Fix issue with missing raw input filename when running single command

DecodeGenetics · Dec 20, 2021 · 8aac3b9 · 8aac3b9
1 parent 78844fb
commit 8aac3b9
Showing 1 changed file with 4 additions and 2 deletions.
diff --git a/src/Ratatosk.cpp b/src/Ratatosk.cpp
@@ -435,9 +435,11 @@ bool check_ProgramOptions(Correct_Opt& opt) {
 
     if (!opt.filenames_helper_long_in.empty()) ret = ret && check_files(opt.filenames_helper_long_in, true, true);
     if (!opt.filenames_short_all.empty()) ret = ret && check_files(opt.filenames_short_all, true, true);
-    if (!opt.filenames_long_raw.empty()) ret = ret && check_files(opt.filenames_long_raw, true, true);
     if (!opt.filenames_short_phase.empty()) ret = ret && check_files(opt.filenames_short_phase, true, true);
     if (!opt.filenames_long_phase.empty()) ret = ret && check_files(opt.filenames_long_phase, true, true);
+
+    if (!opt.filenames_long_raw.empty()) ret = ret && check_files(opt.filenames_long_raw, true, true);
+    else opt.filenames_long_raw = opt.filenames_long_in;
 
     if (opt.filename_long_out.length() == 0){
 
@@ -1288,4 +1290,4 @@ int main(int argc, char *argv[]) {
             }
         }
     }
-}
+}