/**
 ** Copyright (c) 2007-2010 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.
 **
 **/

#include <cstdio>
#include <cstdlib>
#include "smallRna/TrimmerInput.h"
#include "smallRna/Trimmer.h"
#include "smallRna/TrimmerProcess.h"

int main(int argc, char * argv[])
{
    int status = OKAY;

    if ((argc > 1) && (argv[1][0] == '?'))
    {
        CTrimmerInput::PrintHelp(argv[0]);
        exit(0);
    }

    CTrimmerInput input(argc, argv, status);
    if (status != 0) {
        exit(0);
    }
    /******************************
    Start up the trimmer algorithm
    ******************************/
    CTrimmer trimmer;
    status = trimmer.Setup(input.adaptorString, input.simmatrix);

    if (status != 0) {
        printf("Error setting up trimmer. Status=%d\n", status);
        exit(0);
    }

    /******************************
    Write the banner
    ******************************/
    //input.WriteBanner();

    /******************************
    Run the trimming process
    ******************************/
    CTrimmerProcess process(input);
    process.Run(trimmer);
}