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Added ROD for 1KG SNP calls 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@988 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-06-11 19:53:51 +00:00
parent ffffe3b2f6
commit 032d0436e6
1 changed files with 58 additions and 0 deletions
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58
java/src/org/broadinstitute/sting/gatk/refdata/KGenomesSNPROD.java 100755
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package org.broadinstitute.sting.gatk.refdata;
import java.util.*;
import java.util.regex.MatchResult;
import java.util.regex.Pattern;
import java.util.regex.Matcher;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.IOException;
import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.xReadLines;
import org.broadinstitute.sting.utils.cmdLine.Argument;
import org.apache.log4j.Logger;
/**
* loc ref alt EM_alt_freq discovery_likelihood discovery_null discovery_prior discovery_lod EM_N n_ref n_het n_hom
* chr1:1104840 A N 0.000000 -85.341265 -85.341265 0.000000 0.000000 324.000000 162 0 0
* chr1:1104841 C N 0.000000 -69.937928 -69.937928 0.000000 0.000000 324.000000 162 0 0
* chr1:1104842 A N 0.000000 -84.816002 -84.816002 0.000000 0.000000 324.000000 162 0 0
*
*/
public class KGenomesSNPROD extends TabularROD implements SNPCallFromGenotypes {
public KGenomesSNPROD(final String name) {
super(name);
}
public GenomeLoc getLocation() {
loc = new GenomeLoc(this.get("0"), Long.parseLong(this.get("1")));
return loc;
}
public String getRefBasesFWD() { return this.get("2"); }
public char getRefSnpFWD() throws IllegalStateException { return getRefBasesFWD().charAt(0); }
public String getAltBasesFWD() { return this.get("3"); }
public char getAltSnpFWD() throws IllegalStateException { return getAltBasesFWD().charAt(0); }
public boolean isReference() { return getVariationConfidence() < 0.01; }
public boolean isSNP() { return ! isReference(); }
public boolean isInsertion() { return false; }
public boolean isDeletion() { return false; }
public boolean isIndel() { return false; }
public double getMAF() { return Double.parseDouble(this.get("4")); }
public double getHeterozygosity() { return 2 * getMAF() * (1 - getMAF()); }
public boolean isGenotype() { return false; }
public double getVariationConfidence() { return Double.parseDouble(this.get("8")); }
public double getConsensusConfidence() { return -1; }
public List<String> getGenotype() throws IllegalStateException { throw new IllegalStateException(); }
public int getPloidy() throws IllegalStateException { return 2; }
public boolean isBiallelic() { return true; }
// SNPCallFromGenotypes interface
public int nIndividuals() { return -1; }
public int nHomRefGenotypes() { return -1; }
public int nHetGenotypes() { return -1; }
public int nHomVarGenotypes() { return -1; }
public List<Genotype> getGenotypes() { return null; }
}