89 lines
3.1 KiB
Java
89 lines
3.1 KiB
Java
package org.broadinstitute.sting.playground.fourbasecaller;
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import java.io.File;
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/**
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* BasecallingReadModel represents the statistical models for
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* all bases in all cycles. It allows for easy, one-pass
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* training via the addTrainingPoint() method, and for the
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* computation of the 4x4 likelihood matrix or the 1x4
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* probability vector (with contextual components marginalized
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* out of the likelihood matrix).
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*
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* @author Kiran Garimella
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*/
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public class BasecallingReadModel {
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private BasecallingBaseModel[] basemodels = null;
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/**
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* Constructor for BasecallingReadModel.
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*
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* @param readLength the length of the read that this model will support
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*/
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public BasecallingReadModel(int readLength) {
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basemodels = new BasecallingBaseModel[readLength];
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for (int i = 0; i < readLength; i++) {
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basemodels[i] = new BasecallingBaseModel();
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}
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}
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/**
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* Add a single training point to the model.
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*
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* @param cycle the cycle for which this point should be added
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* @param baseCur the current base
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* @param qualCur the current base's quality
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* @param fourintensity the four intensities of the current base
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*/
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public void addMeanPoint(int cycle, char baseCur, byte qualCur, double[] fourintensity) {
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basemodels[cycle].addMeanPoint(baseCur, qualCur, fourintensity);
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}
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public void addCovariancePoint(int cycle, char baseCur, byte qualCur, double[] fourintensity) {
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basemodels[cycle].addCovariancePoint(baseCur, qualCur, fourintensity);
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}
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/**
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* Compute the likelihood matrix for a given cycle.
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*
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* @param cycle the cycle number for the current base
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* @param fourintensity the four intensities for the current cycle's base
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* @return 4x4 matrix of likelihoods
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*/
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public double[] computeLikelihoods(int cycle, double[] fourintensity) {
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return basemodels[cycle].computeLikelihoods(cycle, fourintensity);
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}
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/**
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* Compute the probability distribution for the base at a given cycle.
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*
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* @param cycle the cycle number for the current base
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* @param fourintensity the four intensities for the current cycle's base
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* @return an instance of FourProb, which encodes a base hypothesis, its probability,
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* and the ranking among the other hypotheses
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*/
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public FourProb computeProbabilities(int cycle, double[] fourintensity) {
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double[] likes = computeLikelihoods(cycle, fourintensity);
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double total = 0;
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for (int baseCurIndex = 0; baseCurIndex < 4; baseCurIndex++) { total += likes[baseCurIndex]; }
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for (int baseCurIndex = 0; baseCurIndex < 4; baseCurIndex++) { likes[baseCurIndex] /= total; }
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return new FourProb(likes);
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}
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/**
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* Writes model parameters to a file per cycle.
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*
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* @param dir the directory where the parameters should be written
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*/
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public void write(File dir) {
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for (int cycle = 0; cycle < basemodels.length; cycle++) {
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File outparam = new File(dir.getPath() + "/param." + cycle);
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basemodels[cycle].write(outparam);
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}
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}
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}
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