src/api/BamWriter.h

   1 // ***************************************************************************\r
   2 // BamWriter.h (c) 2009 Michael Str�mberg, Derek Barnett\r
   3 // Marth Lab, Department of Biology, Boston College\r
   4 // All rights reserved.\r
   5 // ---------------------------------------------------------------------------\r
   6 // Last modified: 19 November 2010 (DB)\r
   7 // ---------------------------------------------------------------------------\r
   8 // Provides the basic functionality for producing BAM files\r
   9 // ***************************************************************************\r
  10 \r
  11 #ifndef BAMWRITER_H\r
  12 #define BAMWRITER_H\r
  13 \r
  14 #include <api/api_global.h>\r
  15 #include <api/BamAlignment.h>\r
  16 #include <string>\r
  17 \r
  18 namespace BamTools {\r
  19 \r
  20 namespace Internal {\r
  21     class BamWriterPrivate;\r
  22 } // namespace Internal\r
  23 \r
  24 class API_EXPORT BamWriter {\r
  25 \r
  26     // constructor/destructor\r
  27     public:\r
  28         BamWriter(void);\r
  29         ~BamWriter(void);\r
  30 \r
  31     // public interface\r
  32     public:\r
  33         // closes the alignment archive\r
  34         void Close(void);\r
  35         // opens the alignment archive\r
  36         bool Open(const std::string& filename, \r
  37                   const std::string& samHeader, \r
  38                   const BamTools::RefVector& referenceSequences, \r
  39                   bool writeUncompressed = false);\r
  40         // saves the alignment to the alignment archive\r
  41         void SaveAlignment(const BamTools::BamAlignment& al);\r
  42 \r
  43     // private implementation\r
  44     private:\r
  45         Internal::BamWriterPrivate* d;\r
  46 };\r
  47 \r
  48 } // namespace BamTools\r
  49 \r
  50 #endif // BAMWRITER_H\r