diff options
Diffstat (limited to 'src/param.h')
| -rw-r--r-- | src/param.h | 30 |
1 files changed, 23 insertions, 7 deletions
diff --git a/src/param.h b/src/param.h index 33e2431..45d8c0f 100644 --- a/src/param.h +++ b/src/param.h @@ -19,12 +19,15 @@ #ifndef __PARAM_H__ #define __PARAM_H__ +#include "debug.h" #include "gsl/gsl_matrix.h" #include "gsl/gsl_vector.h" #include <map> #include <set> #include <vector> +#define K_BATCH_SIZE 10000 // #snps used for batched K + using namespace std; class SNPINFO { @@ -110,6 +113,7 @@ class PARAM { public: // IO-related parameters. bool mode_silence; + bool mode_debug = false; int a_mode; // Analysis mode, 1/2/3/4 for Frequentist tests int k_mode; // Kinship read mode: 1: n by n matrix, 2: id/id/k_value; vector<size_t> p_column; // Which phenotype column needs analysis. @@ -135,12 +139,14 @@ public: string file_bf, file_hyp; string path_out; - string file_epm; // Estimated parameter file. - string file_ebv; // Estimated breeding value file. - string file_log; // Log file containing mean estimate. - string file_read; // File containing total number of reads. - string file_gene; // Gene expression file. - string file_snps; // File containing analyzed SNPs or genes. + string file_epm; // Estimated parameter file. + string file_ebv; // Estimated breeding value file. + string file_log; // Log file containing mean estimate. + string file_read; // File containing total number of reads. + string file_gene; // Gene expression file. + string file_snps; // File containing analyzed SNPs or genes. + string file_ksnps; // File SNPs for computing K + string file_gwasnps; // File SNPs for computing GWAS // WJA added. string file_oxford; @@ -152,6 +158,7 @@ public: double r2_level; // LMM-related parameters. + string loco; double l_min; double l_max; size_t n_region; @@ -215,6 +222,7 @@ public: // Number of individuals. size_t ni_total, ni_test, ni_cvt, ni_study, ni_ref; + size_t ni_max = 0; // -nind switch for testing purposes // Number of observed and missing phenotypes. size_t np_obs, np_miss; @@ -305,7 +313,9 @@ public: vector<SNPINFO> snpInfo; // Record SNP information. vector<vector<SNPINFO>> msnpInfo; // Record SNP information. - set<string> setSnps; // Set of snps for analysis. + set<string> setSnps; // Set of snps for analysis (-snps). + set<string> setKSnps; // Set of snps for K (-ksnps and LOCO) + set<string> setGWASnps; // Set of snps for GWA (-gwasnps and LOCO) // Constructor. PARAM(); @@ -351,4 +361,10 @@ public: size_t GetabIndex(const size_t a, const size_t b, const size_t n_cvt); +// Helpers for checking parameters +#define enforce_fexists(fn, msg) \ + if (!fn.empty()) \ + enforce_msg(stat(fn.c_str(), &fileInfo) == 0, \ + ((std::string(__STRING(fn)) + ": " + msg).c_str())); + #endif |