| /dports/biology/plink/plink-ng-79b2df8c/1.9/ |
| H A D | plink_assoc.h | 32 …, double adjust_lambda, uintptr_t unfiltered_marker_ct, uintptr_t* marker_exclude_orig, uintptr_t …
34 …, double adjust_lambda, uintptr_t unfiltered_marker_ct, uintptr_t* marker_exclude_orig, uintptr_t …
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| H A D | plink_calc.h | 62 … distance_wts_noheader, uintptr_t unfiltered_marker_ct, uintptr_t* marker_exclude_orig, uintptr_t*…
68 …int32_t dist_calc_type, uintptr_t unfiltered_marker_ct, uintptr_t* marker_exclude_orig, uint32_t m…
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| H A D | plink_glm.h | 31 …, double adjust_lambda, uintptr_t unfiltered_marker_ct, uintptr_t* marker_exclude_orig, uintptr_t …
34 …, double adjust_lambda, uintptr_t unfiltered_marker_ct, uintptr_t* marker_exclude_orig, uintptr_t …
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| H A D | plink_set.h | 132 …incl, uintptr_t set_ct, uintptr_t unfiltered_marker_ct, uintptr_t* marker_exclude_orig, uintptr_t …
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| H A D | plink_family.h | 105 …, double adjust_lambda, uintptr_t unfiltered_marker_ct, uintptr_t* marker_exclude_orig, uintptr_t …
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| H A D | plink_ld.h | 154 …ame, char* outname_end, uintptr_t unfiltered_marker_ct, uintptr_t* marker_exclude_orig, uintptr_t …
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| H A D | plink_misc.h | 106 …t, uintptr_t marker_ct, uintptr_t unfiltered_marker_ct, uintptr_t* marker_exclude_orig, uintptr_t*…
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| H A D | plink_assoc.c | 6006 uintptr_t* marker_exclude = marker_exclude_orig; in model_assoc()
6165 …if (extract_set_union_unfiltered(sip, nullptr, unfiltered_marker_ct, marker_exclude_orig, &marker_… in model_assoc()
7537 …rm_val, pfilter, output_min_p, mtest_adjust, unfiltered_marker_ct, marker_exclude_orig, marker_ct_… in model_assoc()
8118 uintptr_t* marker_exclude = marker_exclude_orig; in qassoc()
8203 …if (extract_set_union_unfiltered(sip, nullptr, unfiltered_marker_ct, marker_exclude_orig, &marker_… in qassoc()
8884 …rm_val, pfilter, output_min_p, mtest_adjust, unfiltered_marker_ct, marker_exclude_orig, marker_ct_… in qassoc()
9978 uintptr_t marker_uidx = next_unset_unsafe(marker_exclude_orig, 0); in testmiss()
10097 memcpy(marker_exclude, marker_exclude_orig, unfiltered_marker_ctl * sizeof(intptr_t)); in testmiss()
10141 if (IS_SET(marker_exclude_orig, marker_uidx)) { in testmiss()
10142 marker_uidx = next_unset_ul_unsafe(marker_exclude_orig, marker_uidx); in testmiss()
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| H A D | plink_glm.c | 4053 … uint32_t mtest_adjust, uintptr_t unfiltered_marker_ct, uintptr_t* marker_exclude_orig, uintptr_t … in glm_linear_assoc_set_test() argument
4128 …, bedfile, bed_offset, outname, outname_end, unfiltered_marker_ct, marker_exclude_orig, marker_ct_… in glm_linear_assoc_set_test()
4362 …, double adjust_lambda, uintptr_t unfiltered_marker_ct, uintptr_t* marker_exclude_orig, uintptr_t … in glm_linear_assoc() argument
4405 uintptr_t* marker_exclude = marker_exclude_orig; in glm_linear_assoc()
4513 …if (extract_set_union_unfiltered(sip, nullptr, unfiltered_marker_ct, marker_exclude_orig, &marker_… in glm_linear_assoc()
5404 …rm_val, pfilter, output_min_p, mtest_adjust, unfiltered_marker_ct, marker_exclude_orig, marker_ct_… in glm_linear_assoc()
5616 … uint32_t mtest_adjust, uintptr_t unfiltered_marker_ct, uintptr_t* marker_exclude_orig, uintptr_t … in glm_logistic_assoc_set_test() argument
5680 …, bedfile, bed_offset, outname, outname_end, unfiltered_marker_ct, marker_exclude_orig, marker_ct_… in glm_logistic_assoc_set_test()
5933 uintptr_t* marker_exclude = marker_exclude_orig; in glm_logistic_assoc()
6040 …if (extract_set_union_unfiltered(sip, nullptr, unfiltered_marker_ct, marker_exclude_orig, &marker_… in glm_logistic_assoc()
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| H A D | plink_filter.c | 902 uintptr_t* marker_exclude_orig; in filter_qual_scores() local
917 bigstack_alloc_ul(unfiltered_marker_ctl, &marker_exclude_orig)) { in filter_qual_scores()
920 memcpy(marker_exclude_orig, marker_exclude, unfiltered_marker_ctl * sizeof(intptr_t)); in filter_qual_scores()
972 if ((marker_uidx == 0xffffffffU) || is_set(marker_exclude_orig, marker_uidx)) { in filter_qual_scores()
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| H A D | plink_calc.c | 6367 … distance_wts_noheader, uintptr_t unfiltered_marker_ct, uintptr_t* marker_exclude_orig, uintptr_t*… in calc_rel() argument
6375 uintptr_t* marker_exclude = marker_exclude_orig; in calc_rel()
6500 …locate_non_autosomal_markers(chrom_info_ptr, unfiltered_marker_ct, marker_exclude_orig, marker_ct,… in calc_rel()
6507 …_ids, max_marker_id_len, distance_wts_noheader, (marker_exclude == marker_exclude_orig), &marker_e… in calc_rel()
7453 …, uintptr_t bed_offset, uintptr_t unfiltered_marker_ct, uintptr_t* marker_exclude_orig, uint32_t m… in calc_ibm() argument
7459 uintptr_t* marker_exclude = marker_exclude_orig; in calc_ibm()
7499 …locate_non_autosomal_markers(chrom_info_ptr, unfiltered_marker_ct, marker_exclude_orig, marker_ct,… in calc_ibm()
7568 …int32_t dist_calc_type, uintptr_t unfiltered_marker_ct, uintptr_t* marker_exclude_orig, uint32_t m… in calc_distance() argument
7580 uintptr_t* marker_exclude = marker_exclude_orig; in calc_distance()
7678 …locate_non_autosomal_markers(chrom_info_ptr, unfiltered_marker_ct, marker_exclude_orig, marker_ct,… in calc_distance()
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| H A D | plink_family.c | 3799 …, double adjust_lambda, uintptr_t unfiltered_marker_ct, uintptr_t* marker_exclude_orig, uintptr_t … in dfam() argument
3816 uintptr_t* marker_exclude_orig_autosomal = marker_exclude_orig; in dfam()
3929 uii = count_non_autosomal_markers(chrom_info_ptr, marker_exclude_orig, 1, 1); in dfam()
3940 …memcpy(marker_exclude_orig_autosomal, marker_exclude_orig, unfiltered_marker_ctl * sizeof(intptr_t… in dfam()
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| H A D | plink_set.c | 2120 …incl, uintptr_t set_ct, uintptr_t unfiltered_marker_ct, uintptr_t* marker_exclude_orig, uintptr_t … in setdefs_compress() argument
2150 fill_midx_to_idx(marker_exclude_orig, marker_exclude, marker_ct, marker_midx_to_idx); in setdefs_compress()
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| H A D | plink_common.c | 8278 …* chrom_info_ptr, uintptr_t unfiltered_marker_ct, const uintptr_t* marker_exclude_orig, uint32_t m… in conditional_allocate_non_autosomal_markers() argument
8290 …xymt_cts[X_OFFSET] = count_chrom_markers(chrom_info_ptr, marker_exclude_orig, xymt_codes[X_OFFSET]… in conditional_allocate_non_autosomal_markers()
8293 …xymt_cts[Y_OFFSET] = count_chrom_markers(chrom_info_ptr, marker_exclude_orig, xymt_codes[Y_OFFSET]… in conditional_allocate_non_autosomal_markers()
8296 …xymt_cts[MT_OFFSET] = count_chrom_markers(chrom_info_ptr, marker_exclude_orig, xymt_codes[MT_OFFSE… in conditional_allocate_non_autosomal_markers()
8313 memcpy(*marker_exclude_ptr, marker_exclude_orig, unfiltered_marker_ctl * sizeof(intptr_t)); in conditional_allocate_non_autosomal_markers()
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| H A D | plink_ld.c | 7081 …t, uintptr_t marker_ct, uintptr_t unfiltered_marker_ct, uintptr_t* marker_exclude_orig, char* mark… in haploview_blocks() argument
7223 memcpy(marker_exclude, marker_exclude_orig, unfiltered_marker_ctl * sizeof(intptr_t)); in haploview_blocks()
7228 next_unset_ul_unsafe_ck(marker_exclude_orig, &marker_uidx); in haploview_blocks()
12291 …ame, char* outname_end, uintptr_t unfiltered_marker_ct, uintptr_t* marker_exclude_orig, uintptr_t … in set_test_common_init() argument
12330 fill_midx_to_idx(marker_exclude_orig, marker_exclude_mid, marker_ct, marker_midx_to_idx); in set_test_common_init()
12412 …if (extract_set_union_unfiltered(sip, set_incl, unfiltered_marker_ct, marker_exclude_orig, marker_… in set_test_common_init()
12423 …if (setdefs_compress(sip, set_incl, set_ct, unfiltered_marker_ct, marker_exclude_orig, marker_ct_o… in set_test_common_init()
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| H A D | plink_common.h | 2580 …* chrom_info_ptr, uintptr_t unfiltered_marker_ct, const uintptr_t* marker_exclude_orig, uint32_t m…
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| H A D | plink_misc.c | 4209 …t, uintptr_t marker_ct, uintptr_t unfiltered_marker_ct, uintptr_t* marker_exclude_orig, uintptr_t*… in score_report() argument
4303 …retval = populate_id_htable(unfiltered_marker_ct, marker_exclude_orig, marker_ct, marker_ids, max_… in score_report()
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