54 lines
2.1 KiB
Java
54 lines
2.1 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 SequenomROD extends TabularROD implements AllelicVariant {
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public SequenomROD(String name) {
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super(name);
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}
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public GenomeLoc getLocation() {
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long pos = Long.parseLong(this.get("1"));
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return GenomeLocParser.createGenomeLoc(this.get("0"), pos);
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}
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public List<String> getFWDAlleles() {
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return Arrays.asList(this.get("2"));
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}
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public String getFWDRefBases() { return ""; }
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public String getAltBasesFWD() { return getFWDAlleles().get(0); }
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public String getRefBasesFWD() { return ""; }
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public char getRefSnpFWD() { return 'N'; }
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public char getAltSnpFWD() { return getAltBasesFWD().charAt(0); }
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public char getRef() { return 'N'; }
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public List<String> getGenotype() { return getFWDAlleles(); }
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public boolean isGenotype() { return false; }
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public boolean isPointGenotype() { return true; }
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public boolean isIndelGenotype() { return false; }
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public boolean isSNP() { return true; }
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public boolean isReference() { return false; }
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public boolean isInsertion() { return false; }
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public boolean isDeletion() { return false; }
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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 getVariationConfidence() { 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 double getHeterozygosity() { return 0.0; }
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public double getMAF() { return 0.0; }
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public int getPloidy() { return 2; }
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public int length() { return 1; }
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public String toString() {
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StringBuffer sb = new StringBuffer();
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sb.append(getLocation().getContig() + "\t" + getLocation().getStart() + "\t" + getFWDAlleles().get(0));
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return sb.toString();
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}
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}
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