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un-deprecate this ROD and make it implement Genotype 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1240 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-07-14 19:45:41 +00:00
parent 84d407ff3f
commit efcbb16688
1 changed files with 35 additions and 23 deletions
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58
java/src/org/broadinstitute/sting/gatk/refdata/rodGELI.java
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@ -1,13 +1,12 @@
package org.broadinstitute.sting.gatk.refdata;
import java.util.Iterator;
import java.util.*;
import java.io.IOException;
import java.io.File;
import edu.mit.broad.picard.genotype.geli.GeliFileReader;
import edu.mit.broad.picard.genotype.geli.GenotypeLikelihoods;
import edu.mit.broad.picard.genotype.DiploidGenotype;
import edu.mit.broad.picard.variation.KnownVariant;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser;
@ -18,7 +17,7 @@ import net.sf.samtools.util.CloseableIterator;
* This class wraps Picard Geli CHiP data and presents it as a ROD.
*/
public class rodGELI extends BasicReferenceOrderedDatum {
public class rodGELI extends BasicReferenceOrderedDatum implements Genotype {
// ----------------------------------------------------------------------
//
// Constructors
@ -30,8 +29,6 @@ public class rodGELI extends BasicReferenceOrderedDatum {
public rodGELI(final String name, GenotypeLikelihoods gh) {
super(name);
this.gh = gh;
if ( true )
throw new RuntimeException("This class is no longer supported because of issues with GELIs");
}
@Override
@ -96,6 +93,39 @@ public class rodGELI extends BasicReferenceOrderedDatum {
return new rodGELI.rodGELIIterator(name,file);
}
public List<String> getFWDAlleles() {
return new ArrayList<String>();
}
public String getFWDRefBases() {
return "";
}
public char getRef() {
return (char)(gh.getReferenceBase() & 0xff);
}
public boolean isPointGenotype() { return true; }
public boolean isIndelGenotype() { return false; }
public boolean isSNP() { return true; }
public boolean isReference() { return gh.isHomozygousReference(); }
public boolean isInsertion() { return false; }
public boolean isDeletion() { return false; }
public boolean isIndel() { return false; }
public boolean isBiallelic() { return false; }
public boolean isHom() { return gh.isHomozyous(); }
public boolean isHet() { return !isHom(); }
public double getVariantConfidence() {
return gh.getBestToReferenceLod();
}
public double getConsensusConfidence() {
return gh.getBestToSecondBestLod();
}
public static void main(String argv[]) {
String testFile = "NA12878.geli";
@ -115,24 +145,6 @@ public class rodGELI extends BasicReferenceOrderedDatum {
while ( it.hasNext() && counter < 500 ) {
rodGELI rg = it.next();
System.out.println(rg.toString());
/*
System.out.print(p.getLocation().toString());
System.out.print('\t');
if ( p.isIndel() && p.isSNP() ) { System.out.print("Indel+SNP"); }
else {
if ( p.isSNP() ) { System.out.print("SNP"); }
else {
if ( p.isIndel() ) { System.out.print("Indel"); }
else { System.out.print("REF"); }
}
}
System.out.print('\t');
System.out.print(p.getFWDAlleles().get(0)+"/"+p.getFWDAlleles().get(1));
System.out.print('\t');
System.out.println(p.getConsensusConfidence()+"\t"+p.getVariantConfidence());
*/
counter++;
}
}