bcf2pro_file.h

/* An bcf  */

#ifndef _BCF_FILE_H_
#define _BCF_FILE_H_

#include <iostream>
#include <cfloat>
#include <iomanip>
#include <vector>

#include "typedef.h"
#include "datatypes.h"
#include "raw.h"
#include "stream_tools.h"

#include "map_file.h"
#include "locus.h"
#include "bcf2pro.h"


class Bcf2pro_file : public Indexed_file <Locus> {
    using Indexed_file<Locus>::file_index_;

    void read_text(Locus &);    
    void read_text_profile(Locus &locus){Indexed_file<Locus>::read_text(locus);};   

    bool profile_;

    int columns_, offset_;

    using Indexed_file<Locus>::write_text;  
    using Indexed_file<Locus>::out_;    //(const std::ios_base::openmode &);
    using Indexed_file<Locus>::in_; //(const std::ios_base::openmode &);

    using Base_file::open_;
    using Base_file::table_open_;
public:
    Bcf2pro_file(){profile_=false;};
    Bcf2pro_file(bool call){profile_=call;};
    void set_mpileup(const int &, const int &);
/*  Mpileup_file(){
        open_=false;
        table_open_=false;
        read_=false;
        write_=false;
        delim_column_='\t';
        binary_=false;
        filename_="";
        concatenated_=false;
        indexed_=false;
    };          //!< default constructor*/
    using Indexed_file<Locus>::open;
    using Indexed_file<Locus>::set_index;   
    using Indexed_file<Locus>::get_index;   

    using Indexed_file<Locus>::get_pos;
    using Indexed_file<Locus>::write_header;    
    
    Locus read_header_profile(void){return Indexed_file<Locus>::read_header();} 
    Locus read_header(void);            
};

#endif