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: 18 September 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 <string>\r
  18 #include "BamAlignment.h"\r
  19 \r
  20 namespace BamTools {\r
  21 \r
  22 class BamWriter {\r
  23 \r
  24     // constructor/destructor\r
  25     public:\r
  26         BamWriter(void);\r
  27         ~BamWriter(void);\r
  28 \r
  29     // public interface\r
  30     public:\r
  31         // closes the alignment archive\r
  32         void Close(void);\r
  33         // opens the alignment archive\r
  34         bool Open(const std::string& filename, \r
  35                   const std::string& samHeader, \r
  36                   const BamTools::RefVector& referenceSequences, \r
  37                   bool writeUncompressed = false);\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