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Changes the validity declaration from a true to false to a five point scale 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5527 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
corin 2011-03-28 18:31:53 +00:00
parent cdb0bde952
commit f2d84bf746
1 changed files with 10 additions and 11 deletions
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21
java/src/org/broadinstitute/sting/playground/gatk/walkers/validation/DeclareValidityWalker.java
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@ -63,11 +63,11 @@ public class DeclareValidityWalker extends RodWalker<Integer, Integer>{
@Output(doc = "Write bed to this file instead of standard out") @Output(doc = "Write bed to this file instead of standard out")
public PrintStream out; public PrintStream out;
@Argument(fullName = "DeclareFalse", shortName = "isFP", @Argument(fullName = "validity", shortName = "V",
doc = "Argument to create a bed file of with loci annotated as false positive", required = false) doc = "Rank of variant validity on a 0-4 scale where 0 is definitely false positive; 4 is definitely true positive.")
boolean isFP = false; int validity;
@Argument(fullName = "Note", shortName = "N", doc = "Annotation to be included in FP field", required = false) @Argument(fullName = "Note", shortName = "N", doc = "Annotation to be included in FP/TP field", required = false)
String Note ="."; String Note =".";
@Argument(fullName = "Source", shortName = "s", doc = "Institutional source of annotation", required = false) @Argument(fullName = "Source", shortName = "s", doc = "Institutional source of annotation", required = false)
@ -88,7 +88,7 @@ public class DeclareValidityWalker extends RodWalker<Integer, Integer>{
protected String contig; protected String contig;
protected long start; protected long start;
protected long stop; protected long stop;
protected boolean TPorFP; protected int valid;
protected Allele refBase; protected Allele refBase;
protected Allele altBase; protected Allele altBase;
protected String Note; protected String Note;
@ -105,15 +105,15 @@ public class DeclareValidityWalker extends RodWalker<Integer, Integer>{
else {return "unknown";} else {return "unknown";}
} }
public ValidityDeclaration(GenomeLoc Loc, VariantContext Con, Boolean TPorFP, String Note, String Source, String Build){ //Constructor expects 1 based public ValidityDeclaration(GenomeLoc Loc, VariantContext Con, int validity, String Note, String Source, String Build){ //Constructor expects 1 based
this.contig=Loc.getContig(); this.contig=Loc.getContig();
this.start=Loc.getStart()-1; this.start=Loc.getStart()-1;
this.stop=Loc.getStop(); this.stop=Loc.getStop();
this.TPorFP =TPorFP; this.valid =validity;
this.altBase = Con.getAlternateAllele(0); this.altBase = Con.getAlternateAllele(0);
if (Con.getAlternateAlleles().toArray().length >1) if (Con.getAlternateAlleles().toArray().length >1)
{ {
logger.warn("***NOTE: Only the first alternate allele in a VCF will be declared as " +TPorFP+"***"); logger.warn("***NOTE: Only the first alternate allele in a VCF will be declared as " +valid+"***");
} }
this.refBase = Con.getReference(); this.refBase = Con.getReference();
this.Note = Note; this.Note = Note;
@ -126,7 +126,7 @@ public class DeclareValidityWalker extends RodWalker<Integer, Integer>{
} }
public String toString() { public String toString() {
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); return String.format("%s\t%d\t%d\t%s\t%s\t%d\t%s\t%s\t%s\t%s", contig, start, stop, refBase,altBase, validity, user, Build, Note, Source);
} }
} }
/** /**
@ -146,8 +146,7 @@ public class DeclareValidityWalker extends RodWalker<Integer, Integer>{
return 0;} return 0;}
Boolean tpOrFp = !isFP; ValidityDeclaration bedLine = new ValidityDeclaration(ref.getLocus(), current, validity, Note, Source, build);
ValidityDeclaration bedLine = new ValidityDeclaration(ref.getLocus(), current, tpOrFp, Note, Source, build);
out.println(bedLine); out.println(bedLine);
return 1; return 1;
} }