src/api/BamWriter.cpp

   1 // ***************************************************************************\r
   2 // BamWriter.cpp (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: 11 January 2011 (DB)\r
   7 // ---------------------------------------------------------------------------\r
   8 // Provides the basic functionality for producing BAM files\r
   9 // ***************************************************************************\r
  10 \r
  11 #include <api/BamWriter.h>\r
  12 #include <api/internal/BamWriter_p.h>\r
  13 using namespace BamTools;\r
  14 using namespace BamTools::Internal;\r
  15 \r
  16 #include <iostream>\r
  17 using namespace std;\r
  18 \r
  19 // constructor\r
  20 BamWriter::BamWriter(void) {\r
  21     d = new BamWriterPrivate;\r
  22 }\r
  23 \r
  24 // destructor\r
  25 BamWriter::~BamWriter(void) {\r
  26     delete d;\r
  27     d = 0;\r
  28 }\r
  29 \r
  30 // closes the alignment archive\r
  31 void BamWriter::Close(void) {\r
  32     d->Close();\r
  33 }\r
  34 \r
  35 // opens the alignment archive (using std::string SAM header)\r
  36 bool BamWriter::Open(const string& filename,\r
  37                      const string& samHeader,\r
  38                      const RefVector& referenceSequences,\r
  39                      bool isWriteUncompressed)\r
  40 {\r
  41     return d->Open(filename, samHeader, referenceSequences, isWriteUncompressed);\r
  42 }\r
  43 \r
  44 // opens the alignment archive (using SamHeader object)\r
  45 bool BamWriter::Open(const string& filename,\r
  46                      const SamHeader& samHeader,\r
  47                      const RefVector& referenceSequences,\r
  48                      bool isWriteUncompressed)\r
  49 {\r
  50     return d->Open(filename, samHeader.ToString(), referenceSequences, isWriteUncompressed);\r
  51 }\r
  52 \r
  53 // saves the alignment to the alignment archive\r
  54 void BamWriter::SaveAlignment(const BamAlignment& al) {\r
  55     d->SaveAlignment(al);\r
  56 }\r