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/*
* header.h
*
* Created on: Apr 29, 2013
* Author: amarcketta
*/
#ifndef HEADER_H_
#define HEADER_H_
#include <cstring>
#include <string>
#include <map>
#include <vector>
#include "output_log.h"
using namespace std;
extern output_log LOG;
enum Type_enum {Integer=0, Float=1, Character=2, String=3, Flag=4};
class Field_description
{
public:
string Field;
string ID;
int idx;
int N_entries;
string N_entries_str;
string Type_str;
Type_enum Type;
string Description;
string Length;
string Assembly;
string Source;
string Version;
string Other;
Field_description() : Field(""), ID(""), idx(-1), N_entries(0), N_entries_str(""), Type_str(""), Type(Integer), Description(""), Length(""), Assembly(""), Source(""), Version(""), Other("") {};
~Field_description() {};
};
class header
{
public:
unsigned int contig_index;
bool has_contigs;
bool has_genotypes;
bool has_header;
bool has_file_format;
bool has_idx;
vector<string> indv;
vector<string> lines;
vector<Field_description> parsed_lines;
unsigned int N_indv;
map<int, Field_description> INFO_map;
map<int, Field_description> FILTER_map;
map<int, Field_description> FORMAT_map;
map<int, Field_description> CONTIG_map;
map<string, int> CONTIG_reverse_map;
map<string, int> FILTER_reverse_map;
map<string, int> INFO_reverse_map;
map<string, int> FORMAT_reverse_map;
header();
~header() {};
void reprint();
void reparse();
void parse_meta(const string &line, unsigned int &line_index);
void parse_header(const string &line);
int add_INFO_descriptor(const string &in, int index);
int add_FILTER_descriptor(const string &in, int index);
int add_FORMAT_descriptor(const string &in, int index);
void add_CONTIG_descriptor(const string &in, int index);
static void tokenize(const string &in, char token, vector<string> &out);
static int str2int(const string &in, const int missing_value=-1);
static string int2str(const int in, const int missing_value=-1);
static double str2double(const string &in, const double missing_value=-1.0);
static string double2str(const double in, const double missing_value=-1.0);
};
#endif /* HEADER_H_ */
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