text: /*******************************************************************************
   * Copyright (C) 2020 Olivier Delaneau, University of Lausanne
   * Copyright (C) 2020 Simone Rubinacci, University of Lausanne
   *
   * Permission is hereby granted, free of charge, to any person obtaining a copy
   * of this software and associated documentation files (the "Software"), to deal
   * in the Software without restriction, including without limitation the rights
   * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
   * copies of the Software, and to permit persons to whom the Software is
   * furnished to do so, subject to the following conditions:
   *
   * The above copyright notice and this permission notice shall be included in
   * all copies or substantial portions of the Software.
   *
   * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
   * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
   * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
   * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
   * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
   * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
   * SOFTWARE.
   ******************************************************************************/
  
  #ifndef _REPHASER_H
  #define _REPHASER_H
  
  #include <utils/otools.h>
  #include <objects/hmm_parameters.h>
  
  #include <containers/haplotype_set.h>
  #include <containers/variant_map.h>
  
  #include <models/rephase_hmm.h>
  
  class rephaser {
  public:
  	//COMMAND LINE OPTIONS
  	bpo::options_description descriptions;
  	bpo::variables_map options;
  
  	//INTERNAL DATA
  	haplotype_set H;
  	variant_map V;
  	hmm_parameters M;
  
  	//MULTI-THREADING
  	int i_workers, i_jobs;
  	vector < pthread_t > id_workers;
  	pthread_mutex_t mutex_workers;
  
  	//COMPUTE DATA
  	basic_stats statH;
  	vector < rephase_hmm * > HMM;
  
  	//CONSTRUCTOR
  	rephaser();
  	~rephaser();
  
  	//METHODS
  	void rephase_individual(int, int);
  	void rephase_iteration();
  	void rephase_loop();
  
  	//PARAMETERS
  	void declare_options();
  	void parse_command_line(vector < string > &);
  	void check_options();
  	void verbose_options();
  	void verbose_files();
  
  	//FILE I/O
  	void read_files_and_initialise();
  	void rephase(vector < string > &);
  	void write_files_and_finalise();
  };
  
  
  #endif
  
  
  