/dports/biology/plink/plink-ng-79b2df8c/1.9/ |
H A D | plink_rserve.c | 237 if (fwrite_checked(g_textbuf, bufptr - g_textbuf, outfile)) { in rserve_call() 243 fwrite(g_textbuf, 1, (uintptr_t)(bufptr - g_textbuf), outfile); in rserve_call() 247 if (fwrite_checked(g_textbuf, bufptr - g_textbuf, outfile)) { in rserve_call() 256 fwrite(g_textbuf, 1, (uintptr_t)(bufptr - g_textbuf), outfile); in rserve_call() 275 if (fwrite_checked(g_textbuf, bufptr - g_textbuf, outfile)) { in rserve_call() 360 if (fwrite_checked(g_textbuf, bufptr - g_textbuf, outfile)) { in rserve_call() 383 if (fwrite_checked(g_textbuf, bufptr - g_textbuf, outfile)) { in rserve_call() 402 if (fwrite_checked(g_textbuf, bufptr - g_textbuf, outfile)) { in rserve_call() 413 if (fwrite_checked(g_textbuf, bufptr - g_textbuf, outfile)) { in rserve_call() 434 if (fwrite_checked(g_textbuf, bufptr - g_textbuf, outfile)) { in rserve_call() [all …]
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H A D | plink_cluster.c | 675 if (fwrite_checked(g_textbuf, bufptr - g_textbuf, outfile)) { in write_clusters() 2770 if (fwrite_checked(g_textbuf, wptr - g_textbuf, outfile)) { in write_cluster_solution() 2786 if (fwrite_checked(g_textbuf, wptr - g_textbuf, outfile)) { in write_cluster_solution() 3116 g_textbuf[22] = ' '; in mds_plot() 3119 uii = wptr - g_textbuf; in mds_plot() 3142 if (fwrite_checked(g_textbuf, wptr - g_textbuf, outfile)) { in mds_plot() 3154 wptr2 = &(g_textbuf[11]); in mds_plot() 3167 wptr2 = &(g_textbuf[11]); in mds_plot() 3425 g_textbuf[22] = ' '; in mds_plot_eigendecomp() 3428 uii = wptr - g_textbuf; in mds_plot_eigendecomp() [all …]
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H A D | plink_cnv.c | 129 if (!g_textbuf[MAXLINELEN - 1]) { in cnv_intersect_load() 345 if (!fgets(g_textbuf, MAXLINELEN, cnvfile)) { in cnv_first_nonheader_line() 348 if (!g_textbuf[MAXLINELEN - 1]) { in cnv_first_nonheader_line() 353 bufptr = skip_initial_spaces(g_textbuf); in cnv_first_nonheader_line() 357 if (!fgets(g_textbuf, MAXLINELEN, cnvfile)) { in cnv_first_nonheader_line() 474 return fwrite_checked(g_textbuf, wptr2 - g_textbuf, new_mapfile); in cnv_make_map_write() 523 if (!g_textbuf[MAXLINELEN - 1]) { in cnv_make_map() 743 if (!g_textbuf[MAXLINELEN - 1]) { in validate_cnv_map() 762 if (!g_textbuf[MAXLINELEN - 1]) { in validate_cnv_map() 876 if (!fgets(g_textbuf, MAXLINELEN, mapfile)) { in load_cnv_map() [all …]
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H A D | plink_homozyg.c | 532 if (fwrite_checked(g_textbuf, wptr - g_textbuf, outfile)) { in write_main_roh_reports() 1929 if (fwrite_checked(g_textbuf, wptr - g_textbuf, outfile)) { in roh_pool() 1936 fwrite(g_textbuf, 1, wptr - g_textbuf, outfile); in roh_pool() 1941 fwrite(g_textbuf, 1, wptr - g_textbuf, outfile); in roh_pool() 1959 fwrite(g_textbuf, 1, wptr - g_textbuf, outfile); in roh_pool() 2019 if (fwrite_checked(g_textbuf, wptr - g_textbuf, outfile)) { in roh_pool() 2043 fwrite(g_textbuf, 1, wptr - g_textbuf, outfile); in roh_pool() 2050 if (fwrite_checked(g_textbuf, wptr - g_textbuf, outfile)) { in roh_pool() 2056 fwrite(g_textbuf, 1, wptr - g_textbuf, outfile); in roh_pool() 2332 if (fwrite_checked(g_textbuf, wptr - g_textbuf, outfile)) { in roh_pool() [all …]
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H A D | plink_set.c | 298 g_textbuf[MAXLINELEN - 1] = ' '; in load_range_list() 303 if (!g_textbuf[MAXLINELEN - 1]) { in load_range_list() 1735 g_textbuf[0] = '\t'; in write_set() 1754 fwrite(g_textbuf, 1, bufptr - g_textbuf, outfile); in write_set() 3179 if (fwrite_checked(g_textbuf, bufptr2 - g_textbuf, outfile)) { in annotate() 3637 strcpy(g_textbuf, " -- "); in gene_report() 3641 bufptr = &(g_textbuf[4]); in gene_report() 3647 if (fwrite_checked(g_textbuf, bufptr - g_textbuf, outfile)) { in gene_report() 3662 fwrite(g_textbuf, 1, bufptr - g_textbuf, outfile); in gene_report() 3667 fwrite(g_textbuf, 1, bufptr - g_textbuf, outfile); in gene_report() [all …]
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H A D | plink_data.c | 1860 fwrite(g_textbuf, 1, wptr - g_textbuf, outfile); in write_covars() 1950 fwrite(g_textbuf, 1, wptr - g_textbuf, outfile); in write_covars() 2030 fwrite(g_textbuf, 1, wptr - g_textbuf, outfile); in write_covars() 2064 fwrite(g_textbuf, 1, wptr - g_textbuf, outfile); in write_covars() 2081 fwrite(g_textbuf, 1, wptr - g_textbuf, outfile); in write_covars() 4755 fwrite(g_textbuf, 1, bufptr - g_textbuf, outfile_bim); in oxford_to_bed() 6887 fwrite(g_textbuf, 1, cptr - g_textbuf, outfile); in lgen_to_bed() 7329 cptr3 = memcpya(cptr3, g_textbuf, cptr2 - g_textbuf); in transposed_to_bed() 7384 cptr3 = memcpya(cptr3, g_textbuf, cptr2 - g_textbuf); in transposed_to_bed() 13265 fwrite(g_textbuf, 1, wbufptr - g_textbuf, outfile2); in recode() [all …]
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H A D | plink_ld.c | 7674 fwrite(g_textbuf, 1, bufptr - g_textbuf, outfile); in twolocus_write_table() 7703 fwrite(g_textbuf, 1, bufptr - g_textbuf, outfile); in twolocus_write_table() 7714 fwrite(g_textbuf, 1, bufptr - g_textbuf, outfile); in twolocus_write_table() 7720 fwrite(g_textbuf, 1, bufptr - g_textbuf, outfile); in twolocus_write_table() 7731 fwrite(g_textbuf, 1, bufptr - g_textbuf, outfile); in twolocus_write_table() 7737 fwrite(g_textbuf, 1, bufptr - g_textbuf, outfile); in twolocus_write_table() 7748 fwrite(g_textbuf, 1, bufptr - g_textbuf, outfile); in twolocus_write_table() 7757 fwrite(g_textbuf, 1, bufptr - g_textbuf, outfile); in twolocus_write_table() 7767 fwrite(g_textbuf, 1, bufptr - g_textbuf, outfile); in twolocus_write_table() 7771 fwrite(g_textbuf, 1, bufptr - g_textbuf, outfile); in twolocus_write_table() [all …]
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H A D | plink_assoc.c | 484 if (fwrite_checked(g_textbuf, bufptr - g_textbuf, outfile)) { in multcomp() 547 if (fwrite_checked(g_textbuf, bufptr - g_textbuf, outfile)) { in multcomp() 7732 if (fwrite_checked(g_textbuf, wptr - g_textbuf, outfile)) { in model_assoc() 8677 if (fwrite_checked(g_textbuf, wptr - g_textbuf, outfile)) { in qassoc() 9067 if (fwrite_checked(g_textbuf, wptr - g_textbuf, outfile)) { in qassoc() 9554 if (fwrite_checked(g_textbuf, wptr - g_textbuf, outfile)) { in gxe_assoc() 10203 if (fwrite_checked(g_textbuf, wptr - g_textbuf, outfile)) { in testmiss() 10721 if (fwrite_checked(g_textbuf, wptr - g_textbuf, outfile)) { in testmiss() 11198 if (fwrite_checked(g_textbuf, wptr - g_textbuf, outfile)) { in cmh_assoc() 11204 if (fwrite_checked(g_textbuf, wptr - g_textbuf, outfile)) { in cmh_assoc() [all …]
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H A D | plink_lasso.c | 593 char* wptr = g_textbuf; in lasso_lambda() 599 if (fwrite_checked(g_textbuf, wptr - g_textbuf, outfile)) { in lasso_lambda() 602 wptr = g_textbuf; in lasso_lambda() 606 if (fwrite_checked(g_textbuf, wptr - g_textbuf, outfile)) { in lasso_lambda() 1193 g_textbuf[MAXLINELEN] = '\t'; in lasso() 1208 wptr = memcpya(g_textbuf, "COV\t", 4); in lasso() 1212 if (fwrite_checked(g_textbuf, wptr - g_textbuf, outfile)) { in lasso() 1232 wptr2 = dtoa_gx(dxx, '\n', &(g_textbuf[MAXLINELEN + 1])); in lasso() 1237 wptr2 = memcpyl3a(&(g_textbuf[MAXLINELEN + 1]), "NA\n"); in lasso() 1239 if (fwrite_checked(g_textbuf, wptr - g_textbuf, outfile)) { in lasso() [all …]
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H A D | plink_filter.c | 96 g_textbuf[MAXLINELEN - 1] = ' '; in keep_or_remove() 102 if (!g_textbuf[MAXLINELEN - 1]) { in keep_or_remove() 325 char* midbuf = &(g_textbuf[MAXLINELEN]); in extract_exclude_flag_norange() 1221 g_textbuf[MAXLINELEN - 1] = ' '; in load_oblig_missing() 1228 if (!g_textbuf[MAXLINELEN - 1]) { in load_oblig_missing() 1348 if (!g_textbuf[MAXLINELEN - 1]) { in load_oblig_missing() 1488 g_textbuf[MAXLINELEN - 1] = ' '; in filter_samples_file() 1491 if (!g_textbuf[MAXLINELEN - 1]) { in filter_samples_file() 2650 cptr = width_force(4, g_textbuf, chrom_name_write(chrom_info_ptr, chrom_idx, g_textbuf)); in write_missingness_reports() 2692 pzwritep = memcpya(pzwritep, g_textbuf, cptr2 - g_textbuf); in write_missingness_reports() [all …]
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H A D | plink_dosage.c | 387 g_textbuf[MAXLINELEN - 1] = ' '; in dosage_load_score_files() 388 while (fgets(g_textbuf, MAXLINELEN, infile)) { in dosage_load_score_files() 390 if (!g_textbuf[MAXLINELEN - 1]) { in dosage_load_score_files() 394 bufptr = skip_initial_spaces(g_textbuf); in dosage_load_score_files() 430 bufptr = skip_initial_spaces(g_textbuf); in dosage_load_score_files() 1255 if (!g_textbuf[MAXLINELEN - 1]) { in plink1_dosage() 1259 bufptr = skip_initial_spaces(g_textbuf); in plink1_dosage() 1331 bufptr = skip_initial_spaces(g_textbuf); in plink1_dosage() 1549 pzwritep = memcpya(pzwritep, g_textbuf, bufptr - g_textbuf); in plink1_dosage() 1608 if (!g_textbuf[MAXLINELEN - 1]) { in plink1_dosage() [all …]
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H A D | plink_glm.c | 5565 if (fwrite_checked(g_textbuf, wptr - g_textbuf, outfile)) { in glm_linear_assoc() 7001 if (fwrite_checked(g_textbuf, wptr - g_textbuf, outfile)) { in glm_logistic_assoc() 7667 if (fwrite_checked(g_textbuf, wptr - g_textbuf, outfile)) { in glm_linear_nosnp() 7809 if (fwrite_checked(g_textbuf, wptr - g_textbuf, outfile)) { in glm_linear_nosnp() 7827 if (fwrite_checked(g_textbuf, wptr - g_textbuf, outfile)) { in glm_linear_nosnp() 7863 if (fwrite_checked(g_textbuf, wptr - g_textbuf, outfile)) { in glm_linear_nosnp() 7869 if (fwrite_checked(g_textbuf, wptr - g_textbuf, outfile)) { in glm_linear_nosnp() 8460 if (fwrite_checked(g_textbuf, wptr - g_textbuf, outfile)) { in glm_logistic_nosnp() 8593 if (fwrite_checked(g_textbuf, wptr - g_textbuf, outfile)) { in glm_logistic_nosnp() 8611 if (fwrite_checked(g_textbuf, wptr - g_textbuf, outfile)) { in glm_logistic_nosnp() [all …]
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H A D | plink_misc.c | 3246 if (fwrite_checked(g_textbuf, wptr - g_textbuf, outfile)) { in sexcheck() 3598 if (fwrite_checked(g_textbuf, wptr - g_textbuf, outfile)) { in list_duplicate_vars() 4155 if (fwrite_checked(g_textbuf, wptr - g_textbuf, outfile)) { in fst_report() 5831 if (fwrite_checked(g_textbuf, wptr - g_textbuf, outfile)) { in meta_analysis() 5952 g_textbuf[0] = ' '; in meta_analysis() 5953 g_textbuf[1] = 'F'; in meta_analysis() 5956 if (fwrite_checked(g_textbuf, wptr - g_textbuf, outfile)) { in meta_analysis() 6249 wptr = g_textbuf; in meta_analysis() 6262 if (fwrite_checked(g_textbuf, wptr - g_textbuf, outfile)) { in meta_analysis() 6302 g_textbuf[0] = ' '; in meta_analysis() [all …]
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H A D | plink_calc.c | 7196 if (fwrite_checked(g_textbuf, wptr - g_textbuf, outfile)) { in calc_pca() 7307 if (fwrite_checked(g_textbuf, wptr - g_textbuf, outfile)) { in calc_pca() 7376 if (fwrite_checked(g_textbuf, wptr - g_textbuf, outfile)) { in calc_pca() 7396 if (fwrite_checked(g_textbuf, wptr - g_textbuf, outfile)) { in calc_pca() 7418 if (fwrite_checked(g_textbuf, wptr - g_textbuf, outfile)) { in calc_pca() 8680 fwrite(g_textbuf, 1, wptr - g_textbuf, outfile); in calc_cluster_neighbor() 8710 fwrite(g_textbuf, 1, wptr - g_textbuf, outfile); in calc_cluster_neighbor() 8732 fwrite(g_textbuf, 1, wptr - g_textbuf, outfile); in calc_cluster_neighbor() 8763 fwrite(g_textbuf, 1, wptr - g_textbuf, outfile); in calc_cluster_neighbor() 8786 fwrite(g_textbuf, 1, wptr - g_textbuf, outfile); in calc_cluster_neighbor() [all …]
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H A D | plink_family.c | 907 if (fwrite_checked(g_textbuf, wptr - g_textbuf, outfile)) { in mendel_error_scan() 961 if (fwrite_checked(g_textbuf, wptr - g_textbuf, outfile)) { in mendel_error_scan() 983 if (fwrite_checked(g_textbuf, wptr - g_textbuf, outfile_l)) { in mendel_error_scan() 1114 if (fwrite_checked(g_textbuf, wptr - g_textbuf, outfile)) { in mendel_error_scan() 1145 if (fwrite_checked(g_textbuf, wptr - g_textbuf, outfile)) { in mendel_error_scan() 1161 if (fwrite_checked(g_textbuf, wptr - g_textbuf, outfile)) { in mendel_error_scan() 1171 if (fwrite_checked(g_textbuf, wptr - g_textbuf, outfile)) { in mendel_error_scan() 4912 if (fwrite_checked(g_textbuf, wptr - g_textbuf, outfile)) { in dfam() 5787 if (fwrite_checked(g_textbuf, bufptr - g_textbuf, outfile)) { in qfam() 5817 if (fwrite_checked(g_textbuf, bufptr - g_textbuf, outfile)) { in qfam() [all …]
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H A D | plink_help.c | 95 strcpy(g_textbuf, cur_params); in help_print() 97 cur_param_start[0] = g_textbuf; in help_print() 98 payload_ptr = strchr(g_textbuf, '\t'); in help_print() 200 memcpyx(g_textbuf, payload_ptr, uii, 0); in help_print() 201 fputs(g_textbuf, stdout); in help_print()
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H A D | plink.c | 482 if (realpath_identical(outname, g_textbuf, &(g_textbuf[FNAMESIZE + 64]))) { in plink() 948 if ((*g_textbuf == '#') || ((uii == 3) && (!memcmp(g_textbuf, "chr", 3)))) { in plink() 2525 g_textbuf[MAXLINELEN - 1] = ' '; in rerun() 2531 if (!g_textbuf[MAXLINELEN - 1]) { in rerun() 2540 if (!g_textbuf[MAXLINELEN - 1]) { in rerun() 2543 if ((g_textbuf[0] >= '0') && (g_textbuf[0] <= '9')) { in rerun() 2562 while (memcmp(g_textbuf, "Options in effect:", 18) || (g_textbuf[18] >= ' ')) { in rerun() 2570 load_ptr = g_textbuf; in rerun() 2641 g_textbuf[loaded_arg_idx++] = 0; in rerun() 3981 logstr(g_textbuf); in main() [all …]
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H A D | plink_common.c | 27 char g_textbuf[TEXTBUF_SIZE]; variable 780 if (!fgets(g_textbuf, MAXLINELEN, fptr)) { in get_next_noncomment() 784 lptr = skip_initial_spaces(g_textbuf); in get_next_noncomment() 9711 g_textbuf[MAXLINELEN - 1] = ' '; in open_and_size_string_list() 9712 while (fgets(g_textbuf, MAXLINELEN, *infile_ptr)) { in open_and_size_string_list() 9714 if (!g_textbuf[MAXLINELEN - 1]) { in open_and_size_string_list() 9718 bufptr = skip_initial_spaces(g_textbuf); in open_and_size_string_list() 9755 while (fgets(g_textbuf, MAXLINELEN, *infile_ptr)) { in load_string_list() 9756 bufptr = skip_initial_spaces(g_textbuf); in load_string_list()
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/dports/biology/plink/plink-ng-79b2df8c/2.0/ |
H A D | plink2_cmdline.cc | 39 char g_textbuf[kTextbufSize]; variable 3185 memcpyx(g_textbuf, payload_iter, line_slen, '\0'); in HelpPrint() 3186 fputs(g_textbuf, stdout); in HelpPrint() 3329 char* rerun_fname = rerun_parameter_present? argv[rerun_argv_pos + 1] : g_textbuf; in Rerun() 3341 char* textbuf = g_textbuf; in Rerun() 3871 if (GetComputerName(g_textbuf, &windows_dw)) in CmdlineParsePhase2() 3873 if (gethostname(g_textbuf, kTextbufSize) != -1) in CmdlineParsePhase2() 3877 logputs_silent(g_textbuf); in CmdlineParsePhase2() 3880 if (unlikely(!getcwd(g_textbuf, kPglFnamesize))) { in CmdlineParsePhase2() 3886 logputs_silent(g_textbuf); in CmdlineParsePhase2()
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H A D | plink2.cc | 697 if (unlikely(!realpath(pgenname, g_textbuf))) in Plink2Core() 706 pgen_rename = RealpathIdentical(outname, g_textbuf, &(g_textbuf[kPglFnamesize + 64])); in Plink2Core() 710 pgen_rename = RealpathIdentical(outname, g_textbuf, &(g_textbuf[kPglFnamesize + 64])); in Plink2Core() 715 memcpy(g_textbuf, pgenname, fname_slen + 1); in Plink2Core() 717 if (unlikely(rename(g_textbuf, pgenname))) { in Plink2Core() 722 memcpy(g_textbuf, pvarname, fname_slen + 1); in Plink2Core() 724 if (unlikely(rename(g_textbuf, pvarname))) { in Plink2Core() 730 memcpy(g_textbuf, psamname, fname_slen + 1); in Plink2Core() 732 if (unlikely(rename(g_textbuf, psamname))) { in Plink2Core() 895 pvar_renamed = RealpathIdentical(outname, g_textbuf, &(g_textbuf[kPglFnamesize + 64])); in Plink2Core() [all …]
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H A D | plink2_matrix_calc.cc | 2705 fname_slen = GetFullPathName(subset_fname, kPglFnamesize, g_textbuf, nullptr); in CalcKingTableSubset() 2708 if (unlikely(!realpath(subset_fname, g_textbuf))) in CalcKingTableSubset() 2714 if (RealpathIdentical(outname, g_textbuf, &(g_textbuf[kPglFnamesize + 64]))) { in CalcKingTableSubset() 2717 memcpy(g_textbuf, subset_fname, fname_slen); in CalcKingTableSubset() 2718 strcpy_k(&(g_textbuf[fname_slen]), "~"); in CalcKingTableSubset() 2719 if (unlikely(rename(subset_fname, g_textbuf))) { in CalcKingTableSubset() 2723 subset_fname = g_textbuf; in CalcKingTableSubset() 4193 write_double_buf = R_CAST(double*, g_textbuf); in CalcGrm() 4381 write_float_buf = R_CAST(float*, g_textbuf); in CalcGrm()
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H A D | plink2_fasta.cc | 489 nlist_write_iter = g_textbuf;
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H A D | plink2_common.cc | 2557 char* token_buf = g_textbuf; in ParseChrRanges() 2979 char* write_iter = g_textbuf; in WriteSampleIdsOverride()
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H A D | plink2_cmdline.h | 131 extern char g_textbuf[];
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/dports/lang/nwcc/nwcc_0.8.3/cpp/ |
H A D | preprocess.c | 75 char g_textbuf[2048]; variable 1737 p = g_textbuf; 1747 x_fprintf(out, g_textbuf);
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