es.cnio.bioinfo.bicycle.BinomialAnnotator.java Source code

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Here is the source code for es.cnio.bioinfo.bicycle.BinomialAnnotator.java

Source

/*
    
Copyright 2012 Daniel Gonzalez Pea, Osvaldo Graa
    
    
This file is part of the bicycle Project. 
    
bicycle Project is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
    
bicycle Project is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU Lesser Public License for more details.
    
You should have received a copy of the GNU Lesser Public License
along with bicycle Project.  If not, see <http://www.gnu.org/licenses/>.
*/

package es.cnio.bioinfo.bicycle;

import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStreamReader;

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

public class BinomialAnnotator {

    public static void main(String[] args) throws IOException, MathException {
        BufferedReader in = new BufferedReader(new InputStreamReader(System.in));

        double p = Double.parseDouble(args[0]);
        String line = null;

        while ((line = in.readLine()) != null) {

            String[] tokens = line.split("\t");
            int reads = Integer.parseInt(tokens[5]);
            int cCount = Integer.parseInt(tokens[4]);
            BinomialDistribution binomial = new BinomialDistributionImpl(reads, p);
            double pval = (reads == 0) ? 1.0d : (1.0d - binomial.cumulativeProbability(cCount - 1));
            if (System.out.checkError()) {
                System.exit(1);
            }
            System.out.println(line + "\t" + pval);

        }
    }
}