| /dports/biology/gemma/GEMMA-0.98.3/src/ |
| H A D | varcov.cpp | 59 window_bp = cPar.window_bp; in CopyFromParam()
177 (snpInfo_sort[t].base_position == -9 && window_bp != 0)) { in CalcNB()
201 (long int) window_bp || in CalcNB()
202 window_bp == 0) && in CalcNB()
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| H A D | varcov.h | 48 size_t window_bp; variable
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| H A D | vc.h | 75 double window_cm, window_bp, window_ns; variable
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| H A D | param.h | 223 size_t window_bp; variable
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| H A D | vc.cpp | 82 window_bp = cPar.window_bp; in CopyFromParam()
1008 const double &window_cm, const double &window_bp, in ReadFile_cor() argument
1166 } else if (window_bp != 0 && d_pos1 != 0 && d_pos2 != 0) { in ReadFile_cor()
1167 bin = min((int)floor(d_pos / window_bp * bin_size), in ReadFile_cor()
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| H A D | param.cpp | 104 randseed(-1), window_cm(0), window_bp(0), window_ns(0), n_block(200), in PARAM()
627 if (window_cm == 0 && window_bp == 0 && window_ns == 0) { in CheckParam()
628 window_bp = 1000000; in CheckParam()
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| H A D | gemma.cpp | 1590 cPar.window_bp = atoi(str.c_str()); in Assign()
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| /dports/biology/plink/plink-ng-79b2df8c/2.0/ |
| H A D | plink2_filter.h | 44 …id_slen, uintptr_t variant_id_htable_size, uint32_t do_exclude, int32_t window_bp, uintptr_t* vari…
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| H A D | plink2_filter.cc | 120 …id_slen, uintptr_t variant_id_htable_size, uint32_t do_exclude, int32_t window_bp, uintptr_t* vari… in SnpFlag() argument
134 if (window_bp == -1) { in SnpFlag()
164 const uint32_t window_bp_u = window_bp; in SnpFlag()
185 …logprintf("--%ssnp%s: %u variant%s remaining.\n", do_exclude? "exclude-" : "", (window_bp == -1)? … in SnpFlag()
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| H A D | plink2.cc | 361 int32_t window_bp; member
1176 if (unlikely(pcp->window_bp != -1)) { in Plink2Core()
1206 …p, raw_variant_ct, max_variant_id_slen, variant_id_htable_size, 0, pcp->window_bp, variant_include… in Plink2Core()
1218 …p, raw_variant_ct, max_variant_id_slen, variant_id_htable_size, 1, pcp->window_bp, variant_include… in Plink2Core()
3539 pc.window_bp = -1;
9517 pc.window_bp = 0x7ffffffe;
9519 pc.window_bp = S_CAST(int32_t, dxx);
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| /dports/biology/plink/plink-ng-79b2df8c/1.9/ |
| H A D | plink_ld.h | 67 uint32_t window_bp; member
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| H A D | plink_ld.c | 36 ldip->window_bp = 0xffffffffU; in ld_epi_init()
1767 if (marker_pos_thresh < window_bp) { in flipscan()
1770 marker_pos_thresh -= window_bp; in flipscan()
5261 uint32_t window_bp = ldip->window_bp; in ld_report_dprime() local
5476 if (cur_marker_pos > window_bp) { in ld_report_dprime()
5477 cur_marker_pos -= window_bp; in ld_report_dprime()
5697 uint32_t window_bp = ldip->window_bp; in ld_report_regular() local
6022 if (cur_marker_pos > window_bp) { in ld_report_regular()
6023 cur_marker_pos -= window_bp; in ld_report_regular()
6339 uint32_t window_bp = ldip->show_tags_bp; in show_tags() local
[all …]
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| H A D | plink.c | 8202 ld_info.window_bp = 2147483646; in main()
8204 ld_info.window_bp = ((int32_t)(dxx * 1000 * (1 + SMALL_EPSILON))); in main()
13087 if (ld_info.window_bp != 0xffffffffU) { in main()
13089 ld_info.flipscan_window_bp = ld_info.window_bp; in main()
13101 if (ld_info.window_bp != 0xffffffffU) { in main()
13103 ld_info.blocks_max_bp = ld_info.window_bp; in main()
13125 } else if (ld_info.window_bp != 0xffffffffU) { in main()
13146 if (ld_info.window_bp == 0xffffffffU) { in main()
13147 ld_info.window_bp = 1000000; in main()
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