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Searched refs:chrom_mask (Results 1 – 13 of 13) sorted by relevance

/dports/biology/plink/plink-ng-79b2df8c/1.9/
H A Dplink_cnv.c106 uintptr_t* chrom_mask = chrom_info_ptr->chrom_mask; in cnv_intersect_load() local
160 if (!IS_SET(chrom_mask, uljj)) { in cnv_intersect_load()
489 uintptr_t* chrom_mask = chrom_info_ptr->chrom_mask; in cnv_make_map() local
552 if ((!is_autogen) && (!IS_SET(chrom_mask, chrom_idx))) { in cnv_make_map()
719 uintptr_t* chrom_mask = chrom_info_ptr->chrom_mask; in validate_cnv_map() local
811 if (!IS_SET(chrom_mask, chrom_idx)) { in validate_cnv_map()
866 uintptr_t* chrom_mask = chrom_info_ptr->chrom_mask; in load_cnv_map() local
896 if (!IS_SET(chrom_mask, chrom_idx)) { in load_cnv_map()
H A Dplink_common.c4408 fill_ulong_zero(CHROM_MASK_WORDS, chrom_info_ptr->chrom_mask); in init_species()
4467 set_bit(chrom_info_ptr->xymt_codes[xymt_idx], chrom_info_ptr->chrom_mask); in init_default_chrom_mask()
4507 uintptr_t* old_alloc = chrom_info_ptr->chrom_mask; in finalize_chrom_info()
4511 chrom_info_ptr->chrom_mask = new_alloc_iter; in finalize_chrom_info()
4547 if (chrom_info_ptr->chrom_mask) { in cleanup_chrom_info()
4551 aligned_free(chrom_info_ptr->chrom_mask); in cleanup_chrom_info()
4552 chrom_info_ptr->chrom_mask = nullptr; in cleanup_chrom_info()
4655 if (!is_set(chrom_info_ptr->chrom_mask, chrom_idx)) { in get_max_chrom_slen()
4669 const uintptr_t* chrom_mask = chrom_info_ptr->chrom_mask; in haploid_chrom_present() local
4672 if (chrom_mask[widx] & haploid_mask[widx]) { in haploid_chrom_present()
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H A Dplink_data.c326 if (!is_set(chrom_info_ptr->chrom_mask, cur_chrom_code)) { in load_map()
742 SET_BIT(from_chrom, chrom_info_ptr->chrom_mask); in load_bim()
758 SET_BIT(to_chrom, chrom_info_ptr->chrom_mask); in load_bim()
770 SET_BIT(snp_chrom, chrom_info_ptr->chrom_mask); in load_bim()
969 if (is_set(chrom_info_ptr->chrom_mask, cur_chrom_code)) { in load_bim()
4022 if (!is_set(chrom_info_ptr->chrom_mask, ii)) { in oxford_to_bed()
4375 if (!is_set(chrom_info_ptr->chrom_mask, cur_chrom_code)) { in oxford_to_bed()
4724 if (!is_set(chrom_info_ptr->chrom_mask, cur_chrom_code)) { in oxford_to_bed()
12776 if (!IS_SET(chrom_info_ptr->chrom_mask, chrom_idx)) { in recode()
15161 uintptr_t* chrom_mask = chrom_info_ptr->chrom_mask; in merge_post_msort_update_maps() local
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H A Dplink_filter.c1181 uint32_t y_present = ((y_code != -2) && is_set(chrom_info_ptr->chrom_mask, y_code)); in load_oblig_missing()
1609 uint32_t y_present = (y_code != -2) && is_set(chrom_info_ptr->chrom_mask, y_code); in mind_filter()
2094 nonmales_needed = (!is_split_chrom) && (ii != -2) && is_set(chrom_info_ptr->chrom_mask, ii); in calc_freqs_and_hwe()
2096 …d = nonmales_needed || ((!is_split_chrom) && (ii != -2) && is_set(chrom_info_ptr->chrom_mask, ii)); in calc_freqs_and_hwe()
2510 uint32_t y_present = (y_code != -2) && is_set(chrom_info_ptr->chrom_mask, y_code); in write_missingness_reports()
H A Dplink_misc.c2447 if ((chrom_idx != -2) && is_set(chrom_info_ptr->chrom_mask, chrom_idx)) { in write_stratified_freqs()
2467 if (cluster_map_nonmale || ((chrom_idx != -2) && is_set(chrom_info_ptr->chrom_mask, chrom_idx))) { in write_stratified_freqs()
2498 if (!is_set(chrom_info_ptr->chrom_mask, chrom_idx)) { in write_stratified_freqs()
2745 if (!is_set(chrom_info_ptr->chrom_mask, chrom_idx)) { in write_cc_freqs()
2905 if (!is_set(chrom_info_ptr->chrom_mask, chrom_idx)) { in write_freqs()
3070 if ((x_code == -2) || (!is_set(chrom_info_ptr->chrom_mask, (uint32_t)x_code))) { in sexcheck()
3137 if ((y_code != -2) && is_set(chrom_info_ptr->chrom_mask, (uint32_t)y_code)) { in sexcheck()
5714 if (!is_set(chrom_info_ptr->chrom_mask, cur_chrom)) { in meta_analysis()
6133 if (!is_set(chrom_info_ptr->chrom_mask, cur_chrom)) { in meta_analysis()
H A Dplink_lasso.c485 …if ((chrom_info_ptr->xymt_codes[MT_OFFSET] != -2) && is_set(chrom_info_ptr->chrom_mask, chrom_info… in lasso_lambda()
1138 …if ((chrom_info_ptr->xymt_codes[MT_OFFSET] != -2) && is_set(chrom_info_ptr->chrom_mask, chrom_info… in lasso()
H A Dplink.c2344 fill_bits(chrom_code_start, chrom_code_end + 1 - chrom_code_start, chrom_mask); in parse_chrom_ranges()
2346 set_bit(chrom_code_start, chrom_mask); in parse_chrom_ranges()
4240 fill_bits(1, chrom_info.autosome_ct, chrom_info.chrom_mask); in main()
4253 fill_bits(1, chrom_info.autosome_ct, chrom_info.chrom_mask); in main()
4254 set_bit(chrom_info.xymt_codes[XY_OFFSET], chrom_info.chrom_mask); in main()
4975 …retval = parse_chrom_ranges(param_ct, '-', &(argv[cur_arg]), chrom_info.chrom_mask, &chrom_info, (… in main()
9650 chrom_info.chrom_mask[uii] &= ~chrom_exclude[uii]; in main()
11007 …} else if ((!are_all_words_zero(chrom_info.chrom_mask, CHROM_MASK_INITIAL_WORDS)) || chrom_info.in… in main()
11737 …if ((!are_all_words_zero(chrom_info.chrom_mask, CHROM_MASK_INITIAL_WORDS)) || chrom_info.incl_excl… in main()
13166 uii = next_set(chrom_info.chrom_mask, 0, CHROM_MASK_INITIAL_WORDS * BITCT); in main()
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H A Dplink_common.h2170 uintptr_t* chrom_mask; // which chromosomes aren't known to be absent? member
2569 if (!is_set(chrom_info_ptr->chrom_mask, chrom_idx)) { in count_chrom_markers()
H A Dplink_assoc.c6321 …-2) && is_set(chrom_info_ptr->chrom_mask, x_code)) || (model_assoc && (((y_code != -2) && is_set(c… in model_assoc()
8112 …chrom_info_ptr->xymt_codes[MT_OFFSET] != -2) && is_set(chrom_info_ptr->chrom_mask, chrom_info_ptr-… in qassoc()
9153 …(chrom_info_ptr->xymt_codes[Y_OFFSET] != -2) && is_set(chrom_info_ptr->chrom_mask, chrom_info_ptr-… in gxe_assoc()
9154 …chrom_info_ptr->xymt_codes[MT_OFFSET] != -2) && is_set(chrom_info_ptr->chrom_mask, chrom_info_ptr-… in gxe_assoc()
10057 if ((y_code == -2) || (!is_set(chrom_info_ptr->chrom_mask, y_code))) { in testmiss()
11124 …if ((chrom_info_ptr->xymt_codes[MT_OFFSET] != -2) && is_set(chrom_info_ptr->chrom_mask, chrom_info… in cmh_assoc()
11467 …if ((chrom_info_ptr->xymt_codes[MT_OFFSET] != -2) && is_set(chrom_info_ptr->chrom_mask, chrom_info… in cmh2_assoc()
H A Dplink_glm.c3579 …(chrom_info_ptr->xymt_codes[X_OFFSET] != -2) && is_set(chrom_info_ptr->chrom_mask, chrom_info_ptr-… in glm_common_init()
4504 …if ((chrom_info_ptr->xymt_codes[MT_OFFSET] != -2) && is_set(chrom_info_ptr->chrom_mask, chrom_info… in glm_linear_assoc()
6031 …if ((chrom_info_ptr->xymt_codes[MT_OFFSET] != -2) && is_set(chrom_info_ptr->chrom_mask, chrom_info… in glm_logistic_assoc()
7156 …if ((chrom_info_ptr->xymt_codes[MT_OFFSET] != -2) && is_set(chrom_info_ptr->chrom_mask, chrom_info… in glm_linear_nosnp()
8017 …if ((chrom_info_ptr->xymt_codes[MT_OFFSET] != -2) && is_set(chrom_info_ptr->chrom_mask, chrom_info… in glm_logistic_nosnp()
H A Dplink_ld.c702 if (!is_set(chrom_info_ptr->chrom_mask, cur_chrom)) { in ld_prune_write()
722 if (!is_set(chrom_info_ptr->chrom_mask, cur_chrom)) { in ld_prune_write()
855 if (is_set(chrom_info_ptr->chrom_mask, 0)) { in ld_prune()
888 if (is_set(chrom_info_ptr->chrom_mask, cur_chrom)) { in ld_prune()
5315 if ((x_code != -2) && is_set(chrom_info_ptr->chrom_mask, x_code)) { in ld_report_dprime()
10479 if (is_set(chrom_info_ptr->chrom_mask, 0)) { in indep_pairphase()
10503 if (is_set(chrom_info_ptr->chrom_mask, cur_chrom)) { in indep_pairphase()
10540 …if ((chrom_info_ptr->xymt_codes[X_OFFSET] != -2) && is_set(chrom_info_ptr->chrom_mask, chrom_info_… in indep_pairphase()
H A Dplink_homozyg.c2546 if ((x_code != -2) && is_set(chrom_info_ptr->chrom_mask, x_code)) { in calc_homozyg()
H A Dplink_set.c475 if (!is_set(chrom_info_ptr->chrom_mask, cur_chrom_code)) { in load_range_list()