Removed Oxford format as per genetics-statistics#46

genenetwork · Oct 5, 2017 · 4d5cb9a · 4d5cb9a
1 parent 86323cc
commit 4d5cb9a
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Showing 10 changed files with 5 additions and 1,931 deletions.
diff --git a/src/gemma.cpp b/src/gemma.cpp
@@ -310,11 +310,6 @@ void GEMMA::PrintHelp(size_t option) {
     cout << "                  rs#2, base_position, chr_number" << endl;
     cout << "                  ..." << endl;
 
-    // WJA added.
-    cout << " -oxford    [prefix]       "
-         << " specify input Oxford genotype bgen file prefix." << endl;
-    cout << "          requires: *.bgen, *.sample files" << endl;
-
     cout << " -gxe      [filename]     "
          << " specify input file that contains a column of environmental "
             "factor for g by e tests"
@@ -793,18 +788,6 @@ void GEMMA::Assign(int argc, char **argv, PARAM &cPar) {
       str.clear();
       str.assign(argv[i]);
       cPar.file_anno = str;
-    }
-
-    // WJA added.
-    else if (strcmp(argv[i], "-oxford") == 0 ||
-             strcmp(argv[i], "--oxford") == 0 || strcmp(argv[i], "-x") == 0) {
-      if (argv[i + 1] == NULL || argv[i + 1][0] == '-') {
-        continue;
-      }
-      ++i;
-      str.clear();
-      str.assign(argv[i]);
-      cPar.file_oxford = str;
     } else if (strcmp(argv[i], "-gxe") == 0) {
       if (argv[i + 1] == NULL || argv[i + 1][0] == '-') {
         continue;
@@ -2047,8 +2030,6 @@ void GEMMA::BatchRun(PARAM &cPar) {
                         &Y_col.vector); // y is the predictor, not the phenotype
       } else if (!cPar.file_bfile.empty()) {
         cLm.AnalyzePlink(W, &Y_col.vector);
-      } else if (!cPar.file_oxford.empty()) {
-        cLm.Analyzebgen(W, &Y_col.vector);
       } else {
         cLm.AnalyzeBimbam(W, &Y_col.vector);
       }
@@ -2763,17 +2744,12 @@ void GEMMA::BatchRun(PARAM &cPar) {
                                    &Y_col.vector, env);
             }
           }
-          // WJA added
-          else if (!cPar.file_oxford.empty()) {
-            cLmm.Analyzebgen(U, eval, UtW, &UtY_col.vector, W, &Y_col.vector);
+          if (cPar.file_gxe.empty()) {
+            cLmm.AnalyzeBimbam(U, eval, UtW, &UtY_col.vector, W,
+                               &Y_col.vector, cPar.setGWASnps);
           } else {
-            if (cPar.file_gxe.empty()) {
-              cLmm.AnalyzeBimbam(U, eval, UtW, &UtY_col.vector, W,
-                                 &Y_col.vector, cPar.setGWASnps);
-            } else {
-              cLmm.AnalyzeBimbamGXE(U, eval, UtW, &UtY_col.vector, W,
-                                    &Y_col.vector, env);
-            }
+            cLmm.AnalyzeBimbamGXE(U, eval, UtW, &UtY_col.vector, W,
+                                  &Y_col.vector, env);
           }
 
           cLmm.WriteFiles();
@@ -2788,8 +2764,6 @@ void GEMMA::BatchRun(PARAM &cPar) {
             } else {
               cMvlmm.AnalyzePlinkGXE(U, eval, UtW, UtY, env);
             }
-          } else if (!cPar.file_oxford.empty()) {
-            cMvlmm.Analyzebgen(U, eval, UtW, UtY);
           } else {
             if (cPar.file_gxe.empty()) {
               cMvlmm.AnalyzeBimbam(U, eval, UtW, UtY);