48 lines
2.3 KiB
Java
48 lines
2.3 KiB
Java
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package org.broadinstitute.sting.gatk.refdata;
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import java.util.*;
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import java.util.regex.MatchResult;
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import java.util.regex.Pattern;
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import java.util.regex.Matcher;
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import java.io.File;
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import java.io.FileNotFoundException;
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import java.io.IOException;
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import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
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import org.broadinstitute.sting.utils.GenomeLoc;
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import org.broadinstitute.sting.utils.Utils;
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import org.broadinstitute.sting.utils.xReadLines;
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import org.broadinstitute.sting.utils.cmdLine.Argument;
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import org.apache.log4j.Logger;
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/**
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* loc ref alt EM_alt_freq discovery_likelihood discovery_null discovery_prior discovery_lod EM_N n_ref n_het n_hom
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* chr1:1104840 A N 0.000000 -85.341265 -85.341265 0.000000 0.000000 324.000000 162 0 0
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* chr1:1104841 C N 0.000000 -69.937928 -69.937928 0.000000 0.000000 324.000000 162 0 0
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* chr1:1104842 A N 0.000000 -84.816002 -84.816002 0.000000 0.000000 324.000000 162 0 0
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*
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*/
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public class PooledEMSNPROD extends TabularROD implements AllelicVariant {
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public PooledEMSNPROD(final String name) {
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super(name);
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}
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//GenomeLoc getLocation();
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public String getRefBasesFWD() { return this.get("ref"); }
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public char getRefSnpFWD() throws IllegalStateException { return getRefBasesFWD().charAt(0); }
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public String getAltBasesFWD() { return this.get("alt"); }
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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 Double.parseDouble(this.get("EM_alt_freq")); }
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public double getHeterozygosity() { return 2 * getMAF() * (1 - getMAF()); }
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public boolean isGenotype() { return false; }
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public double getVariationConfidence() { return Double.parseDouble(this.get("discovery_lod")) * 10; }
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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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}
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