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/*
* bcf_entry.h
*
* Created on: Sep 20, 2012
* Author: Anthony Marcketta
* ($Revision: 1 $)
*/
#include "output_log.h"
#include "entry.h"
#include "header.h"
extern output_log LOG;
class bcf_entry : public entry {
public:
bcf_entry(header &header_obj, vector<bool> &include_individual);
~bcf_entry();
unsigned int N_info;
unsigned int N_format;
unsigned int N_allele;
unsigned int L_shared;
unsigned int L_indiv;
unsigned int line_pos;
void parse_basic_entry(bool parse_ALT=false, bool parse_FILTER=false, bool parse_INFO=false);
void parse_full_entry(bool parse_FORMAT=true);
void parse_genotype_entry(unsigned int indv, bool GT=false, bool GQ=false, bool DP=false, bool FT=false);
void parse_genotype_entries(bool GT=false, bool GQ=false, bool DP=false, bool FT=false);
void set_ALT(const int n_allele);
void set_ALT(const string &in);
void set_FILTER();
void set_FORMAT();
void set_INFO();
void set_indv_GENOTYPE_and_PHASE(unsigned int indv, const pair<string, string> &genotype, char phase);
void set_indv_GENOTYPE_and_PHASE(unsigned int indv, const pair<int, int> &genotype, char phase);
void set_indv_GENOTYPE_and_PHASE(unsigned int indv, const unsigned int &pos, const unsigned int &size);
void set_indv_GENOTYPE_ids(unsigned int indv, const pair<int, int> &in);
void set_indv_GQUALITY(unsigned int indv, const vector<char> &in);
void set_indv_GQUALITY(unsigned int indv, const float &in);
void set_indv_GFILTER(unsigned int indv, const string &in);
void set_indv_GFILTER(unsigned int indv, const vector<char> &in);
void set_indv_PHASE(unsigned int indv, char in);
void set_indv_GENOTYPE_alleles(unsigned int indv, const pair<int, int> &in);
void reset(const vector<char> &data_line);
void add_FORMAT_entry(const string &in, const unsigned int &fmt_key, const unsigned int &pos, const unsigned int &line_pos, const unsigned int &type, const unsigned int &size);
void read_indv_generic_entry(unsigned int indv, const string &FORMAT_id, string &out);
void read_indv_generic_entry(unsigned int indv, const int &idx, string &out);
void read_all_entries(string &out);
void filter_genotypes_by_quality(double min_genotype_quality);
void filter_genotypes_by_depth(int min_depth, int max_depth);
void filter_genotypes_by_filter_status(const set<string> &filter_flags_to_remove, bool remove_all = false);
void print(ostream &out, const set<string> &INFO_to_keep, bool keep_all_INFO=false);
void print_bcf(BGZF* out, const set<string> &INFO_to_keep, bool keep_all_INFO=false);
private:
vector<int> FILTER_str;
unsigned int INFO_pos, FILTER_pos, ALT_pos, FORMAT_pos;
};
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