/dports/biology/plink/plink-ng-79b2df8c/1.9/ |
H A D | plink_misc.c | 495 uint32_t marker_uidx; in apply_cm_map() local 671 uint32_t marker_uidx; in update_marker_cms() local 795 uint32_t marker_uidx; in update_marker_pos() local 948 uintptr_t marker_uidx; in update_marker_names() local 1056 uintptr_t marker_uidx; in update_marker_alleles() local 1236 uintptr_t marker_uidx; in flip_process_token() local 1887 uint32_t marker_uidx; in read_external_freqs() local 2245 uint32_t marker_uidx; in load_ax_alleles() local 2406 uintptr_t marker_uidx; in write_stratified_freqs() local 2864 uint32_t marker_uidx; in write_freqs() local [all …]
|
H A D | plink_filter.c | 267 uintptr_t marker_uidx; in extract_exclude_process_token() local 913 uint32_t marker_uidx; in filter_qual_scores() local 1024 uint32_t marker_uidx = 0; in random_thin_markers() local 1052 uint32_t marker_uidx = 0; in random_thin_markers_ct() local 1202 uintptr_t marker_uidx; in load_oblig_missing() local 1620 uintptr_t marker_uidx; in mind_filter() local 2019 uintptr_t marker_uidx; in calc_freqs_and_hwe() local 2529 uintptr_t marker_uidx; in write_missingness_reports() local 2880 uintptr_t marker_uidx = 0; in hardy_report() local 3067 uint32_t marker_uidx = 0; in enforce_hwe_threshold() local [all …]
|
H A D | plink_lasso.c | 111 uint32_t marker_uidx; in lasso_bigmem() local 513 uint32_t marker_uidx = 0; in lasso_lambda() local 686 uint32_t marker_uidx; in lasso_smallmem() local 1047 uint32_t marker_uidx; in lasso() local
|
H A D | plink_data.c | 218 uintptr_t marker_uidx; in load_map() local 475 uintptr_t marker_uidx; in load_bim() local 2138 uintptr_t marker_uidx; in zero_cluster_init() local 2692 uintptr_t marker_uidx; in sort_and_write_bim() local 2780 uintptr_t marker_uidx; in load_sort_and_write_map() local 2906 uint32_t marker_uidx; in flip_subset_init() local 4001 uint32_t marker_uidx; in oxford_to_bed() local 5250 uintptr_t marker_uidx; in ped_to_bed_multichar_allele() local 5765 uintptr_t marker_uidx; in ped_to_bed() local 7102 uintptr_t marker_uidx; in transposed_to_bed() local [all …]
|
H A D | plink_rserve.c | 56 uintptr_t marker_uidx; in rserve_call() local
|
H A D | plink_homozyg.c | 111 void roh_extend_forward(uint32_t* marker_pos, uintptr_t* marker_exclude, uint32_t marker_uidx, uint… in roh_extend_forward() 128 …t32_t* roh_list, uint32_t* marker_pos, uintptr_t* marker_exclude, uintptr_t marker_uidx, uint32_t … in save_confirmed_roh_extend() 868 …_sample_ct4, uint32_t* marker_uidx_to_cidx, uint32_t chrom_start, uint32_t marker_uidx, uint32_t l… in populate_roh_slots_from_disk() 2486 uintptr_t marker_uidx; in calc_homozyg() local
|
H A D | plink.c | 205 uint32_t marker_uidx = 0; in allelexxxx_recode() local 259 uint32_t marker_uidx = 0; in calc_marker_reverse_bin() local 278 uintptr_t marker_uidx = 0; in swap_reversed_marker_alleles() local 448 uintptr_t marker_uidx; in plink() local
|
H A D | plink_assoc.c | 262 uintptr_t marker_uidx; in multcomp() local 5656 uintptr_t marker_uidx; in model_assoc_set_test() local 6097 uintptr_t marker_uidx; // loading in model_assoc() local 7832 uint32_t marker_uidx; in qassoc_set_test() local 8147 uintptr_t marker_uidx; // loading in qassoc() local 9129 uintptr_t marker_uidx = 0; in gxe_assoc() local 9978 uintptr_t marker_uidx = next_unset_unsafe(marker_exclude_orig, 0); in testmiss() local 10894 uintptr_t marker_uidx = *marker_uidx_ptr; in cluster_assoc_load_one() local 11037 uintptr_t marker_uidx; in cmh_assoc() local 11408 uintptr_t marker_uidx; in cmh2_assoc() local [all …]
|
H A D | plink_ld.c | 706 …for (uint32_t marker_uidx = get_chrom_start_vidx(chrom_info_ptr, cur_chrom); marker_uidx < chrom_e… in ld_prune_write() local 726 …for (uint32_t marker_uidx = get_chrom_start_vidx(chrom_info_ptr, cur_chrom); marker_uidx < chrom_e… in ld_prune_write() local 1521 uintptr_t marker_uidx; in flipscan() local 6353 uintptr_t marker_uidx; in show_tags() local 7101 uintptr_t marker_uidx = 0; in haploview_blocks() local 7914 uintptr_t marker_uidx; in twolocus() local 8397 uintptr_t marker_uidx = marker_uidx_base; in epistasis_linear_regression() local 8873 uintptr_t marker_uidx = marker_uidx_base; in epistasis_logistic_regression() local 9349 uintptr_t marker_uidx = marker_uidx_base; in epistasis_report() local 11870 uintptr_t marker_uidx; in construct_ld_map() local [all …]
|
H A D | plink_calc.c | 4579 uintptr_t marker_uidx; in calc_genome() local 6190 uintptr_t marker_uidx = *marker_uidx_ptr; in block_load() local 6217 void copy_set_allele_freqs(uintptr_t marker_uidx, uintptr_t* marker_exclude, uint32_t block_max_siz… in copy_set_allele_freqs() 6254 uint32_t marker_uidx; in load_distance_wts() local 6371 uintptr_t marker_uidx = 0; in calc_rel() local 7041 uintptr_t marker_uidx; in calc_pca() local 7455 uintptr_t marker_uidx = 0; in calc_ibm() local 7601 uintptr_t marker_uidx; in calc_distance() local
|
H A D | plink_family.c | 699 uintptr_t marker_uidx = ~ZEROLU; in mendel_error_scan() local 1737 uintptr_t marker_uidx = ~ZEROLU; in tdt_poo() local 1995 uintptr_t marker_uidx = ~ZEROLU; in tdt() local 3867 uintptr_t marker_uidx; // loading in dfam() local 5462 uintptr_t marker_uidx; in qfam() local
|
H A D | plink_set.c | 1707 uintptr_t marker_uidx; in write_set() local 1928 uintptr_t marker_uidx = last_uidx; in unpack_set_unfiltered() local
|
H A D | plink_glm.c | 130 uint32_t marker_uidx; in glm_scan_conditions() local 4109 uint32_t marker_uidx; in glm_linear_assoc_set_test() local 4491 uint32_t marker_uidx; in glm_linear_assoc() local 5666 uint32_t marker_uidx; in glm_logistic_assoc_set_test() local 6014 uint32_t marker_uidx; in glm_logistic_assoc() local 7140 uint32_t marker_uidx; in glm_linear_nosnp() local 8002 uint32_t marker_uidx; in glm_logistic_nosnp() local
|
H A D | plink_common.c | 4962 void refresh_chrom_info(const Chrom_info* chrom_info_ptr, uintptr_t marker_uidx, uint32_t* __restri… in refresh_chrom_info() 6405 …uint32_t marker_uidx = next_unset(marker_exclude, chrom_info_ptr->chrom_fo_vidx_start[chrom_fo_idx… in chrom_window_max() local 9582 uintptr_t marker_uidx = next_unset_ul_unsafe(marker_exclude, marker_uidx_start); in haploid_fix_multiple() local
|