105 lines
3.5 KiB
Java
Executable File
105 lines
3.5 KiB
Java
Executable File
package org.broadinstitute.sting.secondarybase;
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import org.broadinstitute.sting.utils.Utils;
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import org.broadinstitute.sting.utils.QualityUtils;
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/**
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* FourProb represents four base hypotheses, their probabilities, and the ranking among one another.
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*
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* @author Kiran Garimella
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*/
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public class FourProb {
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private double[] baseProbs;
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private int[] baseIndices;
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/**
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* Constructor for FourProb.
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*
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* @param baseLikes the unsorted base hypothesis probabilities (in ACGT order).
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*/
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public FourProb(double[][] baseLikes) {
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double[] baseProbs = new double[4];
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for (int baseCurIndex = 0; baseCurIndex < 4; baseCurIndex++) {
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for (int basePrevIndex = 0; basePrevIndex < baseLikes.length; basePrevIndex++) {
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baseProbs[baseCurIndex] += baseLikes[basePrevIndex][baseCurIndex];
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}
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}
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int[] baseIndices = {0, 1, 2, 3};
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Integer[] perm = Utils.SortPermutation(baseProbs);
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double[] ascendingBaseProbs = Utils.PermuteArray(baseProbs, perm);
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int[] ascendingBaseIndices = Utils.PermuteArray(baseIndices, perm);
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this.baseProbs = new double[4];
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this.baseIndices = new int[4];
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for (int i = 0; i < 4; i++) {
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this.baseProbs[i] = ascendingBaseProbs[3 - i];
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this.baseIndices[i] = ascendingBaseIndices[3 - i];
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}
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}
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/**
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* Returns the index of the base at the specified rank.
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*
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* @param rank (0 = best, 3 = worst) the rank of the base whose index should be returned
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* @return the index (0, 1, 2, 3).
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*/
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public int indexAtRank(int rank) { return baseIndices[rank]; }
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/**
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* Returns the base label of the base at the specified rank.
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*
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* @param rank (0 = best, 3 = worst) the rank of the base whose index should be returned
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* @return the base label (A, C, G, T).
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*/
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public char baseAtRank(int rank) { return baseIndexToBase(indexAtRank(rank)); }
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/**
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* Returns the probability of the base at the specified rank.
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*
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* @param rank (0 = best, 3 = worst) the rank of the base whose index should be returned
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* @return the probability of the base (0.0-1.0)
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*/
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public double probAtRank(int rank) { return baseProbs[rank]; }
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/**
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* Returns the quality score of the base at the specified rank.
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*
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* @param rank (0 = best, 3 = worst) the rank of the base whose index should be returned
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* @return the quality score of the base (0-40)
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*/
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public byte qualAtRank(int rank) { return QualityUtils.probToQual(probAtRank(rank)); }
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/**
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* A utility method to convert a base index into a base label.
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*
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* @param baseIndex the index of the base (0, 1, 2, 3).
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* @return A, C, G, T, or '.' if the base index can't be understood.
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*/
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private char baseIndexToBase(int baseIndex) {
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switch (baseIndex) {
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case 0: return 'A';
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case 1: return 'C';
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case 2: return 'G';
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case 3: return 'T';
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default: return '.';
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}
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}
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/**
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* Prettily formats the FourProb info.
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*
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* @return a prettily formatted Sting containing the base and quality score in rank order.
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*/
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public String toString() {
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return (
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"[" + baseAtRank(0) + ":" + qualAtRank(0) + " "
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+ baseAtRank(1) + ":" + qualAtRank(1) + " "
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+ baseAtRank(2) + ":" + qualAtRank(2) + " "
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+ baseAtRank(3) + ":" + qualAtRank(3) + "]"
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);
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}
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}
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