1 // ***************************************************************************
2 // bamtools_utilities.h (c) 2010 Derek Barnett, Erik Garrison
3 // Marth Lab, Department of Biology, Boston College
4 // All rights reserved.
5 // ---------------------------------------------------------------------------
6 // Last modified: 19 November 2010
7 // ---------------------------------------------------------------------------
8 // Provides general utilities used by BamTools sub-tools.
9 // ***************************************************************************
11 #ifndef BAMTOOLS_UTILITIES_H
12 #define BAMTOOLS_UTILITIES_H
14 #include <api/BamAux.h>
15 #include <utils/utils_global.h>
20 #define BAMTOOLS_ASSERT_UNREACHABLE assert( false )
21 #define BAMTOOLS_ASSERT_MESSAGE( condition, message ) if (!( condition )) throw std::runtime_error( message );
28 class UTILS_EXPORT Utilities {
31 // check if a file exists
32 static bool FileExists(const std::string& fname);
34 // Parses a region string, uses reader to do validation (valid ID's, positions), stores in Region struct
35 // Returns success (true/false)
36 static bool ParseRegionString(const std::string& regionString, const BamReader& reader, BamRegion& region);
37 // Same as above, but accepts a BamMultiReader
38 static bool ParseRegionString(const std::string& regionString, const BamMultiReader& reader, BamRegion& region);
41 static void Reverse(std::string& sequence);
42 static void ReverseComplement(std::string& sequence);
45 } // namespace BamTools
47 #endif // BAMTOOLS_UTILITIES_H