/**
 ** Copyright (c) 2007-2009 Illumina, Inc.
 **
 ** This software is covered by the "Illumina Genome Analyzer Software
 ** License Agreement" and the "Illumina Source Code License Agreement",
 ** and certain third party copyright/licenses, and any user of this
 ** source file is bound by the terms therein (see accompanying files
 ** Illumina_Genome_Analyzer_Software_License_Agreement.pdf and
 ** Illumina_Source_Code_License_Agreement.pdf and third party
 ** copyright/license notices).
 **
 ** This file is part of the Consensus Assessment of Sequence And VAriation
 ** (CASAVA) software package.
 **
 ** \file calculateDiversity.cpp
 **
 ** \brief Calculates the diversity in a population of matched fragments.
 **
 ** CalculateDiversity is used to estimate the diversity in the population
 ** of fragment sizes obtained during alignment analysis.
 **
 ** \author Stephen Allan
 **/

#include "alignment/CalculateDiversityOptions.hh"
#include "alignment/DiversityCalculator.hh"

namespace ca = casava::alignment;

void calculateDiversity(const ca::CalculateDiversityOptions &options);

int main(int argc, char *argv[])
{
    casava::common::run(calculateDiversity, argc, argv);
}

void calculateDiversity(const ca::CalculateDiversityOptions &options)
{
    ca::DiversityCalculator diversityCalculator(options.maximumFragmentSize,
                                                options.inputDirectory,
                                                options.outputFile,
                                                options.processLane);
    diversityCalculator.run();
}