C++ library

The egglib-cpp package contains a fully object-oriented C++ library providing efficient implementation of task related with sequence data storage, simulation and polymorphism analysis.

Documentation

The documentation is available as a separate doxygen-generated reference manual.

Writing C++ programs using egglib-cpp

Here are the recommendations for using egglib-cpp in C++ applications:

• egglib-cpp headers will be available in a egglib-cpp/ directory so it is necessary to include them as in the following C++ code:

#include <egglib-cpp/Align.hpp>

• Link your program against egglib-cpp (as in -legglib-cpp). The library is static.
• All egglib-cpp objects are defined in an egglib namespace.

The following example shows how to perform coalescent simulations to obtain and display the average and standard deviation of Tajima’s D over a pre-defined number of replicates and with a fixed number of segregating sites

// test.cpp

#include <iostream>
using namespace std;

#include <egglib-cpp/Arg.hpp>
#include <egglib-cpp/Controller.hpp>
#include <egglib-cpp/DataMatrix.hpp>
#include <egglib-cpp/EggException.hpp>
#include <egglib-cpp/Mutator.hpp>
#include <egglib-cpp/NucleotideDiversity.hpp>
#include <egglib-cpp/ParamSet.hpp>
#include <egglib-cpp/Random.hpp>
using namespace egglib;

const unsigned int NREPETS = 1000;
const double S = 20;

int main(int argn, char* argv[]) {

    try {
        ParamSet paramSet;      // creates a parameter holder
        paramSet.singles(0, 20);  // sets the number of samples
        Random random;          // creates a random number generator
        Controller controller(&paramSet, &random);  // creates the coalescent simulator
        Arg* arg;     // creates a Ancestral Recombination Graph pointer
        Mutator mutator;    // polymorphism generator
        mutator.fixedNumberOfMutations(S);  // fix number of polymorphic sites
        NucleotideDiversity pol; // polymorphism computer
        DataMatrix data;    // alignment object

        double sum=0.;
        double sum2=0.;

        for (unsigned int i=0; i<NREPETS; i++) {
            controller.reset();
            while (controller.step()>1);    // performs simulations
            arg = controller.getArg();      // gets the tree address
            data = mutator.mute(arg, &random);  // performs simulations
            pol.load(data, false, 1, 0, "01", false);  // analyzes binary data
            sum += pol.D();
            sum2 += pol.D()*pol.D();
        }

        cout << "Tajima's D: " << sum/NREPETS;
        cout << " [+- " << sum2/NREPETS - (sum * sum /(NREPETS*NREPETS)) << "]" << endl;
    }
    catch (EggException e) {
        cerr << "The following error occurred: " << e.what() << endl;
        return -1;
    }
    return 0;
}

This program can be compiled with the following commands:

g++ -c test.cpp
g++ -o test test.o -legglib-cpp