43 lines
1.5 KiB
Java
43 lines
1.5 KiB
Java
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package org.broadinstitute.sting.gatk.refdata;
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import org.broadinstitute.sting.utils.GenomeLoc;
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import org.broadinstitute.sting.utils.GenomeLocParser;
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import java.util.*;
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public class SimpleIndelROD extends TabularROD implements Genotype {
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public SimpleIndelROD(String name) {
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super(name);
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}
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public GenomeLoc getLocation() {
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return GenomeLocParser.createGenomeLoc(this.get("0"), Long.parseLong(this.get("1")));
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}
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public List<String> getFWDAlleles() {
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String str = this.get("3");
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return Arrays.asList(str.substring(0, str.indexOf(":")));
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}
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public String getFWDRefBases() { return ""; }
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public char getRef() { return 'N'; }
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public boolean isPointGenotype() { return false; }
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public boolean isIndelGenotype() { return true; }
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public boolean isSNP() { return false; }
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public boolean isReference() { return false; }
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public boolean isInsertion() { return this.get("3").charAt(0) == '+'; }
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public boolean isDeletion() { return this.get("3").charAt(0) == '-'; }
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public boolean isIndel() { return false; }
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public double getVariantConfidence() { return 0.0; }
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public double getConsensusConfidence() { return 0.0; }
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public boolean isBiallelic() { return true; }
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public boolean isHom() { return false; }
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public boolean isHet() { return false; }
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public String toString() {
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StringBuffer sb = new StringBuffer();
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sb.append(getLocation() + "\t" + getFWDAlleles().get(0));
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return sb.toString();
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}
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}
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