48 lines
1.6 KiB
Java
48 lines
1.6 KiB
Java
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package org.broadinstitute.sting.playground.fourbasecaller;
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import org.broadinstitute.sting.utils.Utils;
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import org.broadinstitute.sting.utils.QualityUtils;
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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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public FourProb(int[] baseIndices, double[] baseProbs) {
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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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public int indexAtRank(int rank) { return baseIndices[rank]; }
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public char baseAtRank(int rank) { return baseIndexToBase(indexAtRank(rank)); }
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public double probAtRank(int rank) { return baseProbs[rank]; }
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public byte qualAtRank(int rank) { return QualityUtils.probToQual(probAtRank(rank)); }
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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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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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