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/*
* vcf_entry.h
*
* Created on: Aug 19, 2009
* Author: Adam Auton
* ($Revision: 230 $)
*/
#ifndef VCF_ENTRY_H_
#define VCF_ENTRY_H_
#include "entry.h"
#include "output_log.h"
#include "header.h"
extern output_log LOG;
using namespace std;
class vcf_entry : public entry
{
public:
vcf_entry(header &meta_data, vector<bool> &include_individual);
~vcf_entry();
static string convert_line;
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 parse_FORMAT();
void reset(const vector<char> &data_line);
void read_indv_generic_entry(unsigned int indv, const string &FORMAT_id, string &out);
void set_ALT(const string &in);
void set_FILTER(const string &FILTER_str);
void set_FORMAT(const string &in);
void set_INFO(const string &INFO_str);
void add_FORMAT_entry(const string &in, unsigned int pos);
void set_indv_GENOTYPE_and_PHASE(unsigned int indv, const string &in);
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_alleles(unsigned int indv, const pair<string, string> &in);
void set_indv_GENOTYPE_alleles(unsigned int indv, char a1, char a2);
void set_indv_GENOTYPE_ids(unsigned int indv, const pair<int, int> &in);
void set_indv_PHASE(unsigned int indv, char in);
void set_indv_GQUALITY(unsigned int indv, double in);
void set_indv_GFILTER(unsigned int indv, const string &in);
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);
void filter_genotypes_by_depth(int min_depth, int max_depth);
void filter_genotypes_by_quality(double min_genotype_quality);
void filter_genotypes_by_filter_status(const set<string> &filter_flags_to_remove, bool remove_all = false);
private:
string ALT_str, FILTER_str, INFO_str, FORMAT_str, QUAL_str;
vector<string> GENOTYPE_str;
};
#endif /* VCF_ENTRY_H_ */
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