/**
 * Project     : CASAVA
 * Module      : $RCSfile: IndelFinder.cpp,v $
 * @author     : Tony Cox
 * Copyright   : Copyright (c) Illumina 2008, 2009. All rights reserved.
 *
 ** 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).
 *
 */

#include "applications/IndelFinder.hh"

#include "applications/CasavaOptions.hh"
#include "variance/SampleStats.hh"
#include "variance/SingletonEvent.hh"
#include "variance/ClusterFinderImpl.hh"
#include "common/Alignment.hh"
#include "common/Exceptions.hh"
#include "common/PairStats.hh"

#include "variance/IndelFinderImpl.hh"
#include "variance/BamAlignmentReader.hh"


// Next #define prints out all shadows as export lines preceded by comments
// #define LIST_SHADOWS 1

namespace ca {
namespace applications {

using namespace casava::common;
using namespace ca::variance_detection;

//TODO: Refactor
int IndelFinder::run() {

	cout << "# Starting IndelFinder." << endl;
	#ifdef DEBUG_IDF
	cout << "# Input file     : " << _options.inputReadsFilePath() << endl;
	cout << "# minGroupSize   : " << _options.minGroupSize() << endl;
	cout << "# sras threshold : " << _options.srasThreshold() << endl;
	cout << "# pras threshold : " << _options.prasThreshold() << endl;
	cout << "# spRd threshold : " << _options.spReadThreshold() << endl;
        cout << "# isQphred       : " << _options.isQphred << endl;
	#endif

    try {
        // Load PairStats.
        const boost::filesystem::path
            inputReadsFilePath(_options.inputReadsFilePath());
        const boost::filesystem::path
            projDirPath(inputReadsFilePath.parent_path().parent_path().
                        parent_path().parent_path());

        PairStats pairStats(projDirPath);
        pairStats.setNumSds(_options.numLowInsertSizeSds(),
                            _options.numHighInsertSizeSds());

        IndelFinderImpl indelFinder
            ( _options.prasThreshold(),
              _options.srasThreshold(),
              _options.spReadThreshold(),
              _options.outputFilePath(),
              _options.summaryFilePath(),
              _options.isQphred);

        map<string, SampleStats> sampleStats;
        {
            BamAlignmentReader alignmentReader(_options.isFilterUnanchored);
            alignmentReader.Open(_options.inputReadsFilePath(), _options.refSequencePath(), _options.bamRegion());

            cout << "# Computing sample stats." << endl;
            indelFinder.meanBaseQualityGoodPairs(alignmentReader, sampleStats);
        }
        //reads.rewind();

        std::vector<Singleton*> singletons;

        cout << "# Finding good singletons. " << endl;
        {
            BamAlignmentReader alignmentReader(_options.isFilterUnanchored);
            alignmentReader.Open(_options.inputReadsFilePath(), _options.refSequencePath(), _options.bamRegion());
            indelFinder.findGoodSingletons
                ( alignmentReader, pairStats, sampleStats, singletons);
        } // ~scope of alignmentReader




#ifdef LIST_SHADOWS
        for ( vector<Singleton*>::iterator i(singletons.begin());
              i!=singletons.end();++i)
        {
            cout << "# SHADOW" << "\t" << (*i)->minPos_ <<"\t"
                 << (*i)->maxPos_ << "\t"	 << (*i)->alignment_;
        } // ~for
#endif

        indelFinder.generateOutputFile( singletons );

        indelFinder.generateStatsFile( sampleStats );

        //	ClusterFinderImpl clusterFinder
        //	  ( _options.maxDistance(), _options.minGroupSize() );

        //	clusterFinder( singletons );
    } catch(const casava::common::CasavaException& e) {
        cerr << "ERROR:  EXCEPTION: " << e.getContext() << ": " << e.getMessage() << std::endl;
        throw;
    }

	return 0;
} // ~IndelFinder::run()



}
} // end namespace casava{ namespace { applications