));
primitives.add(new BCF2TypedValue(-5.0 / 3.0, BCFType.FLOAT));
primitives.add(new BCF2TypedValue(1.23e3, BCFType.FLOAT));
primitives.add(new BCF2TypedValue(1.23e6, BCFType.FLOAT));
primitives.add(new BCF2TypedValue(1.23e9, BCFType.FLOAT));
primitives.add(new BCF2TypedValue(1.23e12, BCFType.FLOAT));
primitives.add(new BCF2TypedValue(1.23e15, BCFType.FLOAT));
primitives.add(new BCF2TypedValue(-1.23e3, BCFType.FLOAT));
primitives.add(new BCF2TypedValue(-1.23e6, BCFType.FLOAT));
primitives.add(new BCF2TypedValue(-1.23e9, BCFType.FLOAT));
primitives.add(new BCF2TypedValue(-1.23e12, BCFType.FLOAT));
primitives.add(new BCF2TypedValue(-1.23e15, BCFType.FLOAT));
primitives.add(new BCF2TypedValue(Float.MIN_VALUE, BCFType.FLOAT));
primitives.add(new BCF2TypedValue(Float.MAX_VALUE, BCFType.FLOAT));
primitives.add(new BCF2TypedValue(Float.NEGATIVE_INFINITY, BCFType.FLOAT));
primitives.add(new BCF2TypedValue(Float.POSITIVE_INFINITY, BCFType.FLOAT));
primitives.add(new BCF2TypedValue(Float.NaN, BCFType.FLOAT));
primitives.add(new BCF2TypedValue(0.0, BCF2Type.FLOAT));
primitives.add(new BCF2TypedValue(-0.0, BCF2Type.FLOAT));
primitives.add(new BCF2TypedValue(1.0, BCF2Type.FLOAT));
primitives.add(new BCF2TypedValue(-1.0, BCF2Type.FLOAT));
primitives.add(new BCF2TypedValue(1.1, BCF2Type.FLOAT));
primitives.add(new BCF2TypedValue(-1.1, BCF2Type.FLOAT));
primitives.add(new BCF2TypedValue(5.0 / 3.0, BCF2Type.FLOAT));
primitives.add(new BCF2TypedValue(-5.0 / 3.0, BCF2Type.FLOAT));
primitives.add(new BCF2TypedValue(1.23e3, BCF2Type.FLOAT));
primitives.add(new BCF2TypedValue(1.23e6, BCF2Type.FLOAT));
primitives.add(new BCF2TypedValue(1.23e9, BCF2Type.FLOAT));
primitives.add(new BCF2TypedValue(1.23e12, BCF2Type.FLOAT));
primitives.add(new BCF2TypedValue(1.23e15, BCF2Type.FLOAT));
primitives.add(new BCF2TypedValue(-1.23e3, BCF2Type.FLOAT));
primitives.add(new BCF2TypedValue(-1.23e6, BCF2Type.FLOAT));
primitives.add(new BCF2TypedValue(-1.23e9, BCF2Type.FLOAT));
primitives.add(new BCF2TypedValue(-1.23e12, BCF2Type.FLOAT));
primitives.add(new BCF2TypedValue(-1.23e15, BCF2Type.FLOAT));
primitives.add(new BCF2TypedValue(Float.MIN_VALUE, BCF2Type.FLOAT));
primitives.add(new BCF2TypedValue(Float.MAX_VALUE, BCF2Type.FLOAT));
primitives.add(new BCF2TypedValue(Float.NEGATIVE_INFINITY, BCF2Type.FLOAT));
primitives.add(new BCF2TypedValue(Float.POSITIVE_INFINITY, BCF2Type.FLOAT));
primitives.add(new BCF2TypedValue(Float.NaN, BCF2Type.FLOAT));
// strings
//primitives.add(new BCF2TypedValue("", BCFType.CHAR)); <- will be null (which is right)
primitives.add(new BCF2TypedValue("S", BCFType.CHAR));
primitives.add(new BCF2TypedValue("S2", BCFType.CHAR));
primitives.add(new BCF2TypedValue("12345678910", BCFType.CHAR));
primitives.add(new BCF2TypedValue("ABCDEFGHIJKLMNOPQRSTUVWXYZ", BCFType.CHAR));
primitives.add(new BCF2TypedValue("ABCDEFGHIJKLMNOPQRSTUVWXYZABCDEFGHIJKLMNOPQRSTUVWXYZABCDEFGHIJKLMNOPQRSTUVWXYZ", BCFType.CHAR));
primitives.add(new BCF2TypedValue("S", BCF2Type.CHAR));
primitives.add(new BCF2TypedValue("S2", BCF2Type.CHAR));
primitives.add(new BCF2TypedValue("12345678910", BCF2Type.CHAR));
primitives.add(new BCF2TypedValue("ABCDEFGHIJKLMNOPQRSTUVWXYZ", BCF2Type.CHAR));
primitives.add(new BCF2TypedValue("ABCDEFGHIJKLMNOPQRSTUVWXYZABCDEFGHIJKLMNOPQRSTUVWXYZABCDEFGHIJKLMNOPQRSTUVWXYZ", BCF2Type.CHAR));
// missing values
for ( BCFType type : BCFType.values() ) {
for ( BCF2Type type : BCF2Type.values() ) {
primitives.add(new BCF2TypedValue(null, type));
}
forCombinations.add(new BCF2TypedValue(10, BCFType.INT8));
forCombinations.add(new BCF2TypedValue(100, BCFType.INT8));
forCombinations.add(new BCF2TypedValue(-100, BCFType.INT8));
forCombinations.add(new BCF2TypedValue(-128, BCFType.INT16)); // first value in range
forCombinations.add(new BCF2TypedValue( 128, BCFType.INT16)); // first value in range
forCombinations.add(new BCF2TypedValue(-100000, BCFType.INT32));
forCombinations.add(new BCF2TypedValue(100000, BCFType.INT32));
forCombinations.add(new BCF2TypedValue(0.0, BCFType.FLOAT));
forCombinations.add(new BCF2TypedValue(1.23e6, BCFType.FLOAT));
forCombinations.add(new BCF2TypedValue(-1.23e6, BCFType.FLOAT));
forCombinations.add(new BCF2TypedValue("S", BCFType.CHAR));
forCombinations.add(new BCF2TypedValue("ABCDEFGHIJKLMNOPQRSTUVWXYZ", BCFType.CHAR));
forCombinations.add(new BCF2TypedValue("ABCDEFGHIJKLMNOPQRSTUVWXYZABCDEFGHIJKLMNOPQRSTUVWXYZABCDEFGHIJKLMNOPQRSTUVWXYZ", BCFType.CHAR));
forCombinations.add(new BCF2TypedValue(10, BCF2Type.INT8));
forCombinations.add(new BCF2TypedValue(100, BCF2Type.INT8));
forCombinations.add(new BCF2TypedValue(-100, BCF2Type.INT8));
forCombinations.add(new BCF2TypedValue(-128, BCF2Type.INT16)); // first value in range
forCombinations.add(new BCF2TypedValue( 128, BCF2Type.INT16)); // first value in range
forCombinations.add(new BCF2TypedValue(-100000, BCF2Type.INT32));
forCombinations.add(new BCF2TypedValue(100000, BCF2Type.INT32));
forCombinations.add(new BCF2TypedValue(0.0, BCF2Type.FLOAT));
forCombinations.add(new BCF2TypedValue(1.23e6, BCF2Type.FLOAT));
forCombinations.add(new BCF2TypedValue(-1.23e6, BCF2Type.FLOAT));
forCombinations.add(new BCF2TypedValue("S", BCF2Type.CHAR));
forCombinations.add(new BCF2TypedValue("ABCDEFGHIJKLMNOPQRSTUVWXYZ", BCF2Type.CHAR));
forCombinations.add(new BCF2TypedValue("ABCDEFGHIJKLMNOPQRSTUVWXYZABCDEFGHIJKLMNOPQRSTUVWXYZABCDEFGHIJKLMNOPQRSTUVWXYZ", BCF2Type.CHAR));
// missing values
for ( BCFType type : BCFType.values() ) {
for ( BCF2Type type : BCF2Type.values() ) {
forCombinations.add(new BCF2TypedValue(null, type));
}
@ -147,18 +147,18 @@ public class EncoderDecoderUnitTest extends BaseTest {
// --------------------------------------------------------------------------------
private class BCF2TypedValue {
final BCFType type;
final BCF2Type type;
final Object value;
private BCF2TypedValue(final int value, final BCFType type) {
private BCF2TypedValue(final int value, final BCF2Type type) {
this(new Integer(value), type);
}
private BCF2TypedValue(final double value, final BCFType type) {
private BCF2TypedValue(final double value, final BCF2Type type) {
this(new Float(value), type);
}
private BCF2TypedValue(final Object value, final BCFType type) {
private BCF2TypedValue(final Object value, final BCF2Type type) {
this.type = type;
this.value = value;
}
@ -214,7 +214,7 @@ public class EncoderDecoderUnitTest extends BaseTest {
BCF2Decoder decoder = new BCF2Decoder(encoder.getRecordBytes());
final Object decoded = decoder.decodeTypedValue();
if ( tv.type == BCFType.CHAR ) {
if ( tv.type == BCF2Type.CHAR ) {
Assert.assertTrue(decoded instanceof String);
final String decodedString = (String)decoded;
Assert.assertTrue(decodedString.length() == length);
@ -232,7 +232,7 @@ public class EncoderDecoderUnitTest extends BaseTest {
@Test(dataProvider = "BCF2EncodingTestProviderBasicTypes")
public void testBCF2EncodingVectorsWithMissing(final List<BCF2TypedValue> toEncode) throws IOException {
for ( final BCF2TypedValue tv : toEncode ) {
if ( tv.type != BCFType.CHAR ) {
if ( tv.type != BCF2Type.CHAR ) {
for ( final int length : Arrays.asList(2, 5, 10, 15, 20, 25) ) {
final byte td = TypeDescriptor.encodeTypeDescriptor(1, tv.type);
@ -314,7 +314,7 @@ public class EncoderDecoderUnitTest extends BaseTest {
if ( tv.isMissing() )
encoder.encodeTypedMissing(tv.type);
else {
final BCFType encodedType = encoder.encode(tv.value);
final BCF2Type encodedType = encoder.encode(tv.value);
if ( tv.type != null ) // only if we have an expectation
Assert.assertEquals(encodedType, tv.type);
}
@ -345,7 +345,7 @@ public class EncoderDecoderUnitTest extends BaseTest {
private final void myAssertEquals(final BCF2TypedValue tv, final Object decoded) {
if ( tv.value == null ) { // special needs for instanceof double
Assert.assertEquals(decoded, tv.value);
} else if ( tv.type == BCFType.FLOAT ) { // need tolerance for floats, and they aren't null
} else if ( tv.type == BCF2Type.FLOAT ) { // need tolerance for floats, and they aren't null
Assert.assertTrue(decoded instanceof Double);
final float valueFloat = (float)(Float)tv.value;

3
public/java/test/org/broadinstitute/sting/utils/codecs/vcf/IndexFactoryUnitTest.java
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@ -6,7 +6,8 @@ import org.broad.tribble.CloseableTribbleIterator;
import org.broad.tribble.Tribble;
import org.broad.tribble.index.*;
import org.broadinstitute.sting.BaseTest;
import org.broadinstitute.sting.WalkerTest;
import org.broadinstitute.sting.utils.codecs.vcf.writer.StandardVCFWriter;
import org.broadinstitute.sting.utils.codecs.vcf.writer.VCFWriter;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;

5
public/java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFWriterUnitTest.java
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@ -3,8 +3,8 @@ package org.broadinstitute.sting.utils.genotype.vcf;
import org.broad.tribble.AbstractFeatureReader;
import org.broad.tribble.FeatureReader;
import org.broad.tribble.Tribble;
import org.broad.tribble.readers.AsciiLineReader;
import org.broad.tribble.readers.PositionalBufferedStream;
import org.broadinstitute.sting.utils.codecs.vcf.writer.StandardVCFWriter;
import org.broadinstitute.sting.utils.codecs.vcf.writer.VCFWriter;
import org.broadinstitute.sting.utils.variantcontext.*;
import org.broadinstitute.sting.utils.codecs.vcf.*;
import org.broadinstitute.sting.utils.exceptions.UserException;
@ -19,7 +19,6 @@ import org.testng.annotations.Test;
import org.testng.annotations.BeforeClass;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.util.*;