/dports/biology/plink/plink-ng-79b2df8c/1.9/ |
H A D | plink_cnv.c | 106 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()
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H A D | plink_common.c | 4408 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() [all …]
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H A D | plink_data.c | 326 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 [all …]
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H A D | plink_filter.c | 1181 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()
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H A D | plink_misc.c | 2447 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()
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H A D | plink_lasso.c | 485 …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()
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H A D | plink.c | 2344 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() [all …]
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H A D | plink_common.h | 2170 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()
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H A D | plink_assoc.c | 6321 …-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()
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H A D | plink_glm.c | 3579 …(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()
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H A D | plink_ld.c | 702 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()
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H A D | plink_homozyg.c | 2546 if ((x_code != -2) && is_set(chrom_info_ptr->chrom_mask, x_code)) { in calc_homozyg()
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H A D | plink_set.c | 475 if (!is_set(chrom_info_ptr->chrom_mask, cur_chrom_code)) { in load_range_list()
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