BamWriter.h

   1 // ***************************************************************************\r
   2 // BamWriter.h (c) 2009 Michael Strömberg, Derek Barnett\r
   3 // Marth Lab, Department of Biology, Boston College\r
   4 // All rights reserved.\r
   5 // ---------------------------------------------------------------------------\r
   6 // Last modified: 8 December 2009 (DB)\r
   7 // ---------------------------------------------------------------------------\r
   8 // Uses BGZF routines were adapted from the bgzf.c code developed at the Broad\r
   9 // Institute.\r
  10 // ---------------------------------------------------------------------------\r
  11 // Provides the basic functionality for producing BAM files\r
  12 // ***************************************************************************\r
  13 \r
  14 #ifndef BAMWRITER_H\r
  15 #define BAMWRITER_H\r
  16 \r
  17 // C++ includes\r
  18 #include <string>\r
  19 \r
  20 // BamTools includes\r
  21 #include "BamAux.h"\r
  22 \r
  23 namespace BamTools {\r
  24 \r
  25 class BamWriter {\r
  26 \r
  27     // constructor/destructor\r
  28     public:\r
  29         BamWriter(void);\r
  30         ~BamWriter(void);\r
  31 \r
  32     // public interface\r
  33     public:\r
  34         // closes the alignment archive\r
  35         void Close(void);\r
  36         // opens the alignment archive\r
  37         void Open(const std::string& filename, const std::string& samHeader, const BamTools::RefVector& referenceSequences);\r
  38         // saves the alignment to the alignment archive\r
  39         void SaveAlignment(const BamTools::BamAlignment& al);\r
  40 \r
  41     // private implementation\r
  42     private:\r
  43         struct BamWriterPrivate;\r
  44         BamWriterPrivate* d;\r
  45 };\r
  46 \r
  47 } // namespace BamTools\r
  48 \r
  49 #endif // BAMWRITER_H\r