211 lines
7.8 KiB
Java
Executable File
211 lines
7.8 KiB
Java
Executable File
package org.broadinstitute.sting.playground.utils;
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import org.broadinstitute.sting.playground.gatk.walkers.AlleleFrequencyWalker;
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import org.broadinstitute.sting.utils.GenomeLoc;
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import java.util.Arrays;
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public class AlleleFrequencyEstimate {
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public GenomeLoc location;
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public char ref;
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public char alt;
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public int N;
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public double qhat;
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public double qstar;
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public double lodVsRef;
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public double lodVsNextBest;
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public double pBest;
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public double pRef;
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public int depth;
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public String notes;
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public String bases;
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//public double[][] quals;
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public double[] posteriors;
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public String sample_name;
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public int n_ref;
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public int n_het;
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public int n_hom;
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public GenotypeLikelihoods genotypeLikelihoods = null;
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GenomeLoc l;
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public AlleleFrequencyEstimate(GenomeLoc location, char ref, char alt, int N, double qhat, double qstar, double lodVsRef, double lodVsNextBest, double pBest, double pRef, int depth, String bases, double[][] quals, double[] posteriors, String sample_name)
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{
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this.location = location;
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this.ref = ref;
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this.alt = alt;
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this.N = N;
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this.qhat = qhat;
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this.qstar = qstar;
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this.lodVsRef = lodVsRef;
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this.lodVsNextBest = lodVsNextBest;
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this.pBest = pBest;
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this.pRef = pRef;
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this.depth = depth;
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this.notes = "";
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this.bases = bases;
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//this.quals = quals;
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this.posteriors = posteriors;
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this.sample_name = sample_name;
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}
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public boolean isREF() { return (this.lodVsRef <= -5.0); }
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public boolean isSNP() { return (this.lodVsRef >= 5.0); }
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/** Return the most likely genotype. */
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public String genotype()
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{
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int alt_count = (int)(qstar * N);
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int ref_count = N-alt_count;
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char[] alleles = new char[N];
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int i;
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for (i = 0; i < ref_count; i++) { alleles[i] = ref; }
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for (; i < N; i++) { alleles[i] = alt; }
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Arrays.sort(alleles);
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return new String(alleles);
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}
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public double emperical_allele_frequency()
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{
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return (double)Math.round((double)qstar * (double)N) / (double)N;
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}
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public double emperical_allele_frequency(int N)
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{
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return (double)Math.round((double)qstar * (double)N) / (double)N;
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}
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public String asGFFString()
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{
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String s = "";
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s += String.format("%s\tCALLER\tVARIANT\t%s\t%s\t%f\t.\t.\t",
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location.getContig(),
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location.getStart(),
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location.getStart(),
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lodVsRef);
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s += String.format("\t;\tSAMPLE %s", sample_name);
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s += String.format("\t;\tREF %c", ref);
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s += String.format("\t;\tALT %c", alt);
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s += String.format("\t;\tFREQ %f", qstar);
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s += String.format("\t;\tGENOTYPE %s", this.genotype());
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s += String.format("\t;\tDEPTH %d", depth);
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s += String.format("\t;\tLODvsREF %f", lodVsRef);
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s += String.format("\t;\tLODvsNEXTBEST %f", lodVsNextBest);
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s += String.format("\t;\tQHAT %f", qhat);
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s += String.format("\t;\tQSTAR %f", qstar);
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s += String.format("\t;\tBASES %s", bases);
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s += ";\n";
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// add quals.
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return s;
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}
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public static String asTabularStringHeader()
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{
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return "location sample_name ref alt genotype qhat qstar lodVsRef lodVsNextBest depth bases";
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}
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public static String geliHeaderString() {
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return "#Sequence Position ReferenceBase NumberOfReads MaxMappingQuality BestGenotype BtrLod BtnbLod AA AC AG AT CC CG CT GG GT TT";
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}
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public String asGeliString()
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{
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// #Sequence Position ReferenceBase NumberOfReads MaxMappingQuality BestGenotype BtrLod BtnbLod dbSNP AA AC AG AT CC CG CT GG GT TT
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// chr1 7764136 A 48 99 CC 83.650421 9.18159 -92.83638 -18.367548 -96.91729 -96.614204 -9.185958 -23.33643 -23.033337 -101.282059 -101.583092 -101.279999
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// chr pos ref Nreads maxMapQ genotype BtrLod BtnbLod dbSNP AA AC AG AT CC CG CT GG GT TT
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//public double[] posteriors;
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return String.format("%s %16d %c %8d %d %s %.6f %.6f %6.6f %6.6f %6.6f %6.6f %6.6f %6.6f %6.6f %6.6f %6.6f %6.6f",
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location.getContig(),
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location.getStart(),
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ref,
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depth,
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-1,
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genotype(),
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lodVsRef,
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lodVsNextBest,
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posteriors[0],
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posteriors[1],
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posteriors[2],
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posteriors[3],
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posteriors[4],
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posteriors[5],
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posteriors[6],
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posteriors[7],
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posteriors[8],
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posteriors[9]);
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}
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public String asTabularString()
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{
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return String.format("%s %s %c %c %s %f %f %f %f %d %s",
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location,
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sample_name,
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ref,
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alt,
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genotype(),
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qhat,
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qstar,
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lodVsRef,
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lodVsNextBest,
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depth,
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bases);
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}
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public String toString() { return asTabularString(); }
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public String asString() {
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// Print out the called bases
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// Notes: switched from qhat to qstar because qhat doesn't work at n=1 (1 observed base) where having a single non-ref
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// base has you calculate qstar = 0.0 and qhat = 0.49 and that leads to a genotype predicition of AG according
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// to qhat, but AA according to qstar. This needs to be further investigated to see whether we really want
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// to use qstar, but make N (number of chormosomes) switch to n (number of reads at locus) for n=1
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long numNonrefBases = Math.round(qstar * N);
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long numRefBases = N - numNonrefBases;
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if (ref < alt) { // order bases alphabetically
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return AlleleFrequencyWalker.repeat(ref, numRefBases) + AlleleFrequencyWalker.repeat(alt, numNonrefBases);
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}else{
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return AlleleFrequencyWalker.repeat(alt, numNonrefBases) + AlleleFrequencyWalker.repeat(ref, numRefBases);
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}
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}
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public String asPoolTabularString()
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{
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return String.format("%s %c %c %f %f %f %s %f %d %d %d %d",
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location,
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ref,
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alt,
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qstar,
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pBest,
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pRef,
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"NA",
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lodVsRef,
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N,
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n_ref,
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n_het,
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n_hom);
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}
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public double posterior()
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{
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return this.posteriors[(int)this.qstar * this.N];
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}
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public String callType() {
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// Returns a string indicating whether the call is homozygous reference, heterozygous SNP, or homozygous SNP
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String[] callTypeString = {"HomozygousSNP", "HeterozygousSNP", "HomozygousReference"};
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String genotype = genotype();
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int ref_matches = (genotype.charAt(0) == ref ? 1 : 0) + (genotype.charAt(1) == ref ? 1 : 0);
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return callTypeString[ref_matches];
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}
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}
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