1 // ***************************************************************************
2 // bamtools_utilities.h (c) 2010 Derek Barnett, Erik Garrison
3 // Marth Lab, Department of Biology, Boston College
4 // ---------------------------------------------------------------------------
5 // Last modified: 9 June 2011
6 // ---------------------------------------------------------------------------
7 // Provides general utilities used by BamTools sub-tools.
8 // ***************************************************************************
10 #ifndef BAMTOOLS_UTILITIES_H
11 #define BAMTOOLS_UTILITIES_H
13 #include <api/BamAux.h>
14 #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 // returns true if 'source' contains 'pattern' or 'c'
32 static bool Contains(const std::string& source, const std::string& pattern);
33 static bool Contains(const std::string& source, const char c);
35 // returns true if 'source' ends with 'pattern' or 'c'
36 static bool EndsWith(const std::string& source, const std::string& pattern);
37 static bool EndsWith(const std::string& source, const char c);
39 // check if a file exists
40 static bool FileExists(const std::string& fname);
42 // Parses a region string, uses reader to do validation (valid ID's, positions), stores in Region struct
43 // Returns success (true/false)
44 static bool ParseRegionString(const std::string& regionString,
45 const BamReader& reader,
47 // Same as above, but accepts a BamMultiReader
48 static bool ParseRegionString(const std::string& regionString,
49 const BamMultiReader& reader,
53 static void Reverse(std::string& sequence);
54 static void ReverseComplement(std::string& sequence);
56 // split string on delimiter character (or string of allowed delimiters)
57 static std::vector<std::string> Split(const std::string& source, const char delim);
58 static std::vector<std::string> Split(const std::string& source, const std::string& delims);
60 // returns true if 'source' starts with 'pattern' or 'c'
61 static bool StartsWith(const std::string& source, const std::string& pattern);
62 static bool StartsWith(const std::string &source, const char c);
65 } // namespace BamTools
67 #endif // BAMTOOLS_UTILITIES_H