| /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
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| 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
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| 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
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| 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
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| H A D | plink_rserve.c | 56 uintptr_t marker_uidx; in rserve_call() local
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| 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
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| 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
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| 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
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| 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
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| 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
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| 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
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| 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
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| 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
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| 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
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