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 // 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 #include <api/api_global.h>\r
  18 #include <api/BamAlignment.h>\r
  19 #include <string>\r
  20 \r
  21 namespace BamTools {\r
  22 \r
  23 class API_EXPORT BamWriter {\r
  24 \r
  25     // constructor/destructor\r
  26     public:\r
  27         BamWriter(void);\r
  28         ~BamWriter(void);\r
  29 \r
  30     // public interface\r
  31     public:\r
  32         // closes the alignment archive\r
  33         void Close(void);\r
  34         // opens the alignment archive\r
  35         bool Open(const std::string& filename, \r
  36                   const std::string& samHeader, \r
  37                   const BamTools::RefVector& referenceSequences, \r
  38                   bool writeUncompressed = false);\r
  39         // saves the alignment to the alignment archive\r
  40         void SaveAlignment(const BamTools::BamAlignment& al);\r
  41 \r
  42     // private implementation\r
  43     private:\r
  44         struct BamWriterPrivate;\r
  45         BamWriterPrivate* d;\r
  46 };\r
  47 \r
  48 } // namespace BamTools\r
  49 \r
  50 #endif // BAMWRITER_H\r