// -*- mode: c++; indent-tabs-mode: nil; -*-
//

/// \file

#ifndef ALIGN_CONTIG_HH_
#define ALIGN_CONTIG_HH_

/**
 * Project     : CASAVA
 * Module      : $RCSfile: AlignContig.hh,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/Application.hh"

// compile with this macro to get verbose output
//#define DEBUG_ALCTG

namespace ca { namespace  applications {
/**
 * @class AlignContig
 *
 * @brief Wrapper for AlignContig functionality.
 *
 */

class AlignContig : public ca::applications::Application {
public:
	AlignContig(CasavaOptions &options) : Application(options){ }
	virtual ~AlignContig() {}
	/**
	 * Runs this applications: reads contigs and aligns them using gapped alignment + affine gap costs
	 *
	 * @return status
	 */
	int run();

	// reads the next contig header 
	bool readNextHeader(char* header, /*static*/ const int bufSize, FILE* pContigs, int& contigNum, int& readsInContig, int& genomeStart, int& genomeEnde);

};

}} // end namespace casava{ namespace { applications

#endif /*ALIGN_CONTIG_HH_*/