src/utils/bamtools_utilities.h

   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: 26 January 2011
   7 // ---------------------------------------------------------------------------
   8 // Provides general utilities used by BamTools sub-tools.
   9 // ***************************************************************************
  10
  11 #ifndef BAMTOOLS_UTILITIES_H
  12 #define BAMTOOLS_UTILITIES_H
  13
  14 #include <api/BamAux.h>
  15 #include <utils/utils_global.h>
  16 #include <cassert>
  17 #include <stdexcept>
  18 #include <string>
  19
  20 #define BAMTOOLS_ASSERT_UNREACHABLE assert( false )
  21 #define BAMTOOLS_ASSERT_MESSAGE( condition, message ) if (!( condition )) throw std::runtime_error( message );
  22
  23 namespace BamTools {
  24
  25 class BamReader;
  26 class BamMultiReader;
  27
  28 class UTILS_EXPORT Utilities {
  29
  30     public:
  31         // check if a file exists
  32         static bool FileExists(const std::string& fname);
  33
  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,
  37                                       const BamReader& reader,
  38                                       BamRegion& region);
  39         // Same as above, but accepts a BamMultiReader
  40         static bool ParseRegionString(const std::string& regionString,
  41                                       const BamMultiReader& reader,
  42                                       BamRegion& region);
  43
  44         // sequence utilities
  45         static void Reverse(std::string& sequence);
  46         static void ReverseComplement(std::string& sequence);
  47 };
  48
  49 } // namespace BamTools
  50
  51 #endif // BAMTOOLS_UTILITIES_H