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/*
* parameters.cpp
*
* Created on: Nov 11, 2009
* Author: Adam Auton
* ($Revision: 249 $)
*/
// Class for reading in, checking and storing user parameters
#ifndef PARAMETERS_H_
#define PARAMETERS_H_
#include <algorithm>
#include <cstdio>
#include <cstdlib>
#include <iostream>
#include <limits>
#include <string>
#include <vector>
#include <set>
#include <stdint.h>
#include <unistd.h>
#include "output_log.h"
extern output_log LOG;
using namespace std;
const string VCFTOOLS_VERSION="v0.1.12";
static const uint8_t bgzf_magic[19] = "\037\213\010\4\0\0\0\0\0\377\6\0\102\103\2\0\0\0"; //just compare the first 16 chars? though
static const uint8_t gzip_magic[2] = {0x1f,0x8b};
class parameters
{
public:
bool stream_in;
bool bcf_format;
bool BED_exclude;
string BED_file;
set<string> chrs_to_exclude;
set<string> chrs_to_keep;
bool derived;
bool diff_discordance_matrix;
string diff_file;
bool diff_file_bcf;
bool diff_file_compressed;
bool diff_indv_discordance;
string diff_indv_map_file;
bool diff_site_discordance;
bool diff_switch_error;
int end_pos;
string exclude_positions_file;
string FORMAT_id_to_extract;
set<string> geno_filter_flags_to_exclude;
string geno_rsq_position_list;
string hap_rsq_position_list;
vector<string> weir_fst_populations;
int fst_window_size;
int fst_window_step;
string indv_exclude_file;
string indv_keep_file;
set<string> indv_to_exclude;
set<string> indv_to_keep;
vector<string> INFO_to_extract;
bool invert_mask;
bool keep_only_indels;
int ld_bp_window_size;
int ld_snp_window_size;
int ld_bp_window_min;
int ld_snp_window_min;
int min_mac;
double min_maf;
string mask_file;
int max_alleles;
int max_genotype_depth;
int max_mac;
double max_maf;
double max_mean_depth;
int max_missing_call_count;
int max_non_ref_ac;
double max_non_ref_af;
int max_N_indv;
int min_alleles;
int min_genotype_depth;
double min_genotype_quality;
double min_HWE_pvalue;
int min_interSNP_distance;
int min_kept_mask_value;
double min_mean_depth;
int min_non_ref_ac;
double min_non_ref_af;
double min_quality;
double min_r2;
double min_site_call_rate;
int num_outputs;
bool output_012_matrix;
bool output_as_IMPUTE;
bool output_as_ldhat_phased;
bool output_as_ldhat_unphased;
bool output_BEAGLE_genotype_likelihoods_GL;
bool output_BEAGLE_genotype_likelihoods_PL;
bool output_counts;
bool output_filter_summary;
bool output_freq;
bool output_geno_depth;
bool output_geno_chisq;
bool output_geno_rsq;
bool output_hap_rsq;
bool output_het;
bool output_HWE;
bool output_indel_hist;
bool output_indv_depth;
bool output_indv_missingness;
bool output_interchromosomal_hap_rsq;
bool output_interchromosomal_geno_rsq;
bool output_kept_sites;
bool output_LROH;
int output_N_PCA_SNP_loadings;
bool output_PCA;
string output_prefix;
bool output_relatedness_Yang;
bool output_relatedness_Manichaikul;
bool output_removed_sites;
bool output_singletons;
bool output_site_depth;
bool output_site_mean_depth;
bool output_site_missingness;
bool output_site_pi;
bool output_site_quality;
int output_SNP_density_bin_size;
int output_Tajima_D_bin_size;
int output_TsTv_bin_size;
bool output_TsTv_by_count;
bool output_TsTv_by_qual;
bool output_TsTv_summary;
bool phased_only;
bool PCA_no_normalisation;
int pi_window_size;
int pi_window_step;
bool plink_output;
bool plink_tped_output;
string positions_file;
bool recode;
bool recode_bcf;
set<string> recode_INFO_to_keep;
bool recode_all_INFO;
bool remove_all_filtered_genotypes;
bool remove_all_filtered_sites;
bool remove_indels;
set<string> site_filter_flags_to_exclude;
set<string> site_filter_flags_to_keep;
set<string> site_INFO_flags_to_keep;
set<string> site_INFO_flags_to_remove;
string snps_to_exclude_file;
string snps_to_keep_file;
set<string> snps_to_keep;
int start_pos;
bool stream_err;
bool stream_out;
bool suppress_allele_output;
string vcf_filename;
bool vcf_format;
bool vcf_compressed;
parameters(int argc, char *argv[]);
~parameters(){};
void read_parameters();
void print_help();
void print_params();
private:
void check_parameters();
static void error(string err_msg, int code);
vector<string> argv;
string get_arg(unsigned int i);
};
#endif /* PARAMETERS_H_ */
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