zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

vcfwriter is in tribble now 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4083 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
aaron 2010-08-23 17:01:04 +00:00
parent 2d3b6d89dc
commit 35b9883dd6
29 changed files with 26 additions and 499 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

4
java/src/org/broadinstitute/sting/gatk/io/storage/VCFWriterStorage.java
View File

@ -1,10 +1,10 @@
package org.broadinstitute.sting.gatk.io.storage;
import org.broad.tribble.vcf.StandardVCFWriter;
import org.broad.tribble.vcf.VCFHeader;
import org.broad.tribble.vcf.VCFHeaderLine;
import org.broad.tribble.util.variantcontext.VariantContext;
import org.broadinstitute.sting.utils.genotype.vcf.VCFWriter;
import org.broadinstitute.sting.utils.genotype.vcf.StandardVCFWriter;
import org.broad.tribble.vcf.VCFWriter;
import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub;

3
java/src/org/broadinstitute/sting/gatk/io/stubs/VCFWriterArgumentTypeDescriptor.java
View File

@ -25,13 +25,12 @@
package org.broadinstitute.sting.gatk.io.stubs;
import org.broad.tribble.vcf.VCFWriter;
import org.broadinstitute.sting.commandline.*;
import org.broadinstitute.sting.utils.genotype.vcf.VCFWriter;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import java.io.File;
import java.io.OutputStream;
import java.lang.annotation.Annotation;
import java.util.List;
import java.util.Arrays;

3
java/src/org/broadinstitute/sting/gatk/io/stubs/VCFWriterStub.java
View File

@ -31,10 +31,9 @@ import java.io.OutputStream;
import org.broad.tribble.util.variantcontext.VariantContext;
import org.broad.tribble.vcf.VCFHeader;
import org.broad.tribble.vcf.VCFWriter;
import org.broadinstitute.sting.gatk.io.OutputTracker;
import org.broadinstitute.sting.gatk.io.storage.VCFWriterStorage;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.utils.genotype.vcf.VCFWriter;
import net.sf.samtools.SAMFileHeader;
/**

1
java/src/org/broadinstitute/sting/gatk/walkers/VariantsToVCF.java
View File

@ -38,7 +38,6 @@ import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.gatk.refdata.utils.helpers.DbSNPHelper;
import org.broadinstitute.sting.utils.vcf.VCFUtils;
import org.broadinstitute.sting.utils.genotype.vcf.*;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.SampleUtils;

6
java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
View File

@ -26,9 +26,7 @@
package org.broadinstitute.sting.gatk.walkers.annotator;
import org.broad.tribble.util.variantcontext.VariantContext;
import org.broad.tribble.vcf.VCFHeader;
import org.broad.tribble.vcf.VCFHeaderLine;
import org.broad.tribble.vcf.VCFCompoundHeaderLine;
import org.broad.tribble.vcf.*;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext;
@ -46,8 +44,6 @@ import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.CommandLineUtils;
import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.utils.vcf.VCFUtils;
import org.broadinstitute.sting.utils.genotype.vcf.VCFWriter;
import org.broadinstitute.sting.utils.genotype.vcf.StandardVCFWriter;
import java.util.*;
import java.io.PrintStream;

2
java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java
View File

@ -40,8 +40,6 @@ import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.CommandLineUtils;
import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.utils.vcf.VCFUtils;
import org.broadinstitute.sting.utils.genotype.vcf.VCFWriter;
import org.broadinstitute.sting.utils.genotype.vcf.StandardVCFWriter;
import java.util.*;
import java.io.PrintStream;

2
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/BatchedCallsMerger.java
View File

@ -25,13 +25,13 @@
package org.broadinstitute.sting.gatk.walkers.genotyper;
import org.broad.tribble.util.variantcontext.VariantContext;
import org.broad.tribble.vcf.VCFWriter;
import org.broadinstitute.sting.gatk.contexts.*;
import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedData;
import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.commandline.*;
import org.broadinstitute.sting.utils.genotype.vcf.VCFWriter;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileupImpl;

1
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
View File

@ -34,7 +34,6 @@ import org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotatorEngine;
import org.broadinstitute.sting.utils.*;
import org.broadinstitute.sting.commandline.*;
import org.broadinstitute.sting.utils.vcf.VCFUtils;
import org.broadinstitute.sting.utils.genotype.vcf.*;
import java.util.*;
import java.io.PrintStream;

2
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
View File

@ -27,6 +27,7 @@ package org.broadinstitute.sting.gatk.walkers.genotyper;
import org.apache.log4j.Logger;
import org.broad.tribble.util.variantcontext.VariantContext;
import org.broad.tribble.vcf.VCFWriter;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.gatk.filters.BadMateFilter;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
@ -39,7 +40,6 @@ import org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotatorEngine;
import org.broadinstitute.sting.utils.sam.AlignmentUtils;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.genotype.vcf.VCFWriter;
import org.broadinstitute.sting.utils.pileup.*;
import org.broad.tribble.vcf.VCFConstants;

2
java/src/org/broadinstitute/sting/gatk/walkers/sequenom/SequenomValidationConverter.java
View File

@ -40,8 +40,6 @@ import org.broadinstitute.sting.utils.QualityUtils;
import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.utils.genotype.vcf.VCFWriter;
import org.broadinstitute.sting.utils.genotype.vcf.StandardVCFWriter;
import java.util.*;
import java.io.PrintStream;

4
java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java
View File

@ -28,6 +28,8 @@ package org.broadinstitute.sting.gatk.walkers.varianteval;
import org.apache.log4j.Logger;
import org.broad.tribble.util.variantcontext.MutableVariantContext;
import org.broad.tribble.util.variantcontext.VariantContext;
import org.broad.tribble.vcf.StandardVCFWriter;
import org.broad.tribble.vcf.VCFWriter;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
@ -48,8 +50,6 @@ import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.utils.genotype.vcf.VCFWriter;
import org.broadinstitute.sting.utils.genotype.vcf.StandardVCFWriter;
import org.broadinstitute.sting.utils.text.XReadLines;
import java.io.File;

2
java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyVariantCuts.java
View File

@ -36,8 +36,6 @@ import org.broadinstitute.sting.utils.*;
import org.broadinstitute.sting.utils.collections.ExpandingArrayList;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.utils.vcf.VCFUtils;
import org.broadinstitute.sting.utils.genotype.vcf.VCFWriter;
import org.broadinstitute.sting.utils.genotype.vcf.StandardVCFWriter;
import org.broadinstitute.sting.utils.text.XReadLines;
import java.io.File;

2
java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
View File

@ -40,8 +40,6 @@ import org.broadinstitute.sting.utils.*;
import org.broadinstitute.sting.utils.collections.ExpandingArrayList;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.utils.vcf.VCFUtils;
import org.broadinstitute.sting.utils.genotype.vcf.VCFWriter;
import org.broadinstitute.sting.utils.genotype.vcf.StandardVCFWriter;
import java.io.File;
import java.io.IOException;

1
java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java
View File

@ -41,7 +41,6 @@ import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.utils.vcf.VCFUtils;
import org.broadinstitute.sting.utils.genotype.vcf.*;
import java.util.*;
import java.io.PrintStream;

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

@ -25,8 +25,8 @@
package org.broadinstitute.sting.gatk.walkers.variantutils;
import org.broad.tribble.util.variantcontext.VariantContext;
import org.broadinstitute.sting.utils.genotype.vcf.VCFWriter;
import org.broadinstitute.sting.utils.genotype.vcf.StandardVCFWriter;
import org.broad.tribble.vcf.StandardVCFWriter;
import org.broad.tribble.vcf.VCFWriter;
import org.broadinstitute.sting.utils.vcf.VCFUtils;
import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;

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

@ -25,11 +25,11 @@
package org.broadinstitute.sting.gatk.walkers.variantutils;
import org.broad.tribble.util.variantcontext.VariantContext;
import org.broad.tribble.vcf.StandardVCFWriter;
import org.broad.tribble.vcf.VCFWriter;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.utils.vcf.VCFUtils;
import org.broadinstitute.sting.utils.genotype.vcf.VCFWriter;
import org.broadinstitute.sting.utils.genotype.vcf.StandardVCFWriter;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;

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

@ -26,8 +26,10 @@ package org.broadinstitute.sting.gatk.walkers.variantutils;
import org.broad.tribble.util.variantcontext.Genotype;
import org.broad.tribble.util.variantcontext.VariantContext;
import org.broad.tribble.vcf.StandardVCFWriter;
import org.broad.tribble.vcf.VCFHeader;
import org.broad.tribble.vcf.VCFHeaderLine;
import org.broad.tribble.vcf.VCFWriter;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
@ -41,8 +43,6 @@ import org.broadinstitute.sting.gatk.walkers.RodWalker;
import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.text.XReadLines;
import org.broadinstitute.sting.utils.vcf.VCFUtils;
import org.broadinstitute.sting.utils.genotype.vcf.VCFWriter;
import org.broadinstitute.sting.utils.genotype.vcf.StandardVCFWriter;
import java.util.*;
import java.util.regex.Matcher;

1
java/src/org/broadinstitute/sting/oneoffprojects/walkers/IndelAnnotator.java
View File

@ -18,7 +18,6 @@ import org.broadinstitute.sting.gatk.walkers.RodWalker;
import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.utils.vcf.VCFUtils;
import org.broadinstitute.sting.utils.genotype.vcf.*;
import java.io.File;
import java.io.IOException;

4
java/src/org/broadinstitute/sting/oneoffprojects/walkers/IndelDBRateWalker.java
View File

@ -1,8 +1,10 @@
package org.broadinstitute.sting.oneoffprojects.walkers;
import org.broad.tribble.util.variantcontext.VariantContext;
import org.broad.tribble.vcf.StandardVCFWriter;
import org.broad.tribble.vcf.VCFHeader;
import org.broad.tribble.vcf.VCFHeaderLine;
import org.broad.tribble.vcf.VCFWriter;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
@ -17,8 +19,6 @@ import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.utils.collections.ExpandingArrayList;
import org.broadinstitute.sting.utils.vcf.VCFUtils;
import org.broadinstitute.sting.utils.genotype.vcf.VCFWriter;
import org.broadinstitute.sting.utils.genotype.vcf.StandardVCFWriter;
import java.io.PrintStream;
import java.util.*;

4
java/src/org/broadinstitute/sting/oneoffprojects/walkers/MendelianViolationClassifier.java
View File

@ -3,8 +3,10 @@ package org.broadinstitute.sting.oneoffprojects.walkers;
import org.broad.tribble.util.variantcontext.Allele;
import org.broad.tribble.util.variantcontext.Genotype;
import org.broad.tribble.util.variantcontext.VariantContext;
import org.broad.tribble.vcf.StandardVCFWriter;
import org.broad.tribble.vcf.VCFHeader;
import org.broad.tribble.vcf.VCFHeaderLine;
import org.broad.tribble.vcf.VCFWriter;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
@ -23,8 +25,6 @@ import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.vcf.VCFUtils;
import org.broadinstitute.sting.utils.genotype.vcf.VCFWriter;
import org.broadinstitute.sting.utils.genotype.vcf.StandardVCFWriter;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import java.io.PrintStream;

3
java/src/org/broadinstitute/sting/oneoffprojects/walkers/TestVariantContextWalker.java
View File

@ -26,11 +26,12 @@
package org.broadinstitute.sting.oneoffprojects.walkers;
import org.broad.tribble.util.variantcontext.VariantContext;
import org.broad.tribble.vcf.StandardVCFWriter;
import org.broad.tribble.vcf.VCFWriter;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.*;
import org.broadinstitute.sting.gatk.walkers.RodWalker;
import org.broadinstitute.sting.utils.genotype.vcf.*;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.Output;

2
java/src/org/broadinstitute/sting/oneoffprojects/walkers/VCF4WriterTestWalker.java
View File

@ -14,8 +14,6 @@ import org.broadinstitute.sting.gatk.walkers.RodWalker;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.utils.vcf.VCFUtils;
import org.broadinstitute.sting.utils.genotype.vcf.VCFWriter;
import org.broadinstitute.sting.utils.genotype.vcf.StandardVCFWriter;
import java.io.File;
import java.io.FileInputStream;

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/BeagleOutputToVCFWalker.java
View File

@ -44,8 +44,6 @@ import org.broadinstitute.sting.gatk.walkers.Requires;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.vcf.VCFUtils;
import org.broadinstitute.sting.utils.genotype.vcf.VCFWriter;
import org.broadinstitute.sting.utils.genotype.vcf.StandardVCFWriter;
import org.broad.tribble.vcf.*;
import java.io.*;

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/ReadBackedPhasingWalker.java
View File

@ -39,8 +39,6 @@ import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.utils.*;
import org.broadinstitute.sting.utils.vcf.VCFUtils;
import org.broadinstitute.sting.utils.genotype.vcf.VCFWriter;
import org.broadinstitute.sting.utils.genotype.vcf.StandardVCFWriter;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;

4
java/src/org/broadinstitute/sting/playground/gatk/walkers/TrioGenotyperWalker.java
View File

@ -29,7 +29,9 @@ import org.broad.tribble.util.variantcontext.Allele;
import org.broad.tribble.util.variantcontext.Genotype;
import org.broad.tribble.util.variantcontext.MutableVariantContext;
import org.broad.tribble.util.variantcontext.VariantContext;
import org.broad.tribble.vcf.StandardVCFWriter;
import org.broad.tribble.vcf.VCFConstants;
import org.broad.tribble.vcf.VCFWriter;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@ -43,8 +45,6 @@ import org.broadinstitute.sting.commandline.ArgumentCollection;
import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.utils.QualityUtils;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.genotype.vcf.VCFWriter;
import org.broadinstitute.sting.utils.genotype.vcf.StandardVCFWriter;
import org.broadinstitute.sting.gatk.walkers.varianteval.MendelianViolationEvaluator;
import java.util.*;

4
java/src/org/broadinstitute/sting/playground/gatk/walkers/annotator/GenomicAnnotator.java
View File

@ -43,8 +43,10 @@ import java.util.TreeSet;
import java.util.Map.Entry;
import org.broad.tribble.util.variantcontext.VariantContext;
import org.broad.tribble.vcf.StandardVCFWriter;
import org.broad.tribble.vcf.VCFHeader;
import org.broad.tribble.vcf.VCFHeaderLine;
import org.broad.tribble.vcf.VCFWriter;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
@ -64,8 +66,6 @@ import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.vcf.VCFUtils;
import org.broadinstitute.sting.utils.genotype.vcf.VCFWriter;
import org.broadinstitute.sting.utils.genotype.vcf.StandardVCFWriter;
/**
* Annotates variant calls with information from user-specified tabular files.

2
java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentField.java
View File

@ -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.genotype.vcf.VCFWriter;
import org.broad.tribble.vcf.VCFWriter;
import java.io.File;
import java.io.InputStream;

431
java/src/org/broadinstitute/sting/utils/genotype/vcf/StandardVCFWriter.java
View File

@ -1,431 +0,0 @@
/*
* Copyright (c) 2010, The Broad Institute
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.utils.genotype.vcf;
import org.broad.tribble.vcf.*;
import org.broad.tribble.util.variantcontext.VariantContext;
import org.broad.tribble.util.variantcontext.Allele;
import org.broad.tribble.util.variantcontext.Genotype;
import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.StingException;
import java.io.*;
import java.util.*;
/**
* this class writes VCF files
*/
public class StandardVCFWriter implements VCFWriter {
// the VCF header we're storing
protected VCFHeader mHeader = null;
// the print stream we're writting to
protected BufferedWriter mWriter;
// were filters applied?
protected boolean filtersWereAppliedToContext = false;
/**
* create a VCF writer, given a file to write to
*
* @param location the file location to write to
*/
public StandardVCFWriter(File location) {
FileOutputStream output;
try {
output = new FileOutputStream(location);
} catch (FileNotFoundException e) {
throw new RuntimeException("Unable to create VCF file at location: " + location);
}
mWriter = new BufferedWriter(new OutputStreamWriter(output));
}
/**
* create a VCF writer, given a stream to write to
*
* @param output the file location to write to
*/
public StandardVCFWriter(OutputStream output) {
mWriter = new BufferedWriter(new OutputStreamWriter(output));
}
public void writeHeader(VCFHeader header) {
this.mHeader = header;
try {
// the file format field needs to be written first
mWriter.write(VCFHeader.METADATA_INDICATOR + VCFHeaderVersion.VCF4_0.getFormatString() + "=" + VCFHeaderVersion.VCF4_0.getVersionString() + "\n");
for ( VCFHeaderLine line : header.getMetaData() ) {
if ( line.getKey().equals(VCFHeaderVersion.VCF4_0.getFormatString()) ||
line.getKey().equals(VCFHeaderVersion.VCF3_3.getFormatString()) ||
line.getKey().equals(VCFHeaderVersion.VCF3_2.getFormatString()) )
continue;
// are the records filtered (so we know what to put in the FILTER column of passing records) ?
if ( line instanceof VCFFilterHeaderLine)
filtersWereAppliedToContext = true;
mWriter.write(VCFHeader.METADATA_INDICATOR);
mWriter.write(line.toString());
mWriter.write("\n");
}
// write out the column line
mWriter.write(VCFHeader.HEADER_INDICATOR);
for ( VCFHeader.HEADER_FIELDS field : header.getHeaderFields() ) {
mWriter.write(field.toString());
mWriter.write(VCFConstants.FIELD_SEPARATOR);
}
if ( header.hasGenotypingData() ) {
mWriter.write("FORMAT");
mWriter.write(VCFConstants.FIELD_SEPARATOR);
for ( String sample : header.getGenotypeSamples() ) {
mWriter.write(sample);
mWriter.write(VCFConstants.FIELD_SEPARATOR);
} }
mWriter.write("\n");
mWriter.flush(); // necessary so that writing to an output stream will work
}
catch (IOException e) {
throw new RuntimeException("IOException writing the VCF header", e);
}
}
/**
* attempt to close the VCF file
*/
public void close() {
try {
mWriter.flush();
mWriter.close();
} catch (IOException e) {
throw new RuntimeException("Unable to close VCFFile");
}
}
public void add(VariantContext vc, byte refBase) {
if ( mHeader == null )
throw new IllegalStateException("The VCF Header must be written before records can be added");
try {
vc = VariantContextUtils.createVariantContextWithPaddedAlleles(vc, refBase);
GenomeLoc loc = VariantContextUtils.getLocation(vc);
Map<Allele, String> alleleMap = new HashMap<Allele, String>(vc.getAlleles().size());
alleleMap.put(Allele.NO_CALL, VCFConstants.EMPTY_ALLELE); // convenience for lookup
// CHROM
mWriter.write(loc.getContig());
mWriter.write(VCFConstants.FIELD_SEPARATOR);
// POS
mWriter.write(String.valueOf(loc.getStart()));
mWriter.write(VCFConstants.FIELD_SEPARATOR);
// ID
String ID = vc.hasAttribute(VariantContext.ID_KEY) ? vc.getAttributeAsString(VariantContext.ID_KEY) : VCFConstants.EMPTY_ID_FIELD;
mWriter.write(ID);
mWriter.write(VCFConstants.FIELD_SEPARATOR);
// REF
alleleMap.put(vc.getReference(), "0");
String refString = vc.getReference().getBaseString();
mWriter.write(refString);
mWriter.write(VCFConstants.FIELD_SEPARATOR);
// ALT
if ( vc.isVariant() ) {
Allele altAllele = vc.getAlternateAllele(0);
alleleMap.put(altAllele, "1");
String alt = altAllele.getBaseString();
mWriter.write(alt);
for (int i = 1; i < vc.getAlternateAlleles().size(); i++) {
altAllele = vc.getAlternateAllele(i);
alleleMap.put(altAllele, String.valueOf(i+1));
alt = altAllele.getBaseString();
mWriter.write(",");
mWriter.write(alt);
}
} else {
mWriter.write(VCFConstants.EMPTY_ALTERNATE_ALLELE_FIELD);
}
mWriter.write(VCFConstants.FIELD_SEPARATOR);
// QUAL
if ( !vc.hasNegLog10PError() )
mWriter.write(VCFConstants.MISSING_VALUE_v4);
else
mWriter.write(getQualValue(vc.getPhredScaledQual()));
mWriter.write(VCFConstants.FIELD_SEPARATOR);
// FILTER
String filters = vc.isFiltered() ? Utils.join(";", Utils.sorted(vc.getFilters())) : (filtersWereAppliedToContext || vc.filtersWereApplied() ? VCFConstants.PASSES_FILTERS_v4 : VCFConstants.UNFILTERED);
mWriter.write(filters);
mWriter.write(VCFConstants.FIELD_SEPARATOR);
// INFO
Map<String, String> infoFields = new TreeMap<String, String>();
for ( Map.Entry<String, Object> field : vc.getAttributes().entrySet() ) {
String key = field.getKey();
if ( key.equals(VariantContext.ID_KEY) || key.equals(VariantContext.REFERENCE_BASE_FOR_INDEL_KEY) )
continue;
String outputValue = formatVCFField(field.getValue());
if ( outputValue != null )
infoFields.put(key, outputValue);
}
writeInfoString(infoFields);
// FORMAT
List<String> genotypeAttributeKeys = new ArrayList<String>();
if ( vc.hasGenotypes() ) {
genotypeAttributeKeys.add(VCFConstants.GENOTYPE_KEY);
for ( String key : calcVCFGenotypeKeys(vc) ) {
genotypeAttributeKeys.add(key);
}
} else if ( mHeader.hasGenotypingData() ) {
// this needs to be done in case all samples are no-calls
genotypeAttributeKeys.add(VCFConstants.GENOTYPE_KEY);
}
if ( genotypeAttributeKeys.size() > 0 ) {
String genotypeFormatString = Utils.join(VCFConstants.GENOTYPE_FIELD_SEPARATOR, genotypeAttributeKeys);
mWriter.write(VCFConstants.FIELD_SEPARATOR);
mWriter.write(genotypeFormatString);
addGenotypeData(vc, alleleMap, genotypeAttributeKeys);
}
mWriter.write("\n");
mWriter.flush(); // necessary so that writing to an output stream will work
} catch (IOException e) {
throw new RuntimeException("Unable to write the VCF object to a file");
}
}
private String getQualValue(double qual) {
String s = String.format(VCFConstants.DOUBLE_PRECISION_FORMAT_STRING, qual);
if ( s.endsWith(VCFConstants.DOUBLE_PRECISION_INT_SUFFIX) )
s = s.substring(0, s.length() - VCFConstants.DOUBLE_PRECISION_INT_SUFFIX.length());
return s;
}
/**
* create the info string; assumes that no values are null
*
* @param infoFields a map of info fields
* @throws IOException for writer
*/
protected void writeInfoString(Map<String, String> infoFields) throws IOException {
if ( infoFields.isEmpty() ) {
mWriter.write(VCFConstants.EMPTY_INFO_FIELD);
return;
}
boolean isFirst = true;
for ( Map.Entry<String, String> entry : infoFields.entrySet() ) {
if ( isFirst )
isFirst = false;
else
mWriter.write(VCFConstants.INFO_FIELD_SEPARATOR);
String key = entry.getKey();
mWriter.write(key);
if ( !entry.getValue().equals("") ) {
int numVals = 1;
VCFInfoHeaderLine metaData = mHeader.getInfoHeaderLine(key);
if ( metaData != null )
numVals = metaData.getCount();
// take care of unbounded encoding
if ( numVals == VCFInfoHeaderLine.UNBOUNDED )
numVals = 1;
if ( numVals > 0 ) {
mWriter.write("=");
mWriter.write(entry.getValue());
}
}
}
}
/**
* add the genotype data
*
* @param vc the variant context
* @param genotypeFormatKeys Genotype formatting string
* @param alleleMap alleles for this context
* @throws IOException for writer
*/
private void addGenotypeData(VariantContext vc, Map<Allele, String> alleleMap, List<String> genotypeFormatKeys)
throws IOException {
for ( String sample : mHeader.getGenotypeSamples() ) {
mWriter.write(VCFConstants.FIELD_SEPARATOR);
Genotype g = vc.getGenotype(sample);
if ( g == null ) {
// TODO -- The VariantContext needs to know what the general ploidy is of the samples
// TODO -- We shouldn't be assuming diploid genotypes here!
mWriter.write(VCFConstants.EMPTY_GENOTYPE);
continue;
}
writeAllele(g.getAllele(0), alleleMap);
for (int i = 1; i < g.getPloidy(); i++) {
mWriter.write(g.genotypesArePhased() ? VCFConstants.PHASED : VCFConstants.UNPHASED);
writeAllele(g.getAllele(i), alleleMap);
}
List<String> attrs = new ArrayList<String>(genotypeFormatKeys.size());
for ( String key : genotypeFormatKeys ) {
if ( key.equals(VCFConstants.GENOTYPE_KEY) )
continue;
Object val = g.hasAttribute(key) ? g.getAttribute(key) : VCFConstants.MISSING_VALUE_v4;
// some exceptions
if ( key.equals(VCFConstants.GENOTYPE_QUALITY_KEY) ) {
if ( MathUtils.compareDoubles(g.getNegLog10PError(), Genotype.NO_NEG_LOG_10PERROR) == 0 )
val = VCFConstants.MISSING_VALUE_v4;
else {
val = getQualValue(Math.min(g.getPhredScaledQual(), VCFConstants.MAX_GENOTYPE_QUAL));
}
} else if ( key.equals(VCFConstants.GENOTYPE_FILTER_KEY) ) {
val = g.isFiltered() ? Utils.join(";", Utils.sorted(g.getFilters())) : (g.filtersWereApplied() ? VCFConstants.PASSES_FILTERS_v4 : VCFConstants.UNFILTERED);
}
VCFFormatHeaderLine metaData = mHeader.getFormatHeaderLine(key);
if ( metaData != null ) {
int numInFormatField = metaData.getCount();
if ( numInFormatField > 1 && val.equals(VCFConstants.MISSING_VALUE_v4) ) {
// If we have a missing field but multiple values are expected, we need to construct a new string with all fields.
// For example, if Number=2, the string has to be ".,."
StringBuilder sb = new StringBuilder(VCFConstants.MISSING_VALUE_v4);
for ( int i = 1; i < numInFormatField; i++ ) {
sb.append(",");
sb.append(VCFConstants.MISSING_VALUE_v4);
}
val = sb.toString();
}
}
// assume that if key is absent, then the given string encoding suffices
String outputValue = formatVCFField(val);
if ( outputValue != null )
attrs.add(outputValue);
}
// strip off trailing missing values
for (int i = attrs.size()-1; i >= 0; i--) {
if ( isMissingValue(attrs.get(i)) )
attrs.remove(i);
else
break;
}
for (String s : attrs ) {
mWriter.write(VCFConstants.GENOTYPE_FIELD_SEPARATOR);
mWriter.write(s);
}
}
}
private boolean isMissingValue(String s) {
// we need to deal with the case that it's a list of missing values
return (MathUtils.countOccurrences(VCFConstants.MISSING_VALUE_v4.charAt(0), s) + MathUtils.countOccurrences(',', s) == s.length());
}
private void writeAllele(Allele allele, Map<Allele, String> alleleMap) throws IOException {
String encoding = alleleMap.get(allele);
if ( encoding == null )
throw new StingException("Allele " + allele + " is not an allele in the variant context");
mWriter.write(encoding);
}
private static String formatVCFField(Object val) {
String result;
if ( val == null )
result = VCFConstants.MISSING_VALUE_v4;
else if ( val instanceof Double )
result = String.format(VCFConstants.DOUBLE_PRECISION_FORMAT_STRING, (Double)val);
else if ( val instanceof Boolean )
result = (Boolean)val ? "" : null; // empty string for true, null for false
else if ( val instanceof List ) {
result = formatVCFField(((List)val).toArray());
} else if ( val instanceof Object[] ) {
Object[] array = (Object[])val;
if ( array.length == 0 )
return formatVCFField(null);
StringBuffer sb = new StringBuffer(formatVCFField(array[0]));
for ( int i = 1; i < array.length; i++) {
sb.append(",");
sb.append(formatVCFField(array[i]));
}
result = sb.toString();
} else
result = val.toString();
return result;
}
private static List<String> calcVCFGenotypeKeys(VariantContext vc) {
Set<String> keys = new HashSet<String>();
boolean sawGoodQual = false;
boolean sawGenotypeFilter = false;
for ( Genotype g : vc.getGenotypes().values() ) {
keys.addAll(g.getAttributes().keySet());
if ( g.hasNegLog10PError() )
sawGoodQual = true;
if (g.isFiltered() && g.isCalled())
sawGenotypeFilter = true;
}
if ( sawGoodQual )
keys.add(VCFConstants.GENOTYPE_QUALITY_KEY);
if (sawGenotypeFilter)
keys.add(VCFConstants.GENOTYPE_FILTER_KEY);
return Utils.sorted(new ArrayList<String>(keys));
}
}

19
java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFWriter.java
View File

@ -1,19 +0,0 @@
package org.broadinstitute.sting.utils.genotype.vcf;
import org.broad.tribble.util.variantcontext.VariantContext;
import org.broad.tribble.vcf.*;
/**
* this class writes VCF files
*/
public interface VCFWriter {
public void writeHeader(VCFHeader header);
/**
* attempt to close the VCF file
*/
public void close();
public void add(VariantContext vc, byte refBase);
}