/*
 * Copyright (c) 2014-2015, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail
 * (here and after addressed as Inventors)
 * All Rights Reserved
 *
 * Permission to use, copy, modify and distribute any part of this program for
 * educational, research and non-profit purposes, by non-profit institutions
 * only, without fee, and without a written agreement is hereby granted,
 * provided that the above copyright notice, this paragraph and the following
 * three paragraphs appear in all copies.
 *
 * Those desiring to incorporate this work into commercial products or use for
 * commercial purposes should contact the Inventors using one of the following
 * email addresses: chudakovdm@mail.ru, chudakovdm@gmail.com
 *
 * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT,
 * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS,
 * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN
 * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 *
 * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS
 * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR
 * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO
 * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT
 * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A
 * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY
 * PATENT, TRADEMARK OR OTHER RIGHTS.
 */

package com.milaboratory.oncomigec.core.variant;

import org.apache.commons.math.MathException;
import org.apache.commons.math.distribution.BinomialDistribution;
import org.apache.commons.math.distribution.BinomialDistributionImpl;

import java.io.Serializable;

public class ErrorModel implements Serializable {
    private double order;
    private double cycles, lambda;
    private double propagateProb;

    public ErrorModel() {
        this(1.0, 20, 0.95);
    }

    public ErrorModel(double order, double cycles, double lambda) {
        this.order = order;
        this.cycles = cycles;
        this.lambda = lambda;
        calcPropagateProb();
    }

    public double getLog10PValue(int majorCount, int minorCount, int total) {
        if (majorCount == 0) {
            return 0;
        }

        minorCount = minorCount == 0 ? 1 : minorCount;

        double errorRateBase = Math.pow(1.0 - minorCount / (double) total, 1.0 / cycles),
                errorRate = Math.log(lambda) - Math.log((1.0 + lambda) * errorRateBase - 1);

        BinomialDistribution binomialDistribution = new BinomialDistributionImpl(total,
                errorRate * propagateProb);

        try {
            return -Math.log10(1.0 - binomialDistribution.cumulativeProbability(majorCount) +
                    0.5 * binomialDistribution.probability(majorCount));
        } catch (MathException e) {
            e.printStackTrace();
            return -Math.log10(binomialDistribution.probability(majorCount));
        }
    }

    public double getCycles() {
        return cycles;
    }

    public double getLambda() {
        return lambda;
    }

    public void setCycles(double cycles) {
        this.cycles = cycles;
    }

    public void setLambda(double lambda) {
        this.lambda = lambda;
        calcPropagateProb();
    }

    public double getOrder() {
        return order;
    }

    public void setOrder(double order) {
        this.order = order;
        calcPropagateProb();
    }

    public double getPropagateProb() {
        return propagateProb;
    }

    private void calcPropagateProb() {
        this.propagateProb = lambda * Math.pow(1.0 - lambda, order);
    }
}

@@ -3631,22 +3631,47 @@
 eProb = 
-lambda
+Math.pow((1.0 - lambda), order)
  * Math.
@@ -3674,22 +3674,16 @@
 ath.pow(
-1.0 - 
 lambda, 
@@ -3687,16 +3687,20 @@
 a, order
+ + 1
 );%0A    %7D

Change hot-spot error propagation probability to the one that corresponds to calculations