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| author | Pjotr Prins | 2025-11-23 14:09:24 +0100 |
|---|---|---|
| committer | Pjotr Prins | 2025-11-23 14:09:24 +0100 |
| commit | 8229e4e18dddae7bf570ca37767ff39726eede45 (patch) | |
| tree | 17986d394dbc3a03da9bebe6eba96119dff571dd /src/gemma_io.cpp | |
| parent | ff196955e3ca5bdd671a44f852f42323d3828be2 (diff) | |
| download | pangemma-8229e4e18dddae7bf570ca37767ff39726eede45.tar.gz | |
Diffstat (limited to 'src/gemma_io.cpp')
| -rw-r--r-- | src/gemma_io.cpp | 10 |
1 files changed, 6 insertions, 4 deletions
diff --git a/src/gemma_io.cpp b/src/gemma_io.cpp index fddfd79..7d1f0ca 100644 --- a/src/gemma_io.cpp +++ b/src/gemma_io.cpp @@ -698,7 +698,7 @@ bool ReadFile_geno(const string &file_geno, const set<string> &setSnps, gsl_vector *genotype = gsl_vector_safe_alloc(W->size1); gsl_vector *genotype_miss = gsl_vector_safe_alloc(W->size1); - gsl_matrix *WtW = gsl_matrix_safe_alloc(W->size2, W->size2); + gsl_matrix *WtW = gsl_matrix_safe_alloc(W->size2, W->size2); // Covariates gsl_matrix *WtWi = gsl_matrix_safe_alloc(W->size2, W->size2); gsl_vector *Wtx = gsl_vector_safe_alloc(W->size2); gsl_vector *WtWiWtx = gsl_vector_safe_alloc(W->size2); @@ -746,13 +746,14 @@ bool ReadFile_geno(const string &file_geno, const set<string> &setSnps, // cerr << key << endl; // } while (!safe_get_line(infile, line).eof()) { - // cout << line; + // fetch SNP annotation ch_ptr = strtok_safe2((char *)line.c_str(), " ,\t",infilen); rs = ch_ptr; ch_ptr = strtok_safe2(NULL, " ,\t",infilen); minor = ch_ptr; ch_ptr = strtok_safe2(NULL, " ,\t",infilen); major = ch_ptr; + // genotypes get read below if (setSnps.size() != 0 && setSnps.count(rs) == 0) { // if SNP in geno but not in -snps we add an missing value @@ -792,11 +793,12 @@ bool ReadFile_geno(const string &file_geno, const set<string> &setSnps, c_idv = 0; gsl_vector_set_zero(genotype_miss); auto infilen = file_geno.c_str(); - for (int i = 0; i < ni_total; ++i) { + for (int i = 0; i < ni_total; ++i) { // read genotypes ch_ptr = strtok_safe2(NULL, " ,\t",(string("To many individuals/strains/genometypes in pheno file for ")+infilen).c_str()); if (indicator_idv[i] == 0) continue; + // annotate missing genotypes enforce_msg(ch_ptr,"Problem reading geno file (not enough genotypes in line)"); if (strcmp(ch_ptr, "NA") == 0) { gsl_vector_set(genotype_miss, c_idv, 1); @@ -900,7 +902,7 @@ bool ReadFile_geno(const string &file_geno, const set<string> &setSnps, if (max_g != 2.0) warning_msg("The maximum genotype value is not 2.0 - this is not the BIMBAM standard and will skew l_lme and effect sizes"); - gsl_vector_free(genotype); + gsl_vector_free(genotype); // we don't hang on to the genotypes gsl_vector_free(genotype_miss); gsl_matrix_free(WtW); gsl_matrix_free(WtWi); |