We have merged LibraryComplexity into parent jar and now recommend exporting Java memory options

/*

 * The MIT License (MIT)

 *

 * Copyright (c) 2011-2015 Broad Institute, Aiden Lab

 *

 * 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.

 *

 * Based on PicardTools 

 * Juicer version 1.5

 */

import java.text.NumberFormat;

import java.text.ParseException;

import java.util.Locale;

import java.io.FileReader;

import java.io.BufferedReader;

import java.io.IOException;

import java.io.File;

class LibraryComplexity {

  public static void main(String[] args) {

    if (args.length != 2 && args.length != 3 && args.length != 1) {

      System.out.println("Usage: java LibraryComplexity <directory> <output file>");

      System.out.println("     : java LibraryComplexity <unique> <pcr> <opt>");

      System.exit(0);

    }

    NumberFormat nf = NumberFormat.getInstance(Locale.US);

    BufferedReader reader = null;

    long readPairs = 0;

    long uniqueReadPairs = 0;

    long opticalDups = 0;

    long totalReadPairs = 0;

    if (args.length == 2 || args.length==1) {

      try {

        File f = new File(args[0] + "/opt_dups.txt");

        if (f.exists()) {

          reader = new BufferedReader(new FileReader(f));

          while (reader.readLine() != null) opticalDups++;

          reader.close();

        }

        f = new File(args[0] + "/merged_nodups.txt");

        if (f.exists()) {

          reader = new BufferedReader(new FileReader(f));

          while (reader.readLine() != null) uniqueReadPairs++;

          reader.close();				

        }

        f = new File(args[0] + "/dups.txt");

        if (f.exists()) {

          reader = new BufferedReader(new FileReader(args[0] + "/dups.txt"));

          while (reader.readLine() != null) readPairs++;

          reader.close();				

          readPairs += uniqueReadPairs; 

        }

        String fname = "inter.txt";

        if (args.length == 2) fname = args[1];

        f = new File(args[0] + "/" + fname);

        if (f.exists()) {

          reader = new BufferedReader(new FileReader(args[0] + "/" + fname));

          String line = reader.readLine();

          boolean done = false;

          while (line != null && !done) {

            if (line.contains("Sequenced Read")) {

              String[] parts = line.split(":");

              try {

                totalReadPairs = nf.parse(parts[1].trim()).longValue();

              }

              catch (ParseException e) {

                totalReadPairs = 0;

              }

              done = true;

            }

            line = reader.readLine(); 

          }

          reader.close();

        }

      } catch (IOException error) {

        System.err.println("Problem counting lines in merged_nodups and dups");

        System.exit(1);

      }

    }

    else {

      try {

        uniqueReadPairs = Integer.valueOf(args[0]);

        readPairs = Integer.valueOf(args[1]);

        opticalDups = Integer.valueOf(args[2]);

      }

      catch (NumberFormatException error) {

        System.err.println("When called with three arguments, must be integers");

        System.exit(1);

      }

      readPairs += uniqueReadPairs;

    }

    NumberFormat decimalFormat = NumberFormat.getPercentInstance();

    decimalFormat.setMinimumFractionDigits(2);

    decimalFormat.setMaximumFractionDigits(2);

    System.out.print("Unique Reads: " + NumberFormat.getInstance().format(uniqueReadPairs) + " ");

    if (totalReadPairs > 0) {

      System.out.println("(" + decimalFormat.format(uniqueReadPairs/(double)totalReadPairs) + ")");

    }

    else {

      System.out.println();

    }

    System.out.print("PCR Duplicates: " + nf.format(readPairs - uniqueReadPairs) + " ");

    if (totalReadPairs > 0) {

      System.out.println("(" + decimalFormat.format((readPairs - uniqueReadPairs)/(double)totalReadPairs) + ")");

    }

    else {

      System.out.println();

    }

    System.out.print("Optical Duplicates: " + nf.format(opticalDups) + " ");

    if (totalReadPairs > 0) {

      System.out.println("(" + decimalFormat.format(opticalDups/(double)totalReadPairs) + ")");

    }

    else {

      System.out.println();

    }

    long result;

    try {

      result = estimateLibrarySize(readPairs, uniqueReadPairs);

    }

    catch (NullPointerException e) {

      result = 0;

    }

    System.out.println("Library Complexity Estimate: " + nf.format(result));

  }

  /**

   * Estimates the size of a library based on the number of paired end molecules 

   * observed and the number of unique pairs observed.

   * <br>

   * Based on the Lander-Waterman equation that states:<br>

   *     C/X = 1 - exp( -N/X )<br>

   * where<br>

   *     X = number of distinct molecules in library<br>

   *     N = number of read pairs<br>

   *     C = number of distinct fragments observed in read pairs<br>

   */

  public static Long estimateLibrarySize(final long readPairs, 

                                         final long uniqueReadPairs) {

    final long readPairDuplicates = readPairs - uniqueReadPairs;

    if (readPairs > 0 && readPairDuplicates > 0) {

	    long n = readPairs;

	    long c = uniqueReadPairs;

	    double m = 1.0, M = 100.0;

	    if (c >= n || f(m*c, c, n) < 0) {

        throw new IllegalStateException("Invalid values for pairs and unique pairs: " + n + ", " + c);

	    }

	    while( f(M*c, c, n) >= 0 ) {

        m = M;

        M *= 10.0;

	    }

	    double r = (m+M)/2.0;

	    double u = f( r * c, c, n );

	    int i = 0;

	    while (u != 0 && i < 1000) {

        if (u > 0) m = r;

        else M = r;

        r = (m+M)/2.0;

        u = f( r * c, c, n );

        i++;

	    }

	    if (i == 1000) {

        System.err.println("Iterated 1000 times, returning estimate");

	    }

	    return (long) (c * (m+M)/2.0);

    }

    else {

	    return null;

    }

  }

  /** Method that is used in the computation of estimated library size. */

  private static double f(double x, double c, double n) {

    return c/x - 1 + Math.exp(-n/x);

  }

}    

#!/bin/sh

#

# Copyright (c) 2015 Aiden Lab

#

# 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.

#

# Juicer version 1.5

java -Djava.awt.headless=true -Djava.library.path=`dirname $0`/lib64 -Xms49152m -Xmx49152m -jar `dirname $0`/juicer_tools.jar $*