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: 17 August 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 // 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         bool Open(const std::string& filename, \r
  38                   const std::string& samHeader, \r
  39                   const BamTools::RefVector& referenceSequences, \r
  40                   bool writeUncompressed = false);\r
  41         // saves the alignment to the alignment archive\r
  42         void SaveAlignment(const BamTools::BamAlignment& al);\r
  43 \r
  44     // private implementation\r
  45     private:\r
  46         struct BamWriterPrivate;\r
  47         BamWriterPrivate* d;\r
  48 };\r
  49 \r
  50 } // namespace BamTools\r
  51 \r
  52 #endif // BAMWRITER_H\r