This is a walker that lets the user generate the bed file for declaring variants true positives or false positives. For use with the IGV crowd sourcing project.
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/*
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* Copyright (c) 2010, The Broad Institute
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*
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* Permission is hereby granted, free of charge, to any person
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* obtaining a copy of this software and associated documentation
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* files (the "Software"), to deal in the Software without
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* restriction, including without limitation the rights to use,
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* copy, modify, merge, publish, distribute, sublicense, and/or sell
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* copies of the Software, and to permit persons to whom the
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* Software is furnished to do so, subject to the following
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* conditions:
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*
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* The above copyright notice and this permission notice shall be
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* included in all copies or substantial portions of the Software.
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* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
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* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
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* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
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* OTHER DEALINGS IN THE SOFTWARE.
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*/
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package org.broadinstitute.sting.playground.gatk.walkers.validation;
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import com.sun.tools.corba.se.idl.constExpr.Not;
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import com.sun.tools.internal.xjc.reader.xmlschema.bindinfo.BIConversion;
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import org.broad.tribble.Feature;
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import org.broad.tribble.util.variantcontext.Genotype;
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import org.broad.tribble.util.variantcontext.VariantContext;
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import org.broad.tribble.vcf.*;
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import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
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import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
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import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
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import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
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import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
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import org.broadinstitute.sting.gatk.walkers.*;
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import org.broadinstitute.sting.commandline.Argument;
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import org.broadinstitute.sting.commandline.Output;
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import org.broadinstitute.sting.utils.GenomeLoc;
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import org.broadinstitute.sting.utils.SampleUtils;
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import org.broadinstitute.sting.utils.bed.BedParser;
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import org.broadinstitute.sting.utils.vcf.VCFUtils;
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import java.io.PrintStream;
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import java.io.Writer;
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import java.util.*;
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/**
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* Declares the validity of variants in a vcf as either true or false. For use with the IGV crowd-sourcing bed generation
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*/
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public class DeclareValidityWalker extends RodWalker<Integer, Integer>{
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@Output(doc = "Write bed to this file instead of standard out")
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public PrintStream out;
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@Argument(fullName = "DeclareFalse", shortName = "isFP",
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doc = "Argument to create a bed file of with loci annotated as false positive", required = false)
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boolean isFP = false;
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@Argument(fullName = "Note", shortName = "N", doc = "Annotation to be included in FP field", required = false)
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String Note =".";
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@Argument(fullName = "Source", shortName = "s", doc = "Source of annotation", required = false)
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String Source = ".";
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@Override
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public Integer reduceInit() {
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return 0; //To change body of implemented methods use File | Settings | File Templates.
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}
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public class ValidityDeclaration{
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protected String contig;
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protected long start;
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protected long stop;
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protected boolean TPorFP;
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protected String Note;
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protected String Source;
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protected String Build;
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protected String user;
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public ValidityDeclaration(GenomeLoc Loc, Boolean TPorFP, String Note, String Source){ //Constructor expects 1 based
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this.contig=Loc.getContig();
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this.start=Loc.getStart()-1;
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this.stop=Loc.getStop()-1;
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this.TPorFP =TPorFP;
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this.Note = Note;
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this.Source = Source;
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this.user = System.getenv("USER");
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//is there a better way to get the build than this?:
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if (this.contig.contains("chr")) {this.Build="hg18";}
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else {this.Build="hg19";}
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}
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public String toString() {
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return String.format("%s\t%d\t%d\t%b positive\t%s\t%s\t%s\t%s\n", contig, start, stop, TPorFP, user, Build, Note, Source);
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}
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}
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/**
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*
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* @param tracker the meta-data tracker
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* @param ref the reference base
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* @param context the context for the given locus
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* @return 1 if the locus was successfully processed, 0 if otherwise
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*/
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public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context){
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if ( tracker == null )
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return 0;
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Boolean tpOrFp = !isFP;
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ValidityDeclaration bedLine = new ValidityDeclaration(ref.getLocus(), tpOrFp, Note, Source);
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out.append(bedLine.toString());
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return 1;
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}
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public Integer reduce(Integer counter, Integer sum) {
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return counter+sum;
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}
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}
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