/dports/biology/plink/plink-ng-79b2df8c/1.9/ |
H A D | plink_misc.c | 476 int32_t apply_cm_map(char* cm_map_fname, char* cm_map_chrname, uintptr_t unfiltered_marker_ct, uint… in apply_cm_map() 654 …_htable_size, char* marker_ids, uintptr_t max_marker_id_len, uintptr_t unfiltered_marker_ct, doubl… in update_marker_cms() 932 …er_id_htable_size, char* marker_ids, uintptr_t max_marker_id_len, uintptr_t unfiltered_marker_ct) { in update_marker_names() 1037 …_htable_size, char* marker_ids, uintptr_t max_marker_id_len, uintptr_t unfiltered_marker_ct, uintp… in update_marker_alleles() 1257 …_htable_size, char* marker_ids, uintptr_t max_marker_id_len, uintptr_t unfiltered_marker_ct, uintp… in flip_strand() 1711 uint32_t calc_plink_maxsnp(uint32_t unfiltered_marker_ct, uintptr_t* marker_exclude, uint32_t marke… in calc_plink_maxsnp() 1863 int32_t read_external_freqs(char* freqname, uintptr_t unfiltered_marker_ct, uintptr_t* marker_exclu… in read_external_freqs() 2224 int32_t load_ax_alleles(Two_col_params* axalleles, uintptr_t unfiltered_marker_ct, uintptr_t* marke… in load_ax_alleles() 3306 int32_t write_snplist(char* outname, char* outname_end, uintptr_t unfiltered_marker_ct, uintptr_t* … in write_snplist() 3377 int32_t write_var_ranges(char* outname, char* outname_end, uintptr_t unfiltered_marker_ct, uintptr_… in write_var_ranges() [all …]
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H A D | plink_filter.c | 318 …t do_exclude, char* marker_ids, uintptr_t max_marker_id_len, uintptr_t unfiltered_marker_ct, uintp… in extract_exclude_flag_norange() 894 …_no_variants, char* marker_ids, uintptr_t max_marker_id_len, uintptr_t unfiltered_marker_ct, uintp… in filter_qual_scores() 1022 uint32_t random_thin_markers(double thin_keep_prob, uintptr_t unfiltered_marker_ct, uintptr_t* mark… in random_thin_markers() 1049 int32_t random_thin_markers_ct(uint32_t thin_keep_ct, uintptr_t unfiltered_marker_ct, uintptr_t* ma… in random_thin_markers_ct() 1159 int32_t load_oblig_missing(FILE* bedfile, uintptr_t bed_offset, uintptr_t unfiltered_marker_ct, uin… in load_oblig_missing() 1587 …ffset, char* outname, char* outname_end, double mind_thresh, uintptr_t unfiltered_marker_ct, uintp… in mind_filter() 2490 … plink_maxfid, uint32_t plink_maxiid, uint32_t plink_maxsnp, uintptr_t unfiltered_marker_ct, uintp… in write_missingness_reports() 2876 …eport(char* outname, char* outname_end, double output_min_p, uintptr_t unfiltered_marker_ct, uintp… in hardy_report() 3065 uint32_t enforce_hwe_threshold(double hwe_thresh, uintptr_t unfiltered_marker_ct, uintptr_t* marker… in enforce_hwe_threshold() 3142 …orce_minor_allele_thresholds(double min_maf, double max_maf, uintptr_t unfiltered_marker_ct, uintp… in enforce_minor_allele_thresholds() [all …]
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H A D | plink_set.c | 588 int32_t extract_exclude_range(char* fname, uint32_t* marker_pos, uintptr_t unfiltered_marker_ct, ui… in extract_exclude_range() 992 int32_t define_sets(Set_info* sip, uintptr_t unfiltered_marker_ct, uintptr_t* marker_exclude, uint3… in define_sets() 1690 …* sip, char* outname, char* outname_end, uint32_t marker_ct, uintptr_t unfiltered_marker_ct, uintp… in write_set() 1925 void unpack_set_unfiltered(uintptr_t marker_ct, uintptr_t unfiltered_marker_ct, uintptr_t* marker_e… in unpack_set_unfiltered() 2094 …act_set_union_unfiltered(Set_info* sip, uintptr_t* set_incl, uintptr_t unfiltered_marker_ct, uintp… in extract_set_union_unfiltered() 2120 …mpress(Set_info* sip, uintptr_t* set_incl, uintptr_t set_ct, uintptr_t unfiltered_marker_ct, uintp… in setdefs_compress()
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H A D | plink_rserve.c | 33 …g, FILE* bedfile, uintptr_t bed_offset, uintptr_t marker_ct, uintptr_t unfiltered_marker_ct, uintp… in rserve_call()
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H A D | plink_data.c | 74 …_major_to_snp_major(char* sample_major_fname, char* outname, uintptr_t unfiltered_marker_ct, uintp… in sample_major_to_snp_major() 208 uintptr_t unfiltered_marker_ct = 0; in load_map() local 421 uintptr_t unfiltered_marker_ct = 0; in load_bim() local 2488 int32_t update_marker_chroms(Two_col_params* update_chr, uintptr_t unfiltered_marker_ct, uintptr_t*… in update_marker_chroms() 2681 int32_t sort_and_write_bim(uint32_t* map_reverse, char* outname, uintptr_t unfiltered_marker_ct, ui… in sort_and_write_bim() 2766 …apfile, uint32_t map_cols, char* outname, char* outname_end, uintptr_t unfiltered_marker_ct, uintp… in load_sort_and_write_map() 3027 …t32_t mergex, uint32_t splitx_bound1, uint32_t splitx_bound2, uint32_t unfiltered_marker_ct, uintp… in merge_or_split_x() 5737 uintptr_t unfiltered_marker_ct = 0; in ped_to_bed() local 6414 uintptr_t unfiltered_marker_ct = 0; in lgen_to_bed() local 11463 …_size, char* recode_allele_name, char*** allele_missing_ptr, uintptr_t unfiltered_marker_ct, uintp… in recode_allele_load() [all …]
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H A D | plink_ld.c | 638 …2_t cur_uidx, Chrom_info* chrom_info_ptr, uint32_t chrom_code_end, uint32_t unfiltered_marker_ct) { in ld_prune_next_valid_chrom_start() 652 …ptr, uint32_t ld_window_size, uint32_t* cur_window_size_ptr, uintptr_t unfiltered_marker_ct, uintp… in ld_prune_start_chrom() 752 …p, FILE* bedfile, uintptr_t bed_offset, uintptr_t marker_ct, uintptr_t unfiltered_marker_ct, uintp… in ld_prune() 2182 …threads, Ld_info* ldip, FILE* bedfile, uintptr_t bed_offset, uintptr_t unfiltered_marker_ct, uintp… in ld_report_matrix() 5670 …threads, Ld_info* ldip, FILE* bedfile, uintptr_t bed_offset, uintptr_t unfiltered_marker_ct, uintp… in ld_report_regular() 6315 …p, FILE* bedfile, uintptr_t bed_offset, uintptr_t marker_ct, uintptr_t unfiltered_marker_ct, uintp… in show_tags() 7081 …p, FILE* bedfile, uintptr_t bed_offset, uintptr_t marker_ct, uintptr_t unfiltered_marker_ct, uintp… in haploview_blocks() 7886 …p, FILE* bedfile, uintptr_t bed_offset, uintptr_t marker_ct, uintptr_t unfiltered_marker_ct, uintp… in twolocus() 10407 …p, FILE* bedfile, uintptr_t bed_offset, uintptr_t marker_ct, uintptr_t unfiltered_marker_ct, uintp… in indep_pairphase() 11332 …fset, char* outname, char* outname_end, double output_min_p, uintptr_t unfiltered_marker_ct, uintp… in test_mishap() [all …]
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H A D | plink_lasso.c | 432 …* pheno_nm, const uintptr_t* covar_nm, uintptr_t bed_offset, uintptr_t unfiltered_marker_ct, uintp… in lasso_lambda() 994 …ile, uintptr_t bed_offset, char* outname, char* outname_end, uintptr_t unfiltered_marker_ct, uintp… in lasso()
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H A D | plink.c | 204 …lexxxx_recode(uint32_t allelexxxx, char** marker_allele_ptrs, uint32_t unfiltered_marker_ct, uintp… in allelexxxx_recode() 258 …rse_bin(uintptr_t* marker_reverse, uintptr_t* marker_exclude, uint32_t unfiltered_marker_ct, uint3… in calc_marker_reverse_bin() 277 void swap_reversed_marker_alleles(uintptr_t unfiltered_marker_ct, uintptr_t* marker_reverse, char**… in swap_reversed_marker_alleles() 325 uintptr_t unfiltered_marker_ct = 0; in plink() local
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H A D | plink_family.c | 683 …k_maxiid, uint32_t plink_maxsnp, uint32_t allow_no_variants, uintptr_t unfiltered_marker_ct, uintp… in mendel_error_scan() 1730 …fset, char* outname, char* outname_end, double output_min_p, uintptr_t unfiltered_marker_ct, uintp… in tdt_poo() 1983 …e output_min_p, uint32_t mtest_adjust, double adjust_lambda, uintptr_t unfiltered_marker_ct, uintp… in tdt() 3799 …e output_min_p, uint32_t mtest_adjust, double adjust_lambda, uintptr_t unfiltered_marker_ct, uintp… in dfam() 5393 …ile, uintptr_t bed_offset, char* outname, char* outname_end, uintptr_t unfiltered_marker_ct, uintp… in qfam() 5982 …ile, uintptr_t bed_offset, char* outname, char* outname_end, uintptr_t unfiltered_marker_ct, uintp… in make_pseudocontrols()
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H A D | plink_glm.c | 91 …can_conditions(char* condition_mname, char* condition_fname, uintptr_t unfiltered_marker_ct, uintp… in glm_scan_conditions() 3554 …tr, Range_list* tests_range_list_ptr, uint32_t mtest_adjust, uintptr_t unfiltered_marker_ct, uintp… in glm_common_init() 4053 … double pfilter, double output_min_p, uint32_t mtest_adjust, uintptr_t unfiltered_marker_ct, uintp… in glm_linear_assoc_set_test() 4362 …e output_min_p, uint32_t mtest_adjust, double adjust_lambda, uintptr_t unfiltered_marker_ct, uintp… in glm_linear_assoc() 5616 … double pfilter, double output_min_p, uint32_t mtest_adjust, uintptr_t unfiltered_marker_ct, uintp… in glm_logistic_assoc_set_test() 5896 …e output_min_p, uint32_t mtest_adjust, double adjust_lambda, uintptr_t unfiltered_marker_ct, uintp… in glm_logistic_assoc() 7052 … ci_size, double ci_zt, double pfilter, double output_min_p, uintptr_t unfiltered_marker_ct, uintp… in glm_linear_nosnp() 7915 … ci_size, double ci_zt, double pfilter, double output_min_p, uintptr_t unfiltered_marker_ct, uintp… in glm_logistic_nosnp()
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H A D | plink_calc.c | 4509 …ds, FILE* bedfile, uintptr_t bed_offset, uint32_t marker_ct, uintptr_t unfiltered_marker_ct, uintp… in calc_genome() 6235 int32_t load_distance_wts(char* distance_wts_fname, uintptr_t unfiltered_marker_ct, char* marker_id… in load_distance_wts() 6367 …d, char* distance_wts_fname, uint32_t distance_wts_noheader, uintptr_t unfiltered_marker_ct, uintp… in calc_rel() 6985 …ar* outname_end, uint64_t calculation_type, Rel_info* relip, uintptr_t unfiltered_marker_ct, uintp… in calc_pca() 7453 …ibm(pthread_t* threads, FILE* bedfile, uintptr_t bed_offset, uintptr_t unfiltered_marker_ct, uintp… in calc_ibm() 7568 …nce_exp, uint64_t calculation_type, uint32_t dist_calc_type, uintptr_t unfiltered_marker_ct, uintp… in calc_distance() 8258 …ds, FILE* bedfile, uintptr_t bed_offset, uint32_t marker_ct, uintptr_t unfiltered_marker_ct, uintp… in calc_cluster_neighbor()
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H A D | plink_assoc.c | 5600 … double pfilter, double output_min_p, uint32_t mtest_adjust, uintptr_t unfiltered_marker_ct, uintp… in model_assoc_set_test() 5997 …e output_min_p, uint32_t mtest_adjust, double adjust_lambda, uintptr_t unfiltered_marker_ct, uintp… in model_assoc() 7777 … double pfilter, double output_min_p, uint32_t mtest_adjust, uintptr_t unfiltered_marker_ct, uintp… in qassoc_set_test() 8086 …e output_min_p, uint32_t mtest_adjust, double adjust_lambda, uintptr_t unfiltered_marker_ct, uintp… in qassoc() 9968 …e output_min_p, uint32_t mtest_adjust, double adjust_lambda, uintptr_t unfiltered_marker_ct, uintp… in testmiss() 11005 …e output_min_p, uint32_t mtest_adjust, double adjust_lambda, uintptr_t unfiltered_marker_ct, uintp… in cmh_assoc() 11373 …fset, char* outname, char* outname_end, double output_min_p, uintptr_t unfiltered_marker_ct, uintp… in cmh2_assoc() 11625 …fset, char* outname, char* outname_end, double output_min_p, uintptr_t unfiltered_marker_ct, uintp… in homog_assoc()
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H A D | plink_dosage.c | 563 uintptr_t unfiltered_marker_ct = 0; in plink1_dosage() local
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H A D | plink_homozyg.c | 2426 …hp, FILE* bedfile, uintptr_t bed_offset, uint32_t marker_ct, uintptr_t unfiltered_marker_ct, uintp… in calc_homozyg()
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H A D | plink_common.c | 4977 …const Chrom_info* chrom_info_ptr, const uintptr_t* marker_exclude, uint32_t unfiltered_marker_ct) { in single_chrom_start() 8278 …cate_non_autosomal_markers(const Chrom_info* chrom_info_ptr, uintptr_t unfiltered_marker_ct, const… in conditional_allocate_non_autosomal_markers()
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