114 lines
4.3 KiB
Java
114 lines
4.3 KiB
Java
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package org.broadinstitute.sting.oneoffprojects.multisamplecaller;
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import java.util.HashMap;
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public class IndelLikelihood {
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private String type;
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private String[] alleles;
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private double p;
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private double lod;
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private double pRef;
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private double pHet;
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private double pHom;
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private String alt;
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public IndelLikelihood(String type, String[] alleles, double p, double lod) {
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initialize(type, alleles, p, lod);
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}
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public IndelLikelihood(String[] indels, double indel_alt_freq)
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{
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HashMap<String,Integer> indel_allele_counts = new HashMap<String,Integer>();
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for (int i = 0; i < indels.length; i++) {
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if (! indel_allele_counts.containsKey(indels[i])) {
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indel_allele_counts.put(indels[i], 1);
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} else {
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indel_allele_counts.put(indels[i], indel_allele_counts.get(indels[i])+1);
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}
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}
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Object[] keys = indel_allele_counts.keySet().toArray();
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String[] alleles = new String[keys.length];
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int[] counts = new int[keys.length];
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//double likelihoods[] = new double[keys.length];
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int null_count = 0;
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String max_allele = null;
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int max_count = -1;
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if ((keys.length > 0) && (! ((keys.length == 1) && (((String)keys[0]).equals("null"))))) {
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for (int i = 0; i < keys.length; i++) {
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Integer count = (Integer)indel_allele_counts.get(keys[i]);
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alleles[i] = (String)keys[i];
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counts[i] = count;
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if (alleles[i].equals("null")) { null_count = counts[i]; }
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else if (counts[i] > max_count) { max_count = counts[i]; max_allele = alleles[i]; }
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//System.out.printf("%s[%d] ", keys[i], count);
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}
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//System.out.printf("\n");
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double eps = 1e-3;
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pRef = null_count*Math.log10(1.0 - eps) + max_count*Math.log10(eps) + 2*Math.log10(1-indel_alt_freq);
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pHet = null_count*Math.log10(0.5 - eps/2) + max_count*Math.log10(0.5-eps/2) + Math.log10((1-indel_alt_freq)*indel_alt_freq);
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pHom = null_count*Math.log10(eps) + max_count*Math.log10(1.0 - eps) + 2*Math.log10(indel_alt_freq);
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double lodRef = pRef - Math.max(pHet, pHom);
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double lodHet = pHet - pRef;
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double lodHom = pHom - pRef;
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//System.out.printf("%s/%s %f %f\n", "null", "null", pRef, lodRef);
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//System.out.printf("%s/%s %f %f\n", max_allele, "null", pHet, lodHet);
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//System.out.printf("%s/%s %f %f\n", max_allele, max_allele, pHom, lodHom);
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//System.out.printf("\n");
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if (lodRef > 0) {
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// reference call
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String[] genotype = new String[2];
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genotype[0] = "null";
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genotype[1] = "null";
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//return new IndelLikelihood("ref", genotype, pRef, lodRef);
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initialize("ref", genotype, pRef, lodRef);
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} else if (lodHet > lodHom) {
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// het call
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String[] genotype = new String[2];
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genotype[0] = "null";
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genotype[1] = max_allele;
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//return new IndelLikelihood("het", genotype, pHet, lodHet);
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initialize("het", genotype, pHet, lodHet);
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} else {
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// hom call
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String[] genotype = new String[2];
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genotype[0] = max_allele;
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genotype[1] = max_allele;
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//return new IndelLikelihood("hom", genotype, pHom, lodHom);
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initialize("hom", genotype, pHom, lodHom);
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}
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}
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}
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private void initialize(String type, String[] alleles, double p, double lod) {
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this.type = type;
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this.alleles = alleles;
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this.p = p;
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this.lod = lod;
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}
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public String getAlt() { return alt; }
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public double pRef() { return pRef; }
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public double pHet() { return pHet; }
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public double pHom() { return pHom; }
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public String getType() { return type; }
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public String[] getAlleles() { return alleles; }
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public double getPosteriorProbability() { return p; }
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public double getLOD() { return lod; }
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public String toString() {
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return String.format("%s/%s %f %f", alleles[0], alleles[1], p, lod);
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}
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}
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