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: 8 September 2011
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>
19 #define BAMTOOLS_ASSERT_UNREACHABLE BT_ASSERT_UNREACHABLE
20 #define BAMTOOLS_ASSERT_MESSAGE( condition, message ) BT_ASSERT_X( condition, message )
27 class UTILS_EXPORT Utilities {
30 // returns true if 'source' contains 'pattern' or 'c'
31 static bool Contains(const std::string& source, const std::string& pattern);
32 static bool Contains(const std::string& source, const char c);
34 // returns true if 'source' ends with 'pattern' or 'c'
35 static bool EndsWith(const std::string& source, const std::string& pattern);
36 static bool EndsWith(const std::string& source, const char c);
38 // check if a file exists
39 static bool FileExists(const std::string& fname);
41 // Parses a region string, uses reader to do validation (valid ID's, positions), stores in Region struct
42 // Returns success (true/false)
43 static bool ParseRegionString(const std::string& regionString,
44 const BamReader& reader,
46 // Same as above, but accepts a BamMultiReader
47 static bool ParseRegionString(const std::string& regionString,
48 const BamMultiReader& reader,
52 static void Reverse(std::string& sequence);
53 static void ReverseComplement(std::string& sequence);
55 // split string on delimiter character (or string of allowed delimiters)
56 static std::vector<std::string> Split(const std::string& source, const char delim);
57 static std::vector<std::string> Split(const std::string& source, const std::string& delims);
59 // returns true if 'source' starts with 'pattern' or 'c'
60 static bool StartsWith(const std::string& source, const std::string& pattern);
61 static bool StartsWith(const std::string &source, const char c);
64 } // namespace BamTools
66 #endif // BAMTOOLS_UTILITIES_H