text: 
  /*
   * bampair.h for MSIsensor1.1
   * Copyright (c) 2013 Beifang Niu && Kai Ye CNIC && Xi’an Jiaotong University All Rights Reserved.
   *
   * 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 _BAMPAIRS_H_
  #define _BAMPAIRS_H_
  
  #include <map>
  #include <vector>
  #include <string>
  #include <iostream>
  #include <fstream>
  #include <algorithm>
  
  #include "param.h"
  
  // Bam file pairs
  class BamPairs {
  public:
      BamPairs();
      ~BamPairs();
      // total pairs
      unsigned int totalParis;
      // bam files
      std::string normal_bam;
      std::string tumor_bam;
  
  protected:
      //xxx
  };
  
  #endif //_BAMPAIRS_H_
  
  