Changing namings to bimbam to make clearer

5 files changed, 26 insertions, 23 deletions

diff --git a/src/gemma.cpp b/src/gemma.cpp
index 01e80f7..38b4913 100644
--- a/src/gemma.cpp
+++ b/src/gemma.cpp
@@ -2901,7 +2901,7 @@ void GEMMA::BatchRun(PARAM &cPar) {
     // run bvsr if rho==1
     if (cPar.rho_min == 1 && cPar.rho_max == 1) {
       // read genotypes X (not UtX)
-      cPar.ReadGenotypes(UtX, G, false);
+      cPar.ReadBIMBAMGenotypes(UtX, G, false);
 
       // perform BSLMM analysis
       BSLMM cBslmm;
@@ -2919,7 +2919,7 @@ void GEMMA::BatchRun(PARAM &cPar) {
 
       // read relatedness matrix G
       if (!(cPar.file_kin).empty()) {
-        cPar.ReadGenotypes(UtX, G, false);
+        cPar.ReadBIMBAMGenotypes(UtX, G, false);
 
         // read relatedness matrix G
         ReadFile_kin(cPar.file_kin, cPar.indicator_idv, cPar.mapID2num,
@@ -2933,7 +2933,7 @@ void GEMMA::BatchRun(PARAM &cPar) {
         CenterMatrix(G);
         validate_K(G);
       } else {
-        cPar.ReadGenotypes(UtX, G, true);
+        cPar.ReadBIMBAMGenotypes(UtX, G, true);
       }
 
       // eigen-decomposition and calculate trace_G
@@ -3011,7 +3011,7 @@ void GEMMA::BatchRun(PARAM &cPar) {
       // run bvsr if rho==1
       if (cPar.rho_min == 1 && cPar.rho_max == 1) {
         // read genotypes X (not UtX)
-        cPar.ReadGenotypes(UtX, G, false);
+        cPar.ReadBIMBAMGenotypes(UtX, G, false);
 
         // perform BSLMM analysis
         BSLMM cBslmm;
@@ -3030,7 +3030,7 @@ void GEMMA::BatchRun(PARAM &cPar) {
 
         // read relatedness matrix G
         if (!(cPar.file_kin).empty()) {
-          cPar.ReadGenotypes(UtX, G, false);
+          cPar.ReadBIMBAMGenotypes(UtX, G, false);
 
           // read relatedness matrix G
           ReadFile_kin(cPar.file_kin, cPar.indicator_idv, cPar.mapID2num,
@@ -3045,7 +3045,7 @@ void GEMMA::BatchRun(PARAM &cPar) {
           validate_K(G);
 
         } else {
-          cPar.ReadGenotypes(UtX, G, true);
+          cPar.ReadBIMBAMGenotypes(UtX, G, true);
         }
 
         // eigen-decomposition and calculate trace_G
diff --git a/src/gemma_io.cpp b/src/gemma_io.cpp
index b1bc368..6d33e00 100644
--- a/src/gemma_io.cpp
+++ b/src/gemma_io.cpp
@@ -688,14 +688,14 @@ bool ReadFile_fam(const string &file_fam, vector<vector<int>> &indicator_pheno,
 The function returns a `bool` indicating success/failure, but the real outputs are these three modified reference parameters.
 */
 
-bool ReadFile_geno(const string &file_geno, const set<string> &setSnps,
-                   const gsl_matrix *W, const vector<int> &indicator_idv,
-                   vector<int> &indicator_snp, const double &maf_level,
-                   const double &miss_level, const double &hwe_level,
-                   const double &r2_level, map<string, string> &mapRS2chr,
-                   map<string, long int> &mapRS2bp,
-                   map<string, double> &mapRS2cM, vector<SNPINFO> &snpInfo,
-                   size_t &ns_test) {
+bool ReadFile_bimbam_geno(const string &file_geno, const set<string> &setSnps,
+                          const gsl_matrix *W, const vector<int> &indicator_idv,
+                          vector<int> &indicator_snp, const double &maf_level,
+                          const double &miss_level, const double &hwe_level,
+                          const double &r2_level, map<string, string> &mapRS2chr,
+                          map<string, long int> &mapRS2bp,
+                          map<string, double> &mapRS2cM, vector<SNPINFO> &snpInfo,
+                          size_t &ns_test) {
   checkpoint("read-file-geno",file_geno);
   debug_msg("entered");
   indicator_snp.clear();
diff --git a/src/gemma_io.h b/src/gemma_io.h
index 116c1a5..139f379 100644
--- a/src/gemma_io.h
+++ b/src/gemma_io.h
@@ -59,7 +59,7 @@ bool ReadFile_pheno(const string &file_pheno,
 bool ReadFile_column(const string &file_pheno, vector<int> &indicator_idv,
                      vector<double> &pheno, const int &p_column);
 
-bool ReadFile_geno(const string &file_geno, const set<string> &setSnps,
+bool ReadFile_bimbam_geno(const string &file_geno, const set<string> &setSnps,
                    const gsl_matrix *W, const vector<int> &indicator_idv,
                    vector<int> &indicator_snp, const double &maf_level,
                    const double &miss_level, const double &hwe_level,
diff --git a/src/param.cpp b/src/param.cpp
index 9755579..7e7ff6e 100644
--- a/src/param.cpp
+++ b/src/param.cpp
@@ -318,9 +318,10 @@ void PARAM::ReadFiles(void) {
 
     trim_individuals(indicator_idv, ni_max);
     trim_individuals(indicator_cvt, ni_max);
-    if (ReadFile_geno(file_geno, setSnps, W2, indicator_idv, indicator_snp,
-                      maf_level, miss_level, hwe_level, r2_level, mapRS2chr,
-                      mapRS2bp, mapRS2cM, snpInfo, ns_test) == false) {
+    // The following reads the geno file to get the SNPs
+    if (is_bimbam && ReadFile_bimbam_geno(file_geno, setSnps, W2, indicator_idv, indicator_snp,
+                                          maf_level, miss_level, hwe_level, r2_level, mapRS2chr,
+                                          mapRS2bp, mapRS2cM, snpInfo, ns_test) == false) {
       error = true;
       return;
     }
@@ -424,7 +425,7 @@ void PARAM::ReadFiles(void) {
     string file_name;
     size_t ns_test_tmp;
     while (!safeGetline(infile, file_name).eof()) {
-      if (ReadFile_geno(file_name, setSnps, W4, indicator_idv, indicator_snp,
+      if (ReadFile_bimbam_geno(file_name, setSnps, W4, indicator_idv, indicator_snp,
                         maf_level, miss_level, hwe_level, r2_level, mapRS2chr,
                         mapRS2bp, mapRS2cM, snpInfo, ns_test_tmp) == false) {
         error = true;
@@ -1262,7 +1263,7 @@ void PARAM::PrintSummary() {
   return;
 }
 
-void PARAM::ReadGenotypes(gsl_matrix *UtX, gsl_matrix *K, const bool calc_K) {
+void PARAM::ReadBIMBAMGenotypes(gsl_matrix *UtX, gsl_matrix *K, const bool calc_K) {
   string file_str;
 
   if (!file_bfile.empty()) {
@@ -1272,8 +1273,8 @@ void PARAM::ReadGenotypes(gsl_matrix *UtX, gsl_matrix *K, const bool calc_K) {
       error = true;
     }
   } else {
-    if (ReadFile_geno(file_geno, indicator_idv, indicator_snp, UtX, K,
-                      calc_K) == false) {
+      // Read BIMBAM. Not supposed to be mdb
+      if (is_mdb || ReadFile_geno(file_geno, indicator_idv, indicator_snp, UtX, K, calc_K) == false) {
       error = true;
     }
   }
diff --git a/src/param.h b/src/param.h
index 8d2fba3..0b8ed97 100644
--- a/src/param.h
+++ b/src/param.h
@@ -338,7 +338,7 @@ public:
   void CheckParam();
   void CheckData();
   void PrintSummary();
-  void ReadGenotypes(gsl_matrix *UtX, gsl_matrix *K, const bool calc_K);
+  void ReadBIMBAMGenotypes(gsl_matrix *UtX, gsl_matrix *K, const bool calc_K);
   void CheckCvt();
   void CopyCvt(gsl_matrix *W);
   void CopyA(size_t flag, gsl_matrix *A);
@@ -372,4 +372,6 @@ public:
 
 size_t GetabIndex(const size_t a, const size_t b, const size_t n_cvt);
 
+#define is_bimbam (!is_mdb)
+
 #endif