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options.h
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//////////////////////////////////////////////////////////////////
// //
// PLINK (c) 2005-2009 Shaun Purcell //
// //
// This file is distibuted under the GNU General Public //
// License, Version 2. Please see the file COPYING for more //
// details //
// //
//////////////////////////////////////////////////////////////////
#ifndef __OPTIONS_H__
#define __OPTIONS_H__
#include <string>
#include <vector>
#include "plink.h"
using namespace std;
/* static Options lookup2_options; */
// static Options idhelp_replace_options;
// static Options idhelp_match_options;
// static Options annot_options;
// static Options dosage_options;
//
class OptionSet {
public:
map<string,vector<string> > val;
bool isSet(string s)
{
return val.find(s) != val.end();
}
vector<string> getValues(string s)
{
vector<string> sv;
map<string,vector<string> >::iterator i = val.find(s);
if ( i == val.end() )
return sv;
return i->second;
}
string getValue(string s)
{
map<string,vector<string> >::iterator i = val.find(s);
if ( i == val.end() )
return "";
if ( i->second.size() > 0 )
return i->second[0];
else
return "";
}
void display()
{
map<string,vector<string> >::iterator i = val.begin();
while ( i != val.end() )
{
cout << i->first;
if ( i->second.size() > 0 )
{
cout << " : ";
for ( int k = 0 ; k < i->second.size(); k++)
{
cout << " " << i->second[k] ;
}
}
cout << "\n";
++i;
}
}
};
class Options {
map<string,OptionSet*> opt;
public:
OptionSet * addOption(string s)
{
map<string,OptionSet*>::iterator i = opt.find(s);
if ( i != opt.end() )
return i->second;
OptionSet * o = new OptionSet;
opt.insert(make_pair(s,o));
return o;
}
~Options()
{
map<string,OptionSet*>::iterator i = opt.begin();
while (i != opt.end() )
{
delete i->second;
++i;
}
}
OptionSet * getOptions(string s)
{
map<string,OptionSet*>::iterator i = opt.find(s);
if ( i != opt.end() )
return i->second;
else
{
OptionSet * o = new OptionSet;
return o;
}
}
};
class par {
public:
static bool myfunction;
static Options opt;
static bool verbose;
static bool flag;
static bool dumpped;
static bool debug;
static bool dummy;
static int dummy_nind;
static int dummy_nsnp;
static bool web_check;
static bool tucc;
static bool do_not_load_snps;
static const double epsilon;
static long unsigned int random_seed;
static int simul_ncases;
static int simul_ncontrols;
static string simul_label;
static double simul_prevalence;
static bool simul;
static string simul_file;
static bool simul_tags;
static bool simul_haps;
static bool simul_qt;
static double simul_qt_var;
static bool lookup;
static bool lookup_single_snp;
static bool lookup_to_file;
static string lookup_snp;
static string lookup_gene_name;
static bool lookup_gene;
static bool lookup_multiple_genes;
static int lookup_gene_kb_window;
static int lookup_snp_kb_window;
static bool lookup2;
static string lookup2_cmd;
static bool idhelp;
static string idhelp_output_delimit;
static string idhelp_dictionary;
static bool idhelp_dump_from_dict;
static string idhelp_dump_from_dict_cmd;
static bool idhelp_auto_alias;
static bool idhelp_lookup;
static string idhelp_lookup_string;
static bool idhelp_subset;
static string idhelp_subset_string;
static bool idhelp_replace;
static string idhelp_replace_string;
static bool idhelp_match;
static vector<string> idhelp_match_string;
static bool idhelp_no_dict;
static bool idhelp_list_aliases;
static bool idhelp_alias_update;
static string idhelp_command;
static string idhelp_input;
static bool run_R_script;
static bool run_R_write_script;
static string R_script;
static bool run_R_chisq;
static bool run_R_z;
static int run_R_nsnps;
static int R_port;
static bool recode;
static bool recode_transpose;
static bool recode_long;
static bool recode_long_ref;
static bool recode_mutlist;
static bool recode_12;
static bool recode_AD;
static bool recode_AD_Aonly;
static bool recode_AD_fixed;
static bool recode_allele_coding;
static string recode_allele_coding_file;
static bool recode_1234;
static bool recode_ACGT;
static bool set_reference_allele;
static string set_reference_allele_file;
static bool lfile_allele_count;
static string recode_delimit;
static string recode_indelimit;
static bool recode_HV;
static bool recode_whap;
static bool recode_fastphase;
static bool recode_structure;
static bool recode_bimbam;
static bool preserve_all_genotypes;
static bool preserve_mendel_errors;
static bool zero_cluster;
static string zero_cluster_filename;
static bool oblig_missing;
static string oblig_missing_filename;
static string oblig_clusters_filename;
static bool loop_over;
static string loop_over_label;
static int loop_counter;
static string loop_over_filename;
static bool list_by_allele;
static bool list_twolocus;
static string twolocus_snp1;
static string twolocus_snp2;
static bool indiv_report;
static string indiv_report_fid;
static string indiv_report_iid;
static bool plist;
static string plist_fid1;
static string plist_iid1;
static string plist_fid2;
static string plist_iid2;
static bool merge_data;
static bool merge_force_strand;
static int merge_mode;
static bool merge_binary;
static bool merge_list;
static string merge_list_filename;
static string merge_pedfile;
static string merge_mapfile;
static string merge_bedfile;
static string merge_bimfile;
static string merge_famfile;
static bool write_snplist;
static bool update_map;
static bool update_cm;
static bool update_chr;
static bool update_name;
static bool update_ids;
static string update_ids_file;
static bool update_sex;
static string update_sex_file;
static bool update_parents;
static string update_parents_file;
static bool update_pheno;
static string update_pheno_file;
static string update_mapfile;
static string range_delimiter;
static bool update_alleles;
static string update_allele_file;
static bool compound_genotype_code;
static string tpedfile;
static string tfamfile;
static bool tfile_input;
static string lpedfile;
static string lfamfile;
static bool lfile_input;
static bool ref_file;
static string ref_file_name;
static bool gvar;
static bool gvar_write;
static bool gvar_to_standard;
static bool load_gvar;
static bool gvar_verbose_association;
static string gmapfile;
static string gfamfile;
static string gvarfile;
static bool gvar_include_all_variants;
static bool gvar_full_report;
static bool flip_strand;
static string flip_file;
static bool flip_subset;
static string flip_subset_file;
static bool read_bitfile;
static bool write_bitfile;
static bool fast_binary;
static string bitfilename;
static string famfile;
static string bitfilename_map;
static bool SNP_major;
static bool out_SNP_major;
static bool compress_file;
static bool uncompress_file;
static string compress_filename;
static bool read_ped;
static string pedfile;
static string mapfile;
static bool ped_from_stdin;
static string fileroot;
static bool map3;
static bool liability;
static bool ped_skip_sex;
static bool ped_skip_parents;
static bool ped_skip_fid;
static bool ped_skip_pheno;
static string output_file_name;
static bool silent;
static bool gplink;
static bool cli;
static string missing_genotype;
static string out_missing_genotype;
static string missing_phenotype;
static string out_missing_phenotype;
static bool missing_genotype_explicit;
static bool missing_phenotype_explicit;
static bool ignore_missing_sex;
static bool pheno_file;
static bool covar_file;
static bool numeric_file;
static bool clist;
static bool no_show_covar;
static bool dump_covar;
static bool dump_covar_with_phenotype;
static bool dump_covar_dummy_coding;
static bool filter_on_covar;
static int nlist_number;
static int clist_number;
static int plist_number;
static bool snp_attrib_filter;
static string snp_attrib_value;
static string snp_attrib_file;
static bool ind_attrib_filter;
static string ind_attrib_value;
static string ind_attrib_file;
static bool multiple_phenotypes;
static string multiple_phenotype_file;
static string make_pheno_filename;
static string make_pheno_value;
static bool make_pheno;
static bool make_pheno_present;
static bool dump_clst;
static bool nlist_selection;
static bool nlist_selection_name;
static bool nlist_selection_number;
static string nlist_selection_string;
static bool clist_selection;
static bool clist_selection_name;
static bool clist_selection_number;
static string clist_selection_string;
static bool plist_selection;
static bool plist_selection_name;
static bool plist_selection_number;
static string plist_selection_string;
static int mult_pheno;
static string name_pheno;
static bool all_pheno;
static int mult_covar;
static int mult_clst;
static int mult_filter;
static string filter_value;
static string number_list_string;
static bool number_list_positive;
static string pheno_filename;
static string covar_filename;
static string nlist_filename;
static string clist_filename;
static string filter_filename;
static bool cm_map;
static double grid;
static double fringe;
static bool singlepoint;
static int inter_grid;
static bool done_global_pihat;
static bool sol_family;
static bool summ_nonfounders;
static bool make_founders;
static bool has_nonfounders;
static bool make_missing_parents;
static bool score_risk;
static string score_risk_file;
static bool score_risk_ranges;
static string score_risk_ranges_file;
static int score_risk_ranges_min;
static bool score_impute_expected;
static bool score_risk_on_qrange;
static string score_qrange_file;
static string score_qfile;
static bool score_test;
static bool profile_sets;
static bool report_missing;
static bool test_missing;
static bool mishap_test;
static int mishap_window;
static bool calcFst;
static bool proxy_assoc;
static bool proxy_glm;
static bool proxy_all;
static bool proxy_full_report;
static bool proxy_error;
static bool proxy_impute;
static bool proxy_impute_replace;
static bool proxy_impute_preserve_genotyped;
static bool proxy_record_dosage;
static bool proxy_impute_genotypic_concordance;
static double proxy_impute_threshold;
static double proxy_info_threshold;
static bool impute_verbose;
static bool proxy_exclude;
static string proxy_exclude_list;
static bool proxy_exclude_from_file;
static bool proxy_reference_only;
static bool proxy_leave_out;
static bool proxy_include_reference;
static bool proxy_CC;
static bool proxy_TDT;
static string proxy_assoc_snp;
static int proxy_window;
static bool proxy_list;
static string proxy_list_file;
static bool proxy_all_list;
static string proxy_all_list_file;
static double proxy_kb;
static double proxy_r2;
static double proxy_maf;
static double proxy_mhf;
static double proxy_geno;
static bool proxy_list_proxies;
static int proxy_maxhap;
static bool proxy_r2_filter;
static double proxy_r2_filter_A;
static double proxy_r2_filter_B;
static double proxy_r2_filter_C;
static int proxy_snp_filter;
static double proxy_kb_planA;
static int proxy_window_planA;
static int proxy_snp_filter_planA;
static double proxy_r2_filter_A_planA;
static double proxy_r2_filter_B_planA;
static double proxy_r2_filter_C_planA;
static double proxy_planB_threshold;
static double proxy_kb_planB;
static int proxy_window_planB;
static int proxy_snp_filter_planB;
static double proxy_r2_filter_A_planB;
static double proxy_r2_filter_B_planB;
static double proxy_r2_filter_C_planB;
static bool greport;
static string greport_results;
static string greport_gene_list;
static bool greport_subset;
static string greport_subset_file;
static bool greport_display_empty;
static bool annot_file;
static string annot_filename;
static bool meta_analysis;
static vector<string> meta_files;
static bool set_screen;
static string set_screen_resultfile;
static bool gettag_mode;
static bool gettag_mode1;
static bool gettag_mode2;
static string gettag_file;
static double gettag_r2;
static int gettag_kb;
static bool gettag_listall;
static bool clumpld;
static bool clumpld_best;
static string clumpld_results;
static string clumpld_column;
static bool clumpld_verbose;
static bool clumpld_indep;
static int clumpld_kb;
static double clumpld_r2;
static double clumpld_p1;
static double clumpld_p2;
static bool clumpld_index1;
static bool clumpld_only_show_replications;
static bool clumpld_only_show_replications_list;
static bool clumpld_annot;
static string clumpld_annot_fields;
static string clumpld_range_file;
static bool clumpld_range_annotate;
static int clumpld_min;
static double min_af;
static double max_af;
static bool make_minor_allele;
static double min_hf;
static double max_hf;
static int min_geno_cell;
static double rarer_maf_threshold;
static double rarer_dist_threshold;
static int rarer_interval;
static bool rare_test;
static bool rare_test_weight1;
static bool rare_test_print_details;
static string rare_test_print_details_snp;
static bool elf_pcmode;
static bool elf_pcmode_2sided;
static bool elf_baseline;
static bool rare_test_score_range;
static double rare_test_score_range_threshold;
static string rare_test_score_results_file;
static string rare_test_score_range_file;
static bool rare_test_summary_controls;
static vector<bool> chr_haploid;
static vector<bool> chr_sex;
static vector<bool> chr_Y;
static vector<string> chr_code;
static map<string,int> chr_map;
static bool species_dog;
static bool species_cow;
static bool species_sheep;
static bool species_horse;
static bool species_rice;
static bool species_mouse;
static int run_start;
static int run_end;
static int run_chr;
static string m1;
static string m2;
static double window;
static bool position_window;
static int from_window;
static int to_window;
static bool qt;
static bool bt;
static bool coding01;
static bool ignore_phenotypes;
static bool filter_cases;
static bool filter_controls;
static bool filter_males;
static bool filter_females;
static bool filter_founders;
static bool filter_nonfounders;
static bool SD;
static bool CP;
static bool affpair;
static bool remove_unaffected_pairs;
static bool fix_prev;
static double fixed_prev;
static string tagfile;
static string mapfile_impute;
static bool make_tags;
static bool impute_tags;
static bool sliding_window;
static string sliding_window_size;
static bool make_blocks;
static bool meta_large_phase;
static bool phase_snps;
static bool phase_hap_all;
static double hap_post_prob;
static double hap_missing_geno;
static double hap_min_phase_prob;
static int hap_max_nf_phases;
static bool display_hap_freqs;
static int haplo_plem_window;
static int haplo_plem_overlap;
static int haplo_plem_original_overlap;
static int haplo_plem_iter;
static bool haplo_plem_verbose;
static bool haplo_plem_follow;
static int haplo_plem_follow_ind;
static string haplo_plem_follow_fid;
static string haplo_plem_follow_iid;
static int haplo_plem_likelihood_iter;
static double haplo_plem_window_prune_phase;
static double haplo_plem_window_tol;
static double haplo_plem_zero_threshold;
static bool haplo_plem_nonzero_threshold;
static int haplo_plem_meta_window;
static double haplo_plem_meta_prune_haplotype;
static double haplo_plem_meta_prune_phase;
static int haplo_plem_meta_iter;
static int haplo_plem_meta_likelihood_iter;
static double haplo_plem_meta_tol;
static bool test_hap_CC;
static bool test_hap_TDT;
static bool test_hap_QTL;
static bool test_hap_only;
static bool test_hap_GLM;
static bool test_hap_GLM_omnibus;
static bool display_phase_probs;
static bool display_phase_probs_wide;
static bool weighted_mm;
static bool chap_test;
static bool chap_sole_variant;
static bool chap_sole_variant_specific_alleles;
static string chap_sole_variant_specific_allele_list;
static bool chap_independent_effect;
static bool chap_haplotype_specific;
static string chap_entity;
static bool chap_specified_groups;
static bool chap_specified_snps;
static string chap_model1;
static string chap_model0;
static bool chap_drop_snps;
static string chap_drop_snps_list;
static bool chap_add_grp_specifics;
static bool assoc_test;
static bool assoc_counts;
static bool assoc_glm;
static bool standard_beta;
static bool assoc_glm_without_main_snp;
static bool assoc_test_alt_perm;
static bool full_model_assoc;
static bool trend_only;
static bool fisher_test;
static bool return_beta;
static bool hap_specific_snps;
static string hap_specific_snps_list;
static bool output_pheno_perm;
static bool qt_means;
static bool conditioning_snp_single;
static string conditioning_snp_name;
static bool conditioning_snps;
static string conditioning_snps_file;
static int xchr_model;
static bool glm_sex_effect;
static bool glm_no_auto_sex_effect;
static bool glm_dominant;
static bool glm_recessive;
static double vif_threshold;
static bool twoDFmodel;
static bool twoDFmodel_hethom;
static bool test_full_model;
static bool simple_interaction;
static vector<int> parameter_list;
static vector<int> test_list;
static bool glm_user_test;
static bool glm_user_parameters;
static bool qt_with_covariates;
static bool model_perm_best;
static bool model_perm_gen;
static bool model_perm_dom;
static bool model_perm_rec;
static bool model_perm_trend;
static bool assoc_gxe;
static bool QTDT_test;
static bool QFAM_total;
static bool QFAM_between;
static bool QFAM_within1;
static bool QFAM_within2;
static bool QFAM_adaptive;
static bool TDT_test;
static bool sibTDT_test;
static bool mating_tests;
static bool dfam_tdt;
static bool dfam_sibs;
static bool dfam_unrelateds;
static bool perm_TDT_basic;
static bool perm_TDT_parent;
static bool discordant_parents;
static bool parent_of_origin;
static bool perm_POO_poo;
static bool perm_POO_pat;
static bool perm_POO_mat;
static bool perm_POO_best;
static bool built_families;
static bool MENDEL_test;
static bool MENDEL_report;
static double MENDEL_snp;
static double MENDEL_ind;
static bool HWD_test;
static bool HWD_report;
static double HWD_limit;
static bool HWD_standard;
static bool HWD_filter_on_all;
static bool CMH_test_1;
static bool CMH_test_2;
static bool CMH_test_ORD;
static bool breslowday;
static bool OR_homog_test;
static double ci_level;
static double ci_zt;
static bool display_ci;
static bool pfilter;
static double pfvalue;
static bool multtest;
static bool use_GC;
static bool fix_lambda;
static double lambda;
static bool qq_plot;
static bool logscale;
static bool ibs_sharing_test;
static bool extract_set;
static bool exclude_set;
static bool snp_range_list;
static bool thin_snps;
static double thin_param;
static bool make_set;
static string make_set_file;
static int make_set_border;
static bool make_set_collapse;
static bool make_set_ignore_group;
static string make_set_collapse_label;
static bool make_set_complement;
static bool write_set;
static bool read_set;
static string exclude_file;
static string extract_file;
static string keep_file;
static string remove_file;
static bool read_snp_qual;
static string snp_qual_file;
static double snp_qual_min;
static double snp_qual_max;
static bool read_geno_qual;
static string geno_qual_file;
static double geno_qual_min;
static double geno_qual_max;
static bool snp_include_from_cl;
static string snp_include_range;
static bool dump_gene;
static string dump_genename;
static bool hotel;
static bool set_test;
static bool set_p2;
static int set_min;
static int set_max;
static bool set_r2;
static double set_r2_val;
static bool set_r2_phase;
static double set_chisq_threshold;
static bool set_r2_write;
static bool set_r2_read;
static string set_r2_read_file;
static string subsetfile;
static bool use_subset;
static string setfile;
static bool set_score;
static double set_score_p;
static double set_step_in;
static bool set_step;
static bool set_table;
static bool permute_within_sol;
static bool boot;
static bool disp_r1;
static bool disp_r2;
static bool disp_r_window;
static int disp_r_window_snp;
static int disp_r_window_kb;
static double disp_r_window_r2;
static bool ld_anchor;
static bool ld_anchor_list;
static bool flip_scan;
static double flip_scan_threshold;
static bool flip_scan_verbose;
static bool prune_ld;
static bool prune_ld_pairwise;
static bool prune_ld_pairwise_maf;
static double prune_ld_vif;
static double prune_ld_r2;
static int prune_ld_win;
static int prune_ld_step;
static bool prune_r2_prefer;
static string prune_r2_prefer_list;
static bool prune_r2_fixed;
static string prune_r2_fixed_list;
static bool calc_SNPSNP_LD;
static string ld_SNP1;
static string ld_SNP1_file;
static string ld_SNP2;
static bool epistasis;
static bool fast_epistasis;
static bool epi_caseonly;
static double epi_caseonly_kb_gap;
static bool epi_filter;
static double epi_alpha1;
static double epi_alpha2;
static bool set_by_set;
static bool epi_genebased;
static bool epi_quickscan;
static bool drop_sets;
static bool inbreeding;
static bool check_sex;
static bool impute_sex;
static double sex_threshold_male;
static double sex_threshold_female;
static bool homo_run;
static bool homo_run_consensus_match;
static bool homo_run_kb;
static bool homo_run_snps;
static double homo_run_density;
static int homo_run_gap;
static bool homo_miss_as_hom;
static int homo_windowSize;
static int homo_windowKB;
static int homo_windowAllowedHet;
static int homo_windowAllowedMissing;
static double homo_threshold;
static int homo_run_length_kb;
static int homo_run_length_snps;
static int homo_run_het;
static bool homo_summary_allelic_match;
static double fuzzy_homo;
static bool homozyg_verbose;
static int pool_size_min;
static bool ibs_run;
static int ibs_run_length_snps;
static int ibs_run_length_kb;
static double ibs_run_density;
static int ibs_inner_run_length_kb;
static int ibs_inner_run_length_snp;
static int ibs_join_kb;
static int ibs_join_snp;
static int ibs_run_missing;
static int ibs_run_0;
static int ibs_inter_snp_distance;
static bool ibs_2only;
static bool miss_run;
static int miss_run_length;
static bool miss_run_length_kb;
static double miss_run_level;
static bool segment_haplotrack;
static string segment_haplotrack_fid1;
static string segment_haplotrack_iid1;
static string segment_haplotrack_fid2;
static string segment_haplotrack_iid2;
static bool mk_datfile;
static bool segment_output;
static bool segment_minimal;
static bool segment_silently_return_groups;
static int segment_current_focal_snp;
static bool segment_overlap;
static bool segment_verbose;
static bool segment_validate;
static bool segment_test_individual;
static bool segment_test_specific_segs;
static bool segment_test_fisher;
static bool segment_test_1sided;
static bool segment_test_force_1sided;
static bool segment_test_ignore_discordant;
static int segment_snp1;
static int segment_snp2;
static string segment_m1;
static string segment_m2;
static bool force_span;
static int segment_length;
static int segment_snp;
static bool segment_output_started;
static bool read_segment_file;
static string read_segment_filename;
static int segment_inter_snp_distance;
static bool multi_output;
static bool gmulti_output;
static bool pihat_filter;
static bool genome_output;
static bool compress_genome;
static bool genome_only_check_rels;
static bool genome_output_minimal;
static bool genome_output_full;
static bool genome_2sets;
static string genome_setlist1;
static string genome_setlist2;
static bool genome_test;
static double genome_test_threshold;
static int genome_test_min_snp;
static bool ibs_test;
static int ibs_test_min_snp;
static bool ibs_test_method2;
static bool summary_ibd_output;
static double IBD_threshold;
static double segment_threshold_start;
static double segment_threshold_finish;
static bool nudge;
static bool bound;
static bool show_impossible_IBD;