/dports/biology/plink/plink-ng-79b2df8c/1.9/ |
H A D | plink_lasso.c | 252 bigstack_alloc_d(col_ct, &xhat); in lasso_bigmem() 463 if (bigstack_alloc_d(sample_valid_ct * LASSO_LAMBDA_BLOCK_SIZE, &rand_matrix) || in lasso_lambda() 464 bigstack_alloc_d(lasso_lambda_iters, &max_empirical_lambdas) || in lasso_lambda() 481 bigstack_alloc_d(sample_valid_ct, &residuals)) { in lasso_lambda() 695 if (bigstack_alloc_d(covar_ct * sample_valid_ct, &covar_data_arr)) { in lasso_smallmem() 736 if (bigstack_alloc_d(covar_ct + marker_ct, &xhat)) { in lasso_smallmem() 748 if (bigstack_alloc_d(sample_valid_ct, &data_window)) { in lasso_smallmem() 840 bigstack_alloc_d(sample_valid_ct, &data_window)) { in lasso_smallmem() 1082 bigstack_alloc_d(sample_valid_ct, &pheno_d_collapsed) || in lasso() 1083 bigstack_alloc_d(sample_valid_ct, &residuals)) { in lasso() [all …]
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H A D | plink_glm.c | 4540 if (bigstack_alloc_d(marker_initial_ct, &g_orig_stats) || in glm_linear_assoc() 4760 if (bigstack_alloc_d(marker_initial_ct, &orig_pvals)) { in glm_linear_assoc() 4842 if (bigstack_alloc_d(sample_valid_ct, &g_perm_pheno_d2)) { in glm_linear_assoc() 6069 if (bigstack_alloc_d(marker_initial_ct, &g_orig_stats) || in glm_logistic_assoc() 7373 bigstack_alloc_d(constraint_ct, &df_buf) || in glm_linear_nosnp() 7390 bigstack_alloc_d(param_ctx - 1, &orig_stats) || in glm_linear_nosnp() 7401 if (bigstack_alloc_d(sample_valid_ct, &g_perm_pheno_d2)) { in glm_linear_nosnp() 7547 if (bigstack_alloc_d(dgels_lwork, &dgels_work)) { in glm_linear_nosnp() 8242 bigstack_alloc_d(param_ctx - 1, &orig_stats)) { in glm_logistic_nosnp() 8355 if (bigstack_alloc_d(param_ct, ¶m_1d_dbuf) || in glm_logistic_nosnp() [all …]
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H A D | plink_dosage.c | 203 bigstack_alloc_d(score_marker_ct, score_effect_sizes_ptr) || in dosage_load_score_files() 1051 bigstack_alloc_d(sample_ct, &covar_d)) { in plink1_dosage() 1383 bigstack_alloc_d(sample_ct, &cur_dosages) || in plink1_dosage() 1449 if (bigstack_alloc_d(sample_ct, &pheno_d2) || in plink1_dosage() 1452 bigstack_alloc_d(param_ct * param_ct, ¶m_2d_buf) || in plink1_dosage() 1453 bigstack_alloc_d(param_ct * param_ct, ¶m_2d_buf2) || in plink1_dosage() 1454 bigstack_alloc_d(param_ct - 1, ®ression_results) || in plink1_dosage() 1455 bigstack_alloc_d(param_ct * sample_ct, &dgels_a) || in plink1_dosage() 1456 bigstack_alloc_d(sample_ct, &dgels_b)) { in plink1_dosage() 1476 if (bigstack_alloc_d(dgels_lwork, &dgels_work)) { in plink1_dosage() [all …]
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H A D | plink_assoc.c | 278 if (bigstack_alloc_d(chi_ct, &sp) || in multcomp() 279 bigstack_alloc_d(chi_ct, &schi) || in multcomp() 370 if (bigstack_alloc_d(chi_ct, &pv_bh) || in multcomp() 371 bigstack_alloc_d(chi_ct, &pv_by) || in multcomp() 372 bigstack_alloc_d(chi_ct, &pv_gc)) { in multcomp() 6299 bigstack_alloc_d(marker_ct, &orig_pvals) || in model_assoc() 11130 if (bigstack_alloc_d(marker_ct, &orig_chisq)) { in cmh_assoc() 11455 if (bigstack_alloc_d(cluster_ct1, &ty_ctrl) || in cmh2_assoc() 11456 bigstack_alloc_d(cluster_ct1, &ty_case) || in cmh2_assoc() 11457 bigstack_alloc_d(cluster_ct1 - 1, &n0) || in cmh2_assoc() [all …]
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H A D | plink_rserve.c | 145 if (bigstack_alloc_d(pheno_nm_ct, &pheno_d2)) { in rserve_call() 164 if (bigstack_alloc_d(pheno_nm_ct * covar_ct, &covar_d2)) { in rserve_call()
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H A D | plink_family.c | 1460 if (bigstack_alloc_d(ulii, &(pri_ptr->rel_space))) { in populate_pedigree_rel_info() 2184 if (bigstack_alloc_d(marker_ct, &orig_chisq)) { in tdt() 4219 if (bigstack_alloc_d(marker_ct, &orig_chisq)) { in dfam() 4408 bigstack_alloc_d(max_thread_ct * perm_vec_cta128, &g_dfam_numers) || in dfam() 4409 bigstack_alloc_d(max_thread_ct * perm_vec_cta128, &g_dfam_denoms)) { in dfam() 4426 if (bigstack_alloc_d(max_thread_ct * perm_vec_ctcl8m, &g_maxt_thread_results)) { in dfam() 4430 if (bigstack_alloc_d(marker_ct * g_perm_vec_ct, &g_mperm_save_all)) { in dfam() 5613 if (bigstack_alloc_d(marker_ct, &orig_beta) || in qfam() 5625 bigstack_alloc_d(marker_ct, &g_orig_stat) || in qfam() 5630 bigstack_alloc_d(lm_ct, &pheno_d2) || in qfam() [all …]
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H A D | plink_calc.c | 2023 if (bigstack_alloc_d(sample_ct, &g_pheno_packed)) { in regress_rel_main() 2403 if (bigstack_alloc_d(ulii, &g_rel_dists)) { in calc_unrelated_herit() 2553 if (bigstack_alloc_d(ulii, &matrix_wkbase)) { in unrelated_herit_batch() 2971 if (bigstack_alloc_d(ll_size, &ll_pool) || in groupdist_calc() 2972 bigstack_alloc_d(lh_size, &lh_pool) || in groupdist_calc() 2973 bigstack_alloc_d(hh_size, &hh_pool) || in groupdist_calc() 7077 if (bigstack_alloc_d(ulii, &rel_dists) || in calc_pca() 7146 bigstack_alloc_d(pc_ct, &cur_var_wts) || in calc_pca() 7148 bigstack_alloc_d(pc_ct, &eigval_inv_sqrts)) { in calc_pca() 7786 if (bigstack_alloc_d(45056, &subset_weights)) { in calc_distance() [all …]
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H A D | plink_cluster.c | 2996 if (bigstack_alloc_d(sample_ct * sample_ct, &main_matrix)) { in mds_plot() 3063 if (bigstack_alloc_d(ulii, &sqrt_eigvals) || in mds_plot() 3064 bigstack_alloc_d(ulii * ulii, &out_u) || in mds_plot() 3065 bigstack_alloc_d(ulii * ulii, &out_v)) { in mds_plot() 3081 if (bigstack_alloc_d(lwork, &work)) { in mds_plot() 3305 if (bigstack_alloc_d(sample_ct * sample_ct, &main_matrix)) { in mds_plot_eigendecomp() 3399 if (bigstack_alloc_d(dim_ct, &sqrt_eigvals)) { in mds_plot_eigendecomp()
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H A D | plink_ld.c | 926 bigstack_alloc_d(window_max, &sums) || in ld_prune() 927 bigstack_alloc_d(window_max, &variance_recips)) { in ld_prune() 945 if (bigstack_alloc_d(window_max * window_max, &cov_matrix) || in ld_prune() 961 if (bigstack_alloc_d(ulii * window_max, &work)) { in ld_prune() 8444 if (bigstack_alloc_d(pheno_nm_ct, &pheno_d2)) { in epistasis_linear_regression() 8493 bigstack_alloc_d(idx1_block_size, &g_epi_phenogeno1); in epistasis_linear_regression() 8498 bigstack_alloc_d(ulii, &g_epi_best_chisq1); in epistasis_linear_regression() 9796 bigstack_alloc_d(ulii, &g_epi_best_chisq1); in epistasis_report() 12438 if (bigstack_alloc_d(set_ct, orig_set_scores_ptr) || in set_test_common_init() 13205 if (bigstack_alloc_d(index_ct, &sorted_pvals) || in clump_reports() [all …]
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H A D | plink_perm.c | 781 if (bigstack_alloc_d(perm_vec_ctcl8m * pheno_nm_ct, &g_perm_vecstd)) { in make_perm_pheno()
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H A D | plink_data.c | 864 if (bigstack_alloc_d(unfiltered_marker_ct, set_allele_freqs_ptr)) { in load_bim() 1411 bigstack_alloc_d(ulii, covar_d_ptr)) { in load_covars() 2795 bigstack_alloc_d(marker_ct, &marker_cms) || in load_sort_and_write_map() 7570 bigstack_alloc_d(marker_ct, &marker_cms) || in transposed_to_bed() 16266 if (bigstack_alloc_d(tot_sample_ct, &pheno_d)) { in merge_datasets() 16520 bigstack_alloc_d(tot_marker_ct, &marker_cms) || in merge_datasets() 16522 bigstack_alloc_d(tot_marker_ct, &marker_cms_tmp) || in merge_datasets()
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H A D | plink_common.h | 1114 HEADER_INLINE int32_t bigstack_alloc_d(uintptr_t ct, double** dp_ptr) { in bigstack_alloc_d() function
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H A D | plink.c | 1755 if (bigstack_alloc_d(ulii, &mds_plot_dmatrix_copy)) { in plink() 1760 if (bigstack_alloc_d((ulii * (ulii - 1)) / 2, &mds_plot_dmatrix_copy)) { in plink() 1784 if (bigstack_alloc_d(ulii, &cluster_sorted_ibs)) { in plink() 1811 if (bigstack_alloc_d((sample_ct * (sample_ct - 1)) / 2, &g_dists)) { in plink()
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H A D | plink_misc.c | 4572 if (bigstack_alloc_d(marker_ct, &effect_sizes_cur)) { in score_report() 4592 if (bigstack_alloc_d(sample_ct, &score_deltas) || in score_report()
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H A D | plink_filter.c | 2914 bigstack_alloc_d(uii * marker_ct, &p_values) || in hardy_report()
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/dports/biology/plink/plink-ng-79b2df8c/2.0/ |
H A D | plink2_adjust.cc | 298 if (unlikely(bigstack_alloc_d(valid_allele_ct, &ln_pv_by))) { in Multcomp() 313 bigstack_alloc_d(valid_allele_ct, &ln_pv_bh) || in Multcomp() 314 bigstack_alloc_d(valid_allele_ct, &ln_pv_gc) || in Multcomp() 315 bigstack_alloc_d(valid_allele_ct, &unadj_sorted_ln_pvals))) { in Multcomp() 764 bigstack_alloc_d(entry_ct, &ln_pvals))) { in AdjustFile()
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H A D | plink2_matrix_calc.cc | 410 if (unlikely(bigstack_alloc_d(king_id_ct - 1, &king_drow))) { in KingCutoffBatch() 4027 bigstack_alloc_d(max_allele_ct, &allele_1copy_buf))) { in CalcGrm() 5003 bigstack_alloc_d(pc_ct, &cur_var_wts) || in CalcPca() 5004 bigstack_alloc_d(pc_ct, &eigval_inv_sqrts))) { in CalcPca() 5035 bigstack_alloc_d(max_allele_ct, &allele_1copy_buf) || in CalcPca() 5036 bigstack_alloc_d(pc_ct, &eigvals) || in CalcPca() 5102 bigstack_alloc_d(qq_col_ct, &ss) || in CalcPca() 5103 bigstack_alloc_d(pca_row_ct * qq_col_ct, &qq) || in CalcPca() 5107 bigstack_alloc_d(gg_size, &g1))) { in CalcPca() 5902 if (unlikely(bigstack_alloc_d(variant_ct, &min_vals))) { in ScoreReport() [all …]
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H A D | plink2_glm.cc | 1734 bigstack_alloc_d(8 * xtx_state - 2 + in GlmAllocFillAndTestCovarsQt() 1737 bigstack_alloc_d(new_covar_ct * (new_covar_ct + 1), &corr_buf))) { in GlmAllocFillAndTestCovarsQt() 1796 bigstack_alloc_d(sample_ct, pheno_d_ptr))) { in GlmAllocFillAndTestPhenoCovarsQt() 1803 bigstack_alloc_d(1 + xtx_state + new_covar_ct, &xt_y_image))) { in GlmAllocFillAndTestPhenoCovarsQt() 1839 bigstack_alloc_d(8 * xtx_state - 3 + in GlmAllocFillAndTestPhenoCovarsCc() 1842 bigstack_alloc_d(new_covar_ct * (new_covar_ct + 1), &corr_buf))) { in GlmAllocFillAndTestPhenoCovarsCc() 9899 if (bigstack_alloc_d(sample_ct * subbatch_size, &ctx->pheno_d)) { in GlmLinearBatch() 11004 bigstack_alloc_d(raw_sample_ct, &cur_covar_vals))) { in GlmMain() 11100 if (unlikely(bigstack_alloc_d(raw_sample_ct, &sex_covar_vals))) { in GlmMain() 12475 if (unlikely(bigstack_alloc_d(cur_allele_ct, &orig_ln_pvals))) { in GlmMain() [all …]
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H A D | plink2_cmdline.h | 483 HEADER_INLINE BoolErr bigstack_alloc_d(uintptr_t ct, double** d_arr_ptr) { in bigstack_alloc_d() function
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H A D | plink2_pvar.cc | 1980 if (unlikely(bigstack_alloc_d(raw_variant_ct, variant_cms_ptr))) { in LoadPvar()
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H A D | plink2_misc.cc | 2803 if (unlikely(bigstack_alloc_d(raw_sample_ct, &shifted_pheno_qt))) { in PhenoVarianceStandardize() 4834 if (unlikely(bigstack_alloc_d(hwe_x_ct + x_xallele_ct, hwe_x_pvals_ptr))) {
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H A D | plink2.cc | 1781 if (unlikely(bigstack_alloc_d(raw_allele_ct - raw_variant_ct, &allele_freqs))) { in Plink2Core() 1828 if (unlikely(bigstack_alloc_d(raw_variant_ct, &imp_r2_vals))) { in Plink2Core()
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H A D | plink2_import.cc | 14397 if (unlikely(bigstack_alloc_d(variant_ct, variant_cms_ptr))) { in LoadMap()
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