integration of SetRegion into BamMultiReader

[bamtools.git] / bamtools_utilities.h

diff --git a/bamtools_utilities.h b/bamtools_utilities.h
index 7d655e69fe2b089bdd97ca90d4a7b92a2273288a..4f6928b6832fb9a3b2299626fed22b40e5611b56 100644 (file)
--- a/bamtools_utilities.h
+++ b/bamtools_utilities.h
@@ -12,29 +12,26 @@
 #define BAMTOOLS_UTILITIES_H
 
 #include <string>
+#include "BamAux.h"
 
 namespace BamTools {
 
 class BamReader;
 class BamMultiReader;
 
-struct Region {
-    int StartChromID;
-    int StopChromID;
-    int StartPosition;
-    int StopPosition;
-};
-
 class Utilities {
   
     public:                          
         // Parses a region string, uses reader to do validation (valid ID's, positions), stores in Region struct
         // Returns success (true/false)
-        static bool ParseRegionString(const std::string& regionString, const BamReader& reader, Region& region);
+        static bool ParseRegionString(const std::string& regionString, const BamReader& reader, BamRegion& region);
         // Same as above, but accepts a BamMultiReader
-        static bool ParseRegionString(const std::string& regionString, const BamMultiReader& reader, Region& region);
+        static bool ParseRegionString(const std::string& regionString, const BamMultiReader& reader, BamRegion& region);
+
+        // check if a file exists
+        static bool FileExists(const std::string& fname); 
 };
 
 } // namespace BamTools
   
-#endif // BAMTOOLS_UTILITIES_H
\ No newline at end of file
+#endif // BAMTOOLS_UTILITIES_H