Main.java Source code

Introduction

Here is the source code for Main.java

Source

//package com.java2s;
/*
 * The MIT License
 *
 * Copyright (c) 2009 The Broad Institute
 *
 * Permission is hereby granted, free of charge, to any person obtaining a copy
 * of this software and associated documentation files (the "Software"), to deal
 * in the Software without restriction, including without limitation the rights
 * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
 * copies of the Software, and to permit persons to whom the Software is
 * furnished to do so, subject to the following conditions:
 *
 * The above copyright notice and this permission notice shall be included in
 * all copies or substantial portions of the Software.
 *
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
 * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
 * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
 * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
 * THE SOFTWARE.
 */

public class Main {
    private static final int QUALITY_MASK = 0x3f;

    /**
     * Convert a pair of likelihoods into a value suitable for passing to baseAndProbDiffToSqValue.
     * @param secondBestLikelihood Probability of the 2nd-best base call.  1 > secondBestLikelihood > thirdBestLikelihood.
     * @param thirdBestLikelihood Probability of the 3rd-best base call.  thirdBestLikelihood > 0.
     * @return ratio of input probabilities for storing in SQ tag.
     */
    public static byte sqScaledProbabilityRatio(final double secondBestLikelihood,
            final double thirdBestLikelihood) {
        if (secondBestLikelihood >= 1.0 || thirdBestLikelihood <= 0 || thirdBestLikelihood > secondBestLikelihood) {
            throw new IllegalArgumentException("Likelihoods out of range.  second best: " + secondBestLikelihood
                    + "; third best: " + thirdBestLikelihood);
        }
        // Cap value at QUALITY_MASK
        return (byte) (Math.min(Math.round(-10.0 * Math.log10(thirdBestLikelihood / secondBestLikelihood)),
                QUALITY_MASK));
    }
}