diff options
| -rw-r--r-- | src/gemma.cpp | 3 | ||||
| -rw-r--r-- | src/lmm.cpp | 11 | ||||
| -rw-r--r-- | src/lmm.h | 6 |
3 files changed, 5 insertions, 15 deletions
diff --git a/src/gemma.cpp b/src/gemma.cpp index 3100b94..94d61a8 100644 --- a/src/gemma.cpp +++ b/src/gemma.cpp @@ -2843,8 +2843,7 @@ void GEMMA::BatchRun(PARAM &cPar) { write(&Y_col.vector, "Y_col"); if (cPar.is_mdb) { - cLmm.mdb_calc_gwa(U, eval, UtW, &UtY_col.vector, W, - &Y_col.vector, cPar.setGWASnps); + cLmm.mdb_calc_gwa(U, eval, UtW, &UtY_col.vector, W, &Y_col.vector); cLmm.CopyToParam(cPar); } else { diff --git a/src/lmm.cpp b/src/lmm.cpp index 1d7485c..375013c 100644 --- a/src/lmm.cpp +++ b/src/lmm.cpp @@ -1882,14 +1882,11 @@ void LMM::mdb_analyze(std::function< SnpNameValues2(size_t) >& fetch_snp, const gsl_matrix *U, const gsl_vector *eval, const gsl_matrix *UtW, const gsl_vector *Uty, const gsl_matrix *W, const gsl_vector *y, - const set<string> gwasnps, size_t num_markers) { vector<SUMSTAT2> sumstat2; clock_t time_start = clock(); checkpoint_nofile("start-lmm-mdb-analyze"); - // Subset/LOCO support - // bool process_gwasnps = gwasnps.size(); // Calculate basic quantities. size_t n_index = (n_cvt + 2 + 1) * (n_cvt + 2) / 2; @@ -1908,8 +1905,6 @@ void LMM::mdb_analyze(std::function< SnpNameValues2(size_t) >& fetch_snp, gsl_matrix *Uab = gsl_matrix_safe_alloc(ni_test, n_index); gsl_vector *ab = gsl_vector_safe_alloc(n_index); - // Create a large matrix with LMM_BATCH_SIZE columns for batched processing - // const size_t msize=(process_gwasnps ? 1 : LMM_BATCH_SIZE); const size_t msize = LMM_BATCH_SIZE; gsl_matrix *Xlarge = gsl_matrix_safe_alloc(inds, msize); gsl_matrix *UtXlarge = gsl_matrix_safe_alloc(inds, msize); @@ -2026,7 +2021,6 @@ void LMM::mdb_analyze(std::function< SnpNameValues2(size_t) >& fetch_snp, auto gs = get<2>(tup); markers.push_back(markerinfo); - // cout << t << " SNP: " << snp << endl; // check whether SNP is included in gwasnps (used by LOCO) /* @@ -2161,8 +2155,7 @@ void LMM::mdb_analyze(std::function< SnpNameValues2(size_t) >& fetch_snp, void LMM::mdb_calc_gwa(const gsl_matrix *U, const gsl_vector *eval, const gsl_matrix *UtW, const gsl_vector *Uty, - const gsl_matrix *W, const gsl_vector *y, - const set<string> gwasnps) { + const gsl_matrix *W, const gsl_vector *y) { checkpoint("mdb-calc-gwa",file_geno); // const auto num_snps = indicator_snp.size(); @@ -2275,7 +2268,7 @@ void LMM::mdb_calc_gwa(const gsl_matrix *U, const gsl_vector *eval, } return make_tuple(success, markerinfo, gs); }; - LMM::mdb_analyze(fetch_snp,U,eval,UtW,Uty,W,y,gwasnps,num_markers); + LMM::mdb_analyze(fetch_snp,U,eval,UtW,Uty,W,y,num_markers); ns_total = ns_test = num_markers; // track global number of snps in original gemma (goes to cPar) } diff --git a/src/lmm.h b/src/lmm.h index af79f5f..f10996d 100644 --- a/src/lmm.h +++ b/src/lmm.h @@ -129,12 +129,10 @@ public: void mdb_analyze(std::function< SnpNameValues2(size_t) >& fetch_snp, const gsl_matrix *U, const gsl_vector *eval, const gsl_matrix *UtW, const gsl_vector *Uty, - const gsl_matrix *W, const gsl_vector *y, - const set<string> gwasnps, size_t num_markers); + const gsl_matrix *W, const gsl_vector *y, size_t num_markers); void mdb_calc_gwa(const gsl_matrix *U, const gsl_vector *eval, const gsl_matrix *UtW, const gsl_vector *Uty, - const gsl_matrix *W, const gsl_vector *y, - const set<string> gwasnps); + const gsl_matrix *W, const gsl_vector *y); void AnalyzeBimbam(const gsl_matrix *U, const gsl_vector *eval, const gsl_matrix *UtW, const gsl_vector *Uty, const gsl_matrix *W, const gsl_vector *y, |