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