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Added getAsMap -> returns the likelihoods as an EnumMap with Genotypes as keys and likelihoods as values.

This commit is contained in:
Laurent Francioli 2011-10-20 12:49:18 +02:00
parent 76dd816e70
commit ef6a6fdfe4
1 changed files with 14 additions and 0 deletions
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14
public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeLikelihoods.java
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@ -25,8 +25,12 @@
package org.broadinstitute.sting.utils.variantcontext; package org.broadinstitute.sting.utils.variantcontext;
import org.broad.tribble.TribbleException; import org.broad.tribble.TribbleException;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
import java.util.EnumMap;
import java.util.Map;
public class GenotypeLikelihoods { public class GenotypeLikelihoods {
public static final boolean CAP_PLS = false; public static final boolean CAP_PLS = false;
public static final int PL_CAP = 255; public static final int PL_CAP = 255;
@ -94,6 +98,16 @@ public class GenotypeLikelihoods {
return likelihoodsAsString_PLs; return likelihoodsAsString_PLs;
} }
public EnumMap<Genotype.Type,Double> getAsMap(boolean normalizeFromLog10){
//Make sure that the log10likelihoods are set
double[] likelihoods = normalizeFromLog10 ? MathUtils.normalizeFromLog10(getAsVector()) : getAsVector();
EnumMap<Genotype.Type,Double> likelihoodsMap = new EnumMap<Genotype.Type, Double>(Genotype.Type.class);
likelihoodsMap.put(Genotype.Type.HOM_REF,likelihoods[Genotype.Type.HOM_REF.ordinal()-1]);
likelihoodsMap.put(Genotype.Type.HET,likelihoods[Genotype.Type.HET.ordinal()-1]);
likelihoodsMap.put(Genotype.Type.HOM_VAR, likelihoods[Genotype.Type.HOM_VAR.ordinal() - 1]);
return likelihoodsMap;
}
private final static double[] parsePLsIntoLikelihoods(String likelihoodsAsString_PLs) { private final static double[] parsePLsIntoLikelihoods(String likelihoodsAsString_PLs) {
if ( !likelihoodsAsString_PLs.equals(VCFConstants.MISSING_VALUE_v4) ) { if ( !likelihoodsAsString_PLs.equals(VCFConstants.MISSING_VALUE_v4) ) {
String[] strings = likelihoodsAsString_PLs.split(","); String[] strings = likelihoodsAsString_PLs.split(",");