42 lines
1.9 KiB
Java
42 lines
1.9 KiB
Java
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package org.broadinstitute.sting.gatk.refdata;
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import java.util.*;
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import org.broadinstitute.sting.utils.GenomeLoc;
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import org.broadinstitute.sting.utils.GenomeLocParser;
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public class SangerSNPROD extends TabularROD implements SNPCallFromGenotypes {
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public SangerSNPROD(final String name) {
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super(name);
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}
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public GenomeLoc getLocation() {
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loc = GenomeLocParser.createGenomeLoc(this.get("0"), Long.parseLong(this.get("1")));
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return loc;
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}
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public String getRefBasesFWD() { return this.get("2"); }
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public char getRefSnpFWD() throws IllegalStateException { return getRefBasesFWD().charAt(0); }
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public String getAltBasesFWD() { return this.get("3"); }
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public char getAltSnpFWD() throws IllegalStateException { return getAltBasesFWD().charAt(0); }
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public boolean isReference() { return getVariationConfidence() < 0.01; }
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public boolean isSNP() { return ! isReference(); }
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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 getMAF() { return -1; }
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public double getHeterozygosity() { return -1; }
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public boolean isGenotype() { return false; }
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public double getVariationConfidence() { return -1; }
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public double getConsensusConfidence() { return -1; }
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public List<String> getGenotype() throws IllegalStateException { throw new IllegalStateException(); }
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public int getPloidy() throws IllegalStateException { return 2; }
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public boolean isBiallelic() { return true; }
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// SNPCallFromGenotypes interface
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public int nIndividuals() { return -1; }
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public int nHomRefGenotypes() { return -1; }
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public int nHetGenotypes() { return -1; }
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public int nHomVarGenotypes() { return -1; }
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public List<Genotype> getGenotypes() { return null; }
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}
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