diff options
Diffstat (limited to 'src/io.cpp')
| -rw-r--r-- | src/io.cpp | 753 |
1 files changed, 0 insertions, 753 deletions
diff --git a/src/io.cpp b/src/io.cpp index 6be01fd..1d75207 100644 --- a/src/io.cpp +++ b/src/io.cpp @@ -2274,759 +2274,6 @@ bool ReadFile_gene(const string &file_gene, vector<double> &vec_read, return true; } -// WJA Added -// Read Oxford sample file. -bool ReadFile_sample(const string &file_sample, - vector<vector<int>> &indicator_pheno, - vector<vector<double>> &pheno, - const vector<size_t> &p_column, vector<int> &indicator_cvt, - vector<vector<double>> &cvt, size_t &n_cvt) { - debug_msg("entered"); - indicator_pheno.clear(); - pheno.clear(); - indicator_cvt.clear(); - - igzstream infile(file_sample.c_str(), igzstream::in); - - if (!infile) { - cout << "error! fail to open sample file: " << file_sample << endl; - return false; - } - - string line; - char *ch_ptr; - - string id; - double p, d; - - vector<double> pheno_row; - vector<int> ind_pheno_row; - int flag_na = 0; - - size_t num_cols = 0; - size_t num_p_in_file = 0; - size_t num_cvt_in_file = 0; - - map<size_t, size_t> mapP2c; - for (size_t i = 0; i < p_column.size(); i++) { - mapP2c[p_column[i]] = i; - pheno_row.push_back(-9); - ind_pheno_row.push_back(0); - } - - // Read header line1. - if (!safeGetline(infile, line).eof()) { - ch_ptr = strtok((char *)line.c_str(), " \t"); - if (strcmp(ch_ptr, "ID_1") != 0) { - return false; - } - ch_ptr = strtok(NULL, " \t"); - if (strcmp(ch_ptr, "ID_2") != 0) { - return false; - } - ch_ptr = strtok(NULL, " \t"); - if (strcmp(ch_ptr, "missing") != 0) { - return false; - } - while (ch_ptr != NULL) { - num_cols++; - ch_ptr = strtok(NULL, " \t"); - } - num_cols--; - } - - vector<map<uint32_t, size_t>> cvt_factor_levels; - - char col_type[num_cols]; - - // Read header line2. - if (!safeGetline(infile, line).eof()) { - ch_ptr = strtok((char *)line.c_str(), " \t"); - if (strcmp(ch_ptr, "0") != 0) { - return false; - } - ch_ptr = strtok(NULL, " \t"); - if (strcmp(ch_ptr, "0") != 0) { - return false; - } - ch_ptr = strtok(NULL, " \t"); - if (strcmp(ch_ptr, "0") != 0) { - return false; - } - size_t it = 0; - ch_ptr = strtok(NULL, " \t"); - if (ch_ptr != NULL) - while (ch_ptr != NULL) { - col_type[it++] = ch_ptr[0]; - if (ch_ptr[0] == 'D') { - cvt_factor_levels.push_back(map<uint32_t, size_t>()); - num_cvt_in_file++; - } - if (ch_ptr[0] == 'C') { - num_cvt_in_file++; - } - if ((ch_ptr[0] == 'P') || (ch_ptr[0] == 'B')) { - num_p_in_file++; - } - ch_ptr = strtok(NULL, " \t"); - } - } - - while (!safeGetline(infile, line).eof()) { - - ch_ptr = strtok((char *)line.c_str(), " \t"); - - for (int it = 0; it < 3; it++) { - ch_ptr = strtok(NULL, " \t"); - } - - size_t i = 0; - size_t p_i = 0; - size_t fac_cvt_i = 0; - - while (i < num_cols) { - - if ((col_type[i] == 'P') || (col_type[i] == 'B')) { - if (mapP2c.count(p_i + 1) != 0) { - if (strcmp(ch_ptr, "NA") == 0) { - ind_pheno_row[mapP2c[p_i + 1]] = 0; - pheno_row[mapP2c[p_i + 1]] = -9; - } else { - p = atof(ch_ptr); - ind_pheno_row[mapP2c[p_i + 1]] = 1; - pheno_row[mapP2c[p_i + 1]] = p; - } - } - p_i++; - } - if (col_type[i] == 'D') { - - // NOTE THIS DOES NOT CHECK TO BE SURE LEVEL - // IS INTEGRAL i.e for atoi error. - if (strcmp(ch_ptr, "NA") != 0) { - uint32_t level = atoi(ch_ptr); - if (cvt_factor_levels[fac_cvt_i].count(level) == 0) { - cvt_factor_levels[fac_cvt_i][level] = - cvt_factor_levels[fac_cvt_i].size(); - } - } - fac_cvt_i++; - } - - ch_ptr = strtok(NULL, " \t"); - i++; - } - - indicator_pheno.push_back(ind_pheno_row); - pheno.push_back(pheno_row); - } - - // Close and reopen the file. - infile.close(); - infile.clear(); - - if (num_cvt_in_file > 0) { - igzstream infile2(file_sample.c_str(), igzstream::in); - - if (!infile2) { - cout << "error! fail to open sample file: " << file_sample << endl; - return false; - } - - // Skip header. - safeGetline(infile2, line); - safeGetline(infile2, line); - - // Pull in the covariates now we now the number of - // factor levels. - while (!safeGetline(infile2, line).eof()) { - - vector<double> v_d; - flag_na = 0; - ch_ptr = strtok((char *)line.c_str(), " \t"); - - for (int it = 0; it < 3; it++) { - ch_ptr = strtok(NULL, " \t"); - } - - size_t i = 0; - size_t fac_cvt_i = 0; - size_t num_fac_levels; - while (i < num_cols) { - - if (col_type[i] == 'C') { - if (strcmp(ch_ptr, "NA") == 0) { - flag_na = 1; - d = -9; - } else { - d = atof(ch_ptr); - } - - v_d.push_back(d); - } - - if (col_type[i] == 'D') { - - // NOTE THIS DOES NOT CHECK TO BE SURE - // LEVEL IS INTEGRAL i.e for atoi error. - num_fac_levels = cvt_factor_levels[fac_cvt_i].size(); - if (num_fac_levels > 1) { - if (strcmp(ch_ptr, "NA") == 0) { - flag_na = 1; - for (size_t it = 0; it < num_fac_levels - 1; it++) { - v_d.push_back(-9); - } - } else { - uint32_t level = atoi(ch_ptr); - for (size_t it = 0; it < num_fac_levels - 1; it++) { - cvt_factor_levels[fac_cvt_i][level] == it + 1 - ? v_d.push_back(1.0) - : v_d.push_back(0.0); - } - } - } - fac_cvt_i++; - } - - ch_ptr = strtok(NULL, " \t"); - i++; - } - - if (flag_na == 0) { - indicator_cvt.push_back(1); - } else { - indicator_cvt.push_back(0); - } - cvt.push_back(v_d); - } - - if (indicator_cvt.empty()) { - n_cvt = 0; - } else { - flag_na = 0; - for (vector<int>::size_type i = 0; i < indicator_cvt.size(); ++i) { - if (indicator_cvt[i] == 0) { - continue; - } - - if (flag_na == 0) { - flag_na = 1; - n_cvt = cvt[i].size(); - } - if (flag_na != 0 && n_cvt != cvt[i].size()) { - cout << "error! number of covariates in row " << i - << " do not match other rows." << endl; - return false; - } - } - } - - infile2.close(); - infile2.clear(); - } - return true; -} - -// WJA Added. -// Read bgen file, the first time. -bool ReadFile_bgen(const string &file_bgen, const set<string> &setSnps, - const gsl_matrix *W, vector<int> &indicator_idv, - vector<int> &indicator_snp, vector<SNPINFO> &snpInfo, - const double &maf_level, const double &miss_level, - const double &hwe_level, const double &r2_level, - size_t &ns_test) { - - debug_msg("entered"); - indicator_snp.clear(); - - ifstream infile(file_bgen.c_str(), ios::binary); - if (!infile) { - cout << "error reading bgen file:" << file_bgen << endl; - return false; - } - - gsl_vector *genotype = gsl_vector_alloc(W->size1); - gsl_vector *genotype_miss = gsl_vector_alloc(W->size1); - gsl_matrix *WtW = gsl_matrix_alloc(W->size2, W->size2); - gsl_matrix *WtWi = gsl_matrix_alloc(W->size2, W->size2); - gsl_vector *Wtx = gsl_vector_alloc(W->size2); - gsl_vector *WtWiWtx = gsl_vector_alloc(W->size2); - gsl_permutation *pmt = gsl_permutation_alloc(W->size2); - - gsl_blas_dgemm(CblasTrans, CblasNoTrans, 1.0, W, W, 0.0, WtW); - int sig; - LUDecomp(WtW, pmt, &sig); - LUInvert(WtW, pmt, WtWi); - - // Read in header. - uint32_t bgen_snp_block_offset; - uint32_t bgen_header_length; - uint32_t bgen_nsamples; - uint32_t bgen_nsnps; - uint32_t bgen_flags; - infile.read(reinterpret_cast<char *>(&bgen_snp_block_offset), 4); - infile.read(reinterpret_cast<char *>(&bgen_header_length), 4); - bgen_snp_block_offset -= 4; - infile.read(reinterpret_cast<char *>(&bgen_nsnps), 4); - bgen_snp_block_offset -= 4; - infile.read(reinterpret_cast<char *>(&bgen_nsamples), 4); - bgen_snp_block_offset -= 4; - infile.ignore(4 + bgen_header_length - 20); - bgen_snp_block_offset -= 4 + bgen_header_length - 20; - infile.read(reinterpret_cast<char *>(&bgen_flags), 4); - bgen_snp_block_offset -= 4; - bool CompressedSNPBlocks = bgen_flags & 0x1; - bool LongIds = bgen_flags & 0x4; - - if (!LongIds) { - return false; - } - - infile.ignore(bgen_snp_block_offset); - - ns_test = 0; - - size_t ns_total = static_cast<size_t>(bgen_nsnps); - - snpInfo.clear(); - string rs; - long int b_pos; - string chr; - string major; - string minor; - string id; - - double v_x, v_w; - int c_idv = 0; - - double maf, geno, geno_old; - size_t n_miss; - size_t n_0, n_1, n_2; - int flag_poly; - - double bgen_geno_prob_AA, bgen_geno_prob_AB; - double bgen_geno_prob_BB, bgen_geno_prob_non_miss; - - // Total number of samples in phenotype file. - size_t ni_total = indicator_idv.size(); - - // Number of samples to use in test. - size_t ni_test = 0; - - uint32_t bgen_N; - uint16_t bgen_LS; - uint16_t bgen_LR; - uint16_t bgen_LC; - uint32_t bgen_SNP_pos; - uint32_t bgen_LA; - std::string bgen_A_allele; - uint32_t bgen_LB; - std::string bgen_B_allele; - uint32_t bgen_P; - size_t unzipped_data_size; - - for (size_t i = 0; i < ni_total; ++i) { - ni_test += indicator_idv[i]; - } - - for (size_t t = 0; t < ns_total; ++t) { - - id.clear(); - rs.clear(); - chr.clear(); - bgen_A_allele.clear(); - bgen_B_allele.clear(); - - infile.read(reinterpret_cast<char *>(&bgen_N), 4); - infile.read(reinterpret_cast<char *>(&bgen_LS), 2); - - id.resize(bgen_LS); - infile.read(&id[0], bgen_LS); - - infile.read(reinterpret_cast<char *>(&bgen_LR), 2); - rs.resize(bgen_LR); - infile.read(&rs[0], bgen_LR); - - infile.read(reinterpret_cast<char *>(&bgen_LC), 2); - chr.resize(bgen_LC); - infile.read(&chr[0], bgen_LC); - - infile.read(reinterpret_cast<char *>(&bgen_SNP_pos), 4); - - infile.read(reinterpret_cast<char *>(&bgen_LA), 4); - bgen_A_allele.resize(bgen_LA); - infile.read(&bgen_A_allele[0], bgen_LA); - - infile.read(reinterpret_cast<char *>(&bgen_LB), 4); - bgen_B_allele.resize(bgen_LB); - infile.read(&bgen_B_allele[0], bgen_LB); - - // Should we switch according to MAF? - minor = bgen_B_allele; - major = bgen_A_allele; - b_pos = static_cast<long int>(bgen_SNP_pos); - - uint16_t unzipped_data[3 * bgen_N]; - - if (setSnps.size() != 0 && setSnps.count(rs) == 0) { - SNPINFO sInfo = { - "-9", rs, -9, -9, minor, major, static_cast<size_t>(-9), - -9, (long int)-9}; - - snpInfo.push_back(sInfo); - indicator_snp.push_back(0); - if (CompressedSNPBlocks) - infile.read(reinterpret_cast<char *>(&bgen_P), 4); - else - bgen_P = 6 * bgen_N; - - infile.ignore(static_cast<size_t>(bgen_P)); - - continue; - } - - if (CompressedSNPBlocks) { - infile.read(reinterpret_cast<char *>(&bgen_P), 4); - uint8_t zipped_data[bgen_P]; - - unzipped_data_size = 6 * bgen_N; - - infile.read(reinterpret_cast<char *>(zipped_data), bgen_P); - int result = uncompress(reinterpret_cast<Bytef *>(unzipped_data), - reinterpret_cast<uLongf *>(&unzipped_data_size), - reinterpret_cast<Bytef *>(zipped_data), - static_cast<uLong>(bgen_P)); - assert(result == Z_OK); - - } else { - bgen_P = 6 * bgen_N; - infile.read(reinterpret_cast<char *>(unzipped_data), bgen_P); - } - - maf = 0; - n_miss = 0; - flag_poly = 0; - geno_old = -9; - n_0 = 0; - n_1 = 0; - n_2 = 0; - c_idv = 0; - gsl_vector_set_zero(genotype_miss); - for (size_t i = 0; i < bgen_N; ++i) { - - // CHECK this set correctly! - if (indicator_idv[i] == 0) { - continue; - } - - bgen_geno_prob_AA = static_cast<double>(unzipped_data[i * 3]) / 32768.0; - bgen_geno_prob_AB = - static_cast<double>(unzipped_data[i * 3 + 1]) / 32768.0; - bgen_geno_prob_BB = - static_cast<double>(unzipped_data[i * 3 + 2]) / 32768.0; - bgen_geno_prob_non_miss = - bgen_geno_prob_AA + bgen_geno_prob_AB + bgen_geno_prob_BB; - - // CHECK 0.1 OK. - if (bgen_geno_prob_non_miss < 0.9) { - gsl_vector_set(genotype_miss, c_idv, 1); - n_miss++; - c_idv++; - continue; - } - - bgen_geno_prob_AA /= bgen_geno_prob_non_miss; - bgen_geno_prob_AB /= bgen_geno_prob_non_miss; - bgen_geno_prob_BB /= bgen_geno_prob_non_miss; - - geno = 2.0 * bgen_geno_prob_BB + bgen_geno_prob_AB; - if (geno >= 0 && geno <= 0.5) { - n_0++; - } - if (geno > 0.5 && geno < 1.5) { - n_1++; - } - if (geno >= 1.5 && geno <= 2.0) { - n_2++; - } - - gsl_vector_set(genotype, c_idv, geno); - - // CHECK WHAT THIS DOES. - if (flag_poly == 0) { - geno_old = geno; - flag_poly = 2; - } - if (flag_poly == 2 && geno != geno_old) { - flag_poly = 1; - } - - maf += geno; - - c_idv++; - } - - maf /= 2.0 * static_cast<double>(ni_test - n_miss); - - SNPINFO sInfo = {chr, rs, -9, b_pos, - minor, major, n_miss, (double)n_miss / (double)ni_test, - maf}; - snpInfo.push_back(sInfo); - - if ((double)n_miss / (double)ni_test > miss_level) { - indicator_snp.push_back(0); - continue; - } - - if ((maf < maf_level || maf > (1.0 - maf_level)) && maf_level != -1) { - indicator_snp.push_back(0); - continue; - } - - if (flag_poly != 1) { - indicator_snp.push_back(0); - continue; - } - - if (hwe_level != 0 && maf_level != -1) { - if (CalcHWE(n_0, n_2, n_1) < hwe_level) { - indicator_snp.push_back(0); - continue; - } - } - - // Filter SNP if it is correlated with W - // unless W has only one column, of 1s. - for (size_t i = 0; i < genotype->size; ++i) { - if (gsl_vector_get(genotype_miss, i) == 1) { - geno = maf * 2.0; - gsl_vector_set(genotype, i, geno); - } - } - - gsl_blas_dgemv(CblasTrans, 1.0, W, genotype, 0.0, Wtx); - gsl_blas_dgemv(CblasNoTrans, 1.0, WtWi, Wtx, 0.0, WtWiWtx); - gsl_blas_ddot(genotype, genotype, &v_x); - gsl_blas_ddot(Wtx, WtWiWtx, &v_w); - - if (W->size2 != 1 && v_w / v_x >= r2_level) { - indicator_snp.push_back(0); - continue; - } - - indicator_snp.push_back(1); - ns_test++; - } - - return true; -} - -// Read oxford genotype file and calculate kinship matrix. -bool bgenKin(const string &file_oxford, vector<int> &indicator_snp, - const int k_mode, const int display_pace, gsl_matrix *matrix_kin) { - debug_msg("entered"); - string file_bgen = file_oxford; - ifstream infile(file_bgen.c_str(), ios::binary); - if (!infile) { - cout << "error reading bgen file:" << file_bgen << endl; - return false; - } - - // Read in header. - uint32_t bgen_snp_block_offset; - uint32_t bgen_header_length; - uint32_t bgen_nsamples; - uint32_t bgen_nsnps; - uint32_t bgen_flags; - infile.read(reinterpret_cast<char *>(&bgen_snp_block_offset), 4); - infile.read(reinterpret_cast<char *>(&bgen_header_length), 4); - bgen_snp_block_offset -= 4; - infile.read(reinterpret_cast<char *>(&bgen_nsnps), 4); - bgen_snp_block_offset -= 4; - infile.read(reinterpret_cast<char *>(&bgen_nsamples), 4); - bgen_snp_block_offset -= 4; - infile.ignore(4 + bgen_header_length - 20); - bgen_snp_block_offset -= 4 + bgen_header_length - 20; - infile.read(reinterpret_cast<char *>(&bgen_flags), 4); - bgen_snp_block_offset -= 4; - bool CompressedSNPBlocks = bgen_flags & 0x1; - - infile.ignore(bgen_snp_block_offset); - - double bgen_geno_prob_AA, bgen_geno_prob_AB; - double bgen_geno_prob_BB, bgen_geno_prob_non_miss; - - uint32_t bgen_N; - uint16_t bgen_LS; - uint16_t bgen_LR; - uint16_t bgen_LC; - uint32_t bgen_SNP_pos; - uint32_t bgen_LA; - std::string bgen_A_allele; - uint32_t bgen_LB; - std::string bgen_B_allele; - uint32_t bgen_P; - size_t unzipped_data_size; - string id; - string rs; - string chr; - double genotype; - - size_t n_miss; - double d, geno_mean, geno_var; - - size_t ni_total = matrix_kin->size1; - gsl_vector *geno = gsl_vector_alloc(ni_total); - gsl_vector *geno_miss = gsl_vector_alloc(ni_total); - - size_t ns_test = 0; - for (size_t t = 0; t < indicator_snp.size(); ++t) { - - if (t % display_pace == 0 || t == (indicator_snp.size() - 1)) { - ProgressBar("Reading bgen SNPs ", t, indicator_snp.size() - 1); - } - - id.clear(); - rs.clear(); - chr.clear(); - bgen_A_allele.clear(); - bgen_B_allele.clear(); - - infile.read(reinterpret_cast<char *>(&bgen_N), 4); - infile.read(reinterpret_cast<char *>(&bgen_LS), 2); - - id.resize(bgen_LS); - infile.read(&id[0], bgen_LS); - - infile.read(reinterpret_cast<char *>(&bgen_LR), 2); - rs.resize(bgen_LR); - infile.read(&rs[0], bgen_LR); - - infile.read(reinterpret_cast<char *>(&bgen_LC), 2); - chr.resize(bgen_LC); - infile.read(&chr[0], bgen_LC); - - infile.read(reinterpret_cast<char *>(&bgen_SNP_pos), 4); - - infile.read(reinterpret_cast<char *>(&bgen_LA), 4); - bgen_A_allele.resize(bgen_LA); - infile.read(&bgen_A_allele[0], bgen_LA); - - infile.read(reinterpret_cast<char *>(&bgen_LB), 4); - bgen_B_allele.resize(bgen_LB); - infile.read(&bgen_B_allele[0], bgen_LB); - - uint16_t unzipped_data[3 * bgen_N]; - - if (indicator_snp[t] == 0) { - if (CompressedSNPBlocks) - infile.read(reinterpret_cast<char *>(&bgen_P), 4); - else - bgen_P = 6 * bgen_N; - - infile.ignore(static_cast<size_t>(bgen_P)); - - continue; - } - - if (CompressedSNPBlocks) { - infile.read(reinterpret_cast<char *>(&bgen_P), 4); - uint8_t zipped_data[bgen_P]; - - unzipped_data_size = 6 * bgen_N; - - infile.read(reinterpret_cast<char *>(zipped_data), bgen_P); - - int result = uncompress(reinterpret_cast<Bytef *>(unzipped_data), - reinterpret_cast<uLongf *>(&unzipped_data_size), - reinterpret_cast<Bytef *>(zipped_data), - static_cast<uLong>(bgen_P)); - assert(result == Z_OK); - - } else { - - bgen_P = 6 * bgen_N; - infile.read(reinterpret_cast<char *>(unzipped_data), bgen_P); - } - - geno_mean = 0.0; - n_miss = 0; - geno_var = 0.0; - gsl_vector_set_all(geno_miss, 0); - - for (size_t i = 0; i < bgen_N; ++i) { - - bgen_geno_prob_AA = static_cast<double>(unzipped_data[i * 3]) / 32768.0; - bgen_geno_prob_AB = - static_cast<double>(unzipped_data[i * 3 + 1]) / 32768.0; - bgen_geno_prob_BB = - static_cast<double>(unzipped_data[i * 3 + 2]) / 32768.0; - // WJA - bgen_geno_prob_non_miss = - bgen_geno_prob_AA + bgen_geno_prob_AB + bgen_geno_prob_BB; - if (bgen_geno_prob_non_miss < 0.9) { - gsl_vector_set(geno_miss, i, 0.0); - n_miss++; - } else { - - bgen_geno_prob_AA /= bgen_geno_prob_non_miss; - bgen_geno_prob_AB /= bgen_geno_prob_non_miss; - bgen_geno_prob_BB /= bgen_geno_prob_non_miss; - - genotype = 2.0 * bgen_geno_prob_BB + bgen_geno_prob_AB; - - gsl_vector_set(geno, i, genotype); - gsl_vector_set(geno_miss, i, 1.0); - geno_mean += genotype; - geno_var += genotype * genotype; - } - } - - geno_mean /= (double)(ni_total - n_miss); - geno_var += geno_mean * geno_mean * (double)n_miss; - geno_var /= (double)ni_total; - geno_var -= geno_mean * geno_mean; - - for (size_t i = 0; i < ni_total; ++i) { - if (gsl_vector_get(geno_miss, i) == 0) { - gsl_vector_set(geno, i, geno_mean); - } - } - - gsl_vector_add_constant(geno, -1.0 * geno_mean); - - if (geno_var != 0) { - if (k_mode == 1) { - gsl_blas_dsyr(CblasUpper, 1.0, geno, matrix_kin); - } else if (k_mode == 2) { - gsl_blas_dsyr(CblasUpper, 1.0 / geno_var, geno, matrix_kin); - } else { - cout << "Unknown kinship mode." << endl; - } - } - - ns_test++; - } - cout << endl; - - gsl_matrix_scale(matrix_kin, 1.0 / (double)ns_test); - - for (size_t i = 0; i < ni_total; ++i) { - for (size_t j = 0; j < i; ++j) { - d = gsl_matrix_get(matrix_kin, j, i); - gsl_matrix_set(matrix_kin, i, j, d); - } - } - - gsl_vector_free(geno); - gsl_vector_free(geno_miss); - - infile.close(); - infile.clear(); - - return true; -} - // Read header to determine which column contains which item. bool ReadHeader_io(const string &line, HEADER &header) { debug_msg("entered"); |