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Updated the walker to specify the build based on the user's input file name if the user does not specify the build. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5459 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
corin 2011-03-17 17:49:17 +00:00
parent 3de300e504
commit 30237e6824
1 changed files with 43 additions and 10 deletions
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53
java/src/org/broadinstitute/sting/playground/gatk/walkers/validation/DeclareValidityWalker.java
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@ -27,6 +27,7 @@ package org.broadinstitute.sting.playground.gatk.walkers.validation;
import com.sun.tools.corba.se.idl.constExpr.Not;
import com.sun.tools.internal.xjc.reader.xmlschema.bindinfo.BIConversion;
import org.broad.tribble.Feature;
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.*;
@ -38,11 +39,14 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.gatk.walkers.DataSource;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.bed.BedParser;
import org.broadinstitute.sting.utils.vcf.VCFUtils;
import javax.activation.*;
import java.beans.VetoableChangeSupport;
import java.io.PrintStream;
import java.io.Writer;
import java.util.*;
@ -52,7 +56,7 @@ import java.util.*;
* Declares the validity of variants in a vcf as either true or false. For use with the IGV crowd-sourcing bed generation
*/
@Requires(value={},referenceMetaData=@RMD(name="validated", type=VariantContext.class))
public class DeclareValidityWalker extends RodWalker<Integer, Integer>{
@ -66,9 +70,13 @@ public class DeclareValidityWalker extends RodWalker<Integer, Integer>{
@Argument(fullName = "Note", shortName = "N", doc = "Annotation to be included in FP field", required = false)
String Note =".";
@Argument(fullName = "Source", shortName = "s", doc = "Source of annotation", required = false)
@Argument(fullName = "Source", shortName = "s", doc = "Institutional source of annotation", required = false)
String Source = ".";
@Argument(fullName = "Build", shortName = "bld", doc = "Genome build", required = false)
String build = ".";
@Override
public Integer reduceInit() {
return 0; //To change body of implemented methods use File | Settings | File Templates.
@ -81,25 +89,44 @@ public class DeclareValidityWalker extends RodWalker<Integer, Integer>{
protected long start;
protected long stop;
protected boolean TPorFP;
protected Allele refBase;
protected Allele altBase;
protected String Note;
protected String Source;
protected String Build;
protected String user;
public ValidityDeclaration(GenomeLoc Loc, Boolean TPorFP, String Note, String Source){ //Constructor expects 1 based
public String getBuild(){
String refPath = getToolkit().getArguments().referenceFile.getPath();
if (refPath.contains("19")) {return "hg19";}
else if (refPath.contains("18")) {return "hg18";}
else if (refPath.contains("36")) {return "b36";}
else if (refPath.contains("37")) {return "b37";}
else {return "unknown";}
}
public ValidityDeclaration(GenomeLoc Loc, VariantContext Con, Boolean TPorFP, String Note, String Source, String Build){ //Constructor expects 1 based
this.contig=Loc.getContig();
this.start=Loc.getStart()-1;
this.stop=Loc.getStop()-1;
this.stop=Loc.getStop();
this.TPorFP =TPorFP;
this.altBase = Con.getAlternateAllele(0);
if (Con.getAlternateAlleles().toArray().length >1)
{
logger.warn("***NOTE: Only the first alternate allele in a VCF will be declared as " +TPorFP+"***");
}
this.refBase = Con.getReference();
this.Note = Note;
this.Source = Source;
this.user = System.getenv("USER");
//is there a better way to get the build than this?:
if (this.contig.contains("chr")) {this.Build="hg18";}
else {this.Build="hg19";}
if (Build == "."){
this.Build=getBuild();
}
else{this.Build = Build; }
}
public String toString() {
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);
return String.format("%s\t%d\t%d\t%s\t%s\t%b positive\t%s\t%s\t%s\t%s", contig, start, stop, refBase,altBase, TPorFP, user, Build, Note, Source);
}
}
/**
@ -113,9 +140,15 @@ public class DeclareValidityWalker extends RodWalker<Integer, Integer>{
if ( tracker == null )
return 0;
VariantContext current = tracker.getVariantContext(ref, "validated", context.getLocation());
if (current == null) {
return 0;}
Boolean tpOrFp = !isFP;
ValidityDeclaration bedLine = new ValidityDeclaration(ref.getLocus(), tpOrFp, Note, Source);
out.append(bedLine.toString());
ValidityDeclaration bedLine = new ValidityDeclaration(ref.getLocus(), current, tpOrFp, Note, Source, build);
out.println(bedLine);
return 1;
}