-// string hardName = globaldata->getHard();
-// string hardFilter = "";
-//
-// ifstream fileHandle;
-// openInputFile(hardName, fileHandle);
-//
-// fileHandle >> hardFilter;
-//
-// if(hardFilter.length() != filter.length()){
-// cout << "The hard filter is not the same length as the alignment: Hard filter will not be applied." << endl;
-// }
-// else{
-// filter = hardFilter;
-// }
+ string hardName = globaldata->getHard();
+ string hardFilter = "";
+
+ ifstream fileHandle;
+ openInputFile(hardName, fileHandle);
+
+ fileHandle >> hardFilter;
+
+ if(hardFilter.length() != filter.length()){
+ cout << "The hard filter is not the same length as the alignment: Hard filter will not be applied." << endl;
+ }
+ else{
+ filter = hardFilter;
+ }