avoid using global variables for local scopes in bed

vgl-hub · Mar 19, 2024 · 3f9cbd0 · 3f9cbd0
1 parent 52563fd
commit 3f9cbd0
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Showing 3 changed files with 3 additions and 14 deletions.
diff --git a/gfalibs b/gfalibs
diff --git a/include/input.h b/include/input.h
@@ -36,8 +36,6 @@ class Input {
 
     std::vector<Instruction> instructions;
 
-    unsigned int begin = 0, end = 0;
-
 public:
 
     void load(UserInputGfastats userInput);

diff --git a/src/input.cpp b/src/input.cpp
@@ -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') {
-Original file line number
+Diff line change
@@ Expand Up / @@ -36,8 +36,6 @@ class Input { @@
         std::vector<Instruction> instructions;
-        unsigned int begin = 0, end = 0;
     public:
         void load(UserInputGfastats userInput);
@@ Expand Down @@