src/utils/bamtools_fasta.h

   1 // ***************************************************************************
   2 // bamtools_fasta.h (c) 2010 Derek Barnett, Erik Garrison
   3 // Marth Lab, Department of Biology, Boston College
   4 // ---------------------------------------------------------------------------
   5 // Last modified: 19 November 2010
   6 // ---------------------------------------------------------------------------
   7 // Provides FASTA reading/indexing functionality.
   8 // ***************************************************************************
   9
  10 #ifndef BAMTOOLS_FASTA_H
  11 #define BAMTOOLS_FASTA_H
  12
  13 #include <utils/utils_global.h>
  14 #include <string>
  15
  16 namespace BamTools {
  17
  18 class UTILS_EXPORT Fasta {
  19
  20     // ctor & dtor
  21     public:
  22         Fasta(void);
  23         ~Fasta(void);
  24
  25     // file-handling methods
  26     public:
  27         bool Close(void);
  28         bool Open(const std::string& filename, const std::string& indexFilename = "");
  29
  30     // sequence access methods
  31     public:
  32         bool GetBase(const int& refID, const int& position, char& base);
  33         bool GetSequence(const int& refId, const int& start, const int& stop, std::string& sequence);
  34
  35     // index-handling methods
  36     public:
  37         bool CreateIndex(const std::string& indexFilename);
  38
  39     // internal implementation
  40     private:
  41         struct FastaPrivate;
  42         FastaPrivate* d;
  43 };
  44
  45 } // BAMTOOLS_FASTA_H
  46
  47 #endif // BAMTOOLS_FASTA_H