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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 <algorithm>
#include <iostream>
#include <iterator>
#include <limits>
#include <map>
#include <set>
#include <sstream>
#include <string>
#include <vector>
#include <cassert>
#include "output_log.h"
extern output_log LOG;
using namespace std;
enum Type_enum {Integer=0, Float=1, Character=2, String=3, Flag=4};
class Field_description
{
public:
string ID;
int N_entries;
Type_enum Type;
string Description;
Field_description() : ID(""), N_entries(0), Type(Integer), Description("") {};
~Field_description() {};
};
class vcf_entry {
public:
vcf_entry(const unsigned int N_indv);
vcf_entry(const unsigned int N_indv, const string &data_line);
~vcf_entry();
const unsigned int N_indv;
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 reset(const string &vcf_data_line);
string get_CHROM() const;
void get_CHROM(string &out) const;
int get_POS() const;
string get_ID() const;
string get_REF() const;
string get_ALT() const;
string get_ALT_allele(int allele_num) const;
void get_allele(int allele_num, string &out) const;
void get_alleles_vector(vector<string> &out) const;
string get_FILTER() const;
void get_FILTER_vector(vector<string> &out) const;
double get_QUAL() const;
string get_INFO(const set<string> &INFO_to_keep) const;
string get_INFO_value(const string &key) const;
string get_FORMAT() const;
void get_indv_GENOTYPE_ids(unsigned int indv, pair<int, int> &out) const;
void get_indv_GENOTYPE_strings(unsigned int indv, pair<string, string> &out) const;
char get_indv_PHASE(unsigned int indv) const;
double get_indv_GQUALITY(unsigned int indv) const;
int get_indv_DEPTH(unsigned int indv) const;
void get_indv_GFILTER(unsigned int indv, string &out) const;
void get_indv_GFILTER_vector(unsigned int indv, vector<string> &out) const;
int get_indv_ploidy(unsigned int indv) const;
bool is_SNP() const;
bool is_biallelic_SNP() const;
bool is_diploid(const vector<bool> &include_indv, const vector<bool> &include_genotype) const;
void read_indv_generic_entry(unsigned int indv, const string &FORMAT_id, string &out);
bool FORMAT_id_exists(const string &FORMAT_id);
unsigned int get_N_alleles() const;
unsigned int get_N_chr(const vector<bool> &include_indv, const vector<bool> &include_genotype) const;
void set_CHROM(const string &in);
void set_POS(const int in);
void set_ID(const string &in);
void set_REF(const string &in);
void set_ALT(const string &in);
void set_QUAL(const double in);
void set_FILTER(const string &FILTER_str);
void set_FORMAT(const string &in);
void set_INFO(const string &INFO_str);
void add_ALT_allele(const string &in);
void add_FILTER_entry(const string &in);
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_DEPTH(unsigned int indv, int in);
void set_indv_GFILTER(unsigned int indv, const string &in);
void add_indv_GFILTER(unsigned int indv, const string &in);
static void add_INFO_descriptor(const string &in);
static void add_FILTER_descriptor(const string &in);
static void add_FORMAT_descriptor(const string &in);
void print(ostream &out);
void print(ostream &out, const set<string> &INFO_to_keep, bool keep_all_INFO=false);
void print(ostream &out, const set<string> &INFO_to_keep, bool keep_all_INFO, const vector<bool> &include_indv, const vector<bool> &include_genotype);
void filter_genotypes_by_depth(vector<bool> &include_genotype_out, int min_depth, int max_depth);
void filter_genotypes_by_quality(vector<bool> &include_genotype_out, double min_genotype_quality);
void filter_genotypes_by_filter_status(vector<bool> &include_genotype_out, const set<string> &filter_flags_to_remove, bool remove_all = false);
void get_allele_counts(vector<int> &out, unsigned int &N_non_missing_chr_out, const vector<bool> &include_indv, const vector<bool> &include_genotype) const;
void get_genotype_counts(const vector<bool> &include_indv, const vector<bool> &include_genotype, unsigned int &out_N_hom1, unsigned int &out_N_het, unsigned int &out_N_hom2) const;
static double SNPHWE(int obs_hets, int obs_hom1, int obs_hom2);
private:
istringstream data_stream;
bool basic_parsed;
bool fully_parsed;
bool parsed_ALT;
bool parsed_FILTER;
bool parsed_INFO;
bool parsed_FORMAT;
string CHROM;
int POS;
string ID;
string REF;
vector<string> ALT;
double QUAL;
vector<string> FILTER;
bool passed_filters;
vector<pair<string, string> > INFO;
vector<string> FORMAT;
vector< pair<int,int> > GENOTYPE;
vector<int> ploidy;
vector<char> PHASE;
vector<double> GQUALITY;
vector<int> DEPTH;
vector< vector<string> > GFILTER;
vector<bool> parsed_GT;
vector<bool> parsed_GQ;
vector<bool> parsed_DP;
vector<bool> parsed_FT;
int GT_idx;
int GQ_idx;
int DP_idx;
int FT_idx;
string ALT_str, FILTER_str, INFO_str, FORMAT_str, QUAL_str;
vector<string> GENOTYPE_str;
map<string, unsigned int> FORMAT_to_idx;
static map<string, Field_description> INFO_map;
static map<string, string> FILTER_map;
static map<string, Field_description> FORMAT_map;
static int str2int(const string &in, const int missing_value=-1);
static double str2double(const string &in, const double missing_value=-1.0);
static string int2str(const int in, const int missing_value=-1);
static string double2str(const double in, const double missing_value=-1.0);
static void tokenize(const string &in, char token, vector<string> &out);
};
#endif /* VCF_ENTRY_H_ */
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