Major update to BamTools version 1.0

[bamtools.git] / src / utils / bamtools_utilities.h

diff --git a/src/utils/bamtools_utilities.h b/src/utils/bamtools_utilities.h
index 4f6928b6832fb9a3b2299626fed22b40e5611b56..3701690fbc6f6a3499dcd3f744d04b5e8e06024f 100644 (file)
--- a/src/utils/bamtools_utilities.h
+++ b/src/utils/bamtools_utilities.h
@@ -3,7 +3,7 @@
 // Marth Lab, Department of Biology, Boston College
 // All rights reserved.
 // ---------------------------------------------------------------------------
-// Last modified: 2 June 2010
+// Last modified: 26 January 2011
 // ---------------------------------------------------------------------------
 // Provides general utilities used by BamTools sub-tools.
 // ***************************************************************************
@@ -11,25 +11,39 @@
 #ifndef BAMTOOLS_UTILITIES_H
 #define BAMTOOLS_UTILITIES_H
 
+#include <api/BamAux.h>
+#include <utils/utils_global.h>
+#include <cassert>
+#include <stdexcept>
 #include <string>
-#include "BamAux.h"
+
+#define BAMTOOLS_ASSERT_UNREACHABLE assert( false )
+#define BAMTOOLS_ASSERT_MESSAGE( condition, message ) if (!( condition )) throw std::runtime_error( message );
 
 namespace BamTools {
 
 class BamReader;
 class BamMultiReader;
 
-class Utilities {
+class UTILS_EXPORT Utilities {
   
-    public:                          
+    public: 
+        // check if a file exists
+        static bool FileExists(const std::string& fname);
+        
         // 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, BamRegion& 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, BamRegion& 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); 
+        // sequence utilities
+        static void Reverse(std::string& sequence);
+        static void ReverseComplement(std::string& sequence);
 };
 
 } // namespace BamTools