/**
 ** 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 demultiplexTile.cpp
 **
 ** \brief Demultiplex samples (per tile).
 **
 ** Entry point for the application that splits the base call directories from
 ** RTA and from the pipeline into a number of subdirectories where every lane
 ** contains at most one sample.
 **
 ** \author Roman Petrovski
 **/

#include "common/Compression.hh"
#include "demultiplex/DemultiplexBclsOptions.hh"
#include "demultiplex/BclToFastqDemultiplexer.hh"

using casava::demultiplex::DemultiplexBclsOptions;

namespace cc=casava::common;

void demultiplex(const DemultiplexBclsOptions &options, const cc::Compression &compressor)
{
    const casava::demultiplex::BarcodeTranslationTable barcodeDirectories(
            options.outputDirectory,
            options.unknownBarcode,
            options.componentMaxMismatches, options.samples, options.barcodes, options.demuxDirNames);

    std::cerr << barcodeDirectories << "\n";
    casava::demultiplex::BclToFastqDemultiplexer demultiplexer(
            options.instrumentName,
            options.runNumber,
            options.flowCellId,
            options.lane,
            options.tiles,
            options.readCycles,
            options.inputReadNumbers,
            options.outputReadNumbers,
            options.barcodeCycles,
            barcodeDirectories,
            options.basecallsDirectory,
            options.outputFormat,
            options.fastqClusterCount,
            options.createMissingFolders,
            options.createDemuxIndex,
            options.intensitiesDirectory,
            options.inputPositionsDir,
            options.inputPositionsFileType,
            options.inputFilterDir,
            options.filterPerRead,
            options.needSeparateControls,
            compressor,
            options.outputSummaryFilePath,
            options.withEamss,
            options.ignoreMissingBcl,
            options.ignoreMissingCtrl,
            options.withFailedReads,
            options.readAdapterSequences);

    demultiplexer.run();
}

void demultiplex(const DemultiplexBclsOptions &options)
{
    if ("gzip" == options.compression)
    {
        demultiplex(options, cc::makeCompressionFilter(options.gzParams));
    }
    else
    {
        demultiplex(options, cc::CompressionFactory::get(options.compression));
    }
}

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