/**
 ** 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 DemultiplexOptions.hh
 **
 ** \brief Command line options for the sample demultiplexer.
 **
 ** \author Come Raczy
 **/

#ifndef CASAVA_DEMULTIPLEX_DEMULTIPLEX_BCLS_OPTIONS_HH
#define CASAVA_DEMULTIPLEX_DEMULTIPLEX_BCLS_OPTIONS_HH

#include <boost/iostreams/filter/gzip.hpp>
#include <boost/filesystem.hpp>

#include "common/Program.hh"

namespace bios=boost::iostreams;

namespace casava
{
namespace demultiplex
{

class DemultiplexBclsOptions : public casava::common::Options
{
public:
    DemultiplexBclsOptions();
    std::string instrumentName;
    unsigned int runNumber;
    std::string flowCellId;
    std::string componentMaxMismatchesString;
    std::vector<unsigned int> componentMaxMismatches;
    unsigned int lane;
    std::vector<unsigned int> tiles;
    std::vector<std::vector<unsigned int> > readCycles;
    std::vector<unsigned int> inputReadNumbers;
    std::vector<unsigned int> outputReadNumbers;
    std::vector<std::string> readCyclesStrings;
    std::vector<unsigned int> barcodeCycles;
    std::string barcodeCyclesString;
    std::vector<std::string> samples;
    std::vector<std::string> barcodes;
    std::vector<std::string> demuxDirNames;
    boost::filesystem::path basecallsDirectory;
    boost::filesystem::path intensitiesDirectory;
    boost::filesystem::path inputPositionsDir;
    std::string inputPositionsFileType;
    boost::filesystem::path inputFilterDir;
    bool filterPerRead;
    bool needSeparateControls;
    boost::filesystem::path outputDirectory;
    boost::filesystem::path outputSummaryFilePath;
    std::string unknownBarcode;
    std::string outputFormat;
    unsigned int fastqClusterCount;
    bool createMissingFolders;
    bool createDemuxIndex;
    std::string compression;
    bios::gzip_params gzParams;
    bool withEamss;
    bool ignoreMissingBcl;
    bool ignoreMissingCtrl;
    bool withFailedReads;
    std::vector<std::string> readAdapterSequences;
private:
    std::string usagePrefix() const {return "Usage: demultiplexBcls [options]";}
    void postProcess(boost::program_options::variables_map &vm);
};

} // namespave demultiplex
} // namespace casava

#endif // CASAVA_DEMULTIPLEX_DEMULTIPLEX_BCLS_OPTIONS_HH