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ROD to represent simple output from IndelGenotyper 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1274 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-07-17 14:36:12 +00:00
parent f978b04633
commit d45c90b166
1 changed files with 43 additions and 0 deletions
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43
java/src/org/broadinstitute/sting/gatk/refdata/SimpleIndelROD.java 100755
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package org.broadinstitute.sting.gatk.refdata;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser;
import java.util.*;
public class SimpleIndelROD extends TabularROD implements Genotype {
public SimpleIndelROD(String name) {
super(name);
}
public GenomeLoc getLocation() {
return GenomeLocParser.createGenomeLoc(this.get("0"), Long.parseLong(this.get("1")));
}
public List<String> getFWDAlleles() {
String str = this.get("3");
return Arrays.asList(str.substring(0, str.indexOf(":")));
}
public String getFWDRefBases() { return ""; }
public char getRef() { return 'N'; }
public boolean isPointGenotype() { return false; }
public boolean isIndelGenotype() { return true; }
public boolean isSNP() { return false; }
public boolean isReference() { return false; }
public boolean isInsertion() { return this.get("3").charAt(0) == '+'; }
public boolean isDeletion() { return this.get("3").charAt(0) == '-'; }
public boolean isIndel() { return false; }
public double getVariantConfidence() { return 0.0; }
public double getConsensusConfidence() { return 0.0; }
public boolean isBiallelic() { return true; }
public boolean isHom() { return false; }
public boolean isHet() { return false; }
public String toString() {
StringBuffer sb = new StringBuffer();
sb.append(getLocation() + "\t" + getFWDAlleles().get(0));
return sb.toString();
}
}