avoid using global variables for local scopes in bed

Author: gf777

gfalibs

@@ -36,8 +36,6 @@ class Input {
 
     std::vector<Instruction> instructions;
 
-    unsigned int begin = 0, end = 0;
-    
 public:
 
     void load(UserInputGfastats userInput);

include/input.h

@@ -61,43 +61,34 @@ void Input::read(InSequences& inSequences) {
     if (!userInput.inBedInclude.empty() || userInput.pipeType == 'i') {
 
         StreamObj streamObj;
-        
         stream = streamObj.openStream(userInput, 'i');
 
         while (getline(*stream, line)) {
 
+            uint64_t begin = 0, end = 0;
             std::istringstream iss(line);
             iss >> bedHeader >> begin >> end;
-            
             userInput.bedIncludeList.pushCoordinates(bedHeader, begin, end);
-            begin = 0, end = 0;
-            
         }
-        
         lg.verbose("Finished reading BED include list");
-        
     }
 
     BedCoordinates bedExcludeList;
 
     if (!userInput.inBedExclude.empty() || userInput.pipeType == 'e') {
 
         StreamObj streamObj;
-        
         stream = streamObj.openStream(userInput, 'e');
 
         while (getline(*stream, line)) {
 
+            uint64_t begin = 0, end = 0;
             std::istringstream iss(line);
             iss >> bedHeader >> begin >> end;
 
             bedExcludeList.pushCoordinates(bedHeader, begin, end);
-            begin = 0, end = 0;
-            
         }
-        
         lg.verbose("Finished reading BED exclude list");
-        
     }
 
     if (!userInput.inSequence.empty() || userInput.pipeType == 'f') {