BamReaderMain.cpp

   1 // BamReaderMain.cpp\r
   2 \r
   3 // Derek Barnett\r
   4 // Marth Lab, Boston College\r
   5 // Last modified: 12 May 2009\r
   6 \r
   7 #include "BamReader.h"\r
   8 \r
   9 // C++ includes\r
  10 #include <iostream>\r
  11 using std::cerr;\r
  12 using std::cout;\r
  13 using std::endl;\r
  14 \r
  15 #include <vector>\r
  16 using std::vector;\r
  17 \r
  18 #include <string>\r
  19 using std::string;\r
  20 \r
  21 int main(int argc, char* argv[]) {\r
  22 \r
  23         // check command line parameters\r
  24         if (argc != 3) {\r
  25                 cerr << endl;\r
  26                 cerr << "Usage: BamReaderTest <bamFile> <bamIndexFile>" << endl;\r
  27                 cerr << endl;\r
  28                 exit(1);\r
  29         }\r
  30 \r
  31         // get filenames from command line\r
  32         const char* bamFilename = argv[1];\r
  33         const char* bamIndexFilename = argv[2];\r
  34 \r
  35         int alignmentsRead = 0;\r
  36         BamAlignment bAlignment;\r
  37         \r
  38         BamReader bReader;\r
  39         cerr << endl << "Opening BAM file (and index)" << endl << endl;\r
  40         bReader.Open(bamFilename, bamIndexFilename);\r
  41 \r
  42         string header = bReader.GetHeaderText();\r
  43         cerr << "Printing header text..." << endl;\r
  44         if ( header.empty() ) {\r
  45                 cerr << "No header provided." << endl << endl;\r
  46         } else {\r
  47                 cerr << "----------------------" << endl;\r
  48                 cerr << "Header Text: " << endl;\r
  49                 cerr << "----------------------" << endl;\r
  50                 cerr << header << endl << endl;\r
  51         }\r
  52 \r
  53         RefVector references = bReader.GetReferenceData();\r
  54         cerr << "Printing references..." << endl;\r
  55         RefVector::const_iterator refIter = references.begin();\r
  56         RefVector::const_iterator refEnd  = references.end();\r
  57         for ( ; refIter != refEnd; ++refIter) {\r
  58                 cerr << "Reference entry: " << endl;\r
  59                 cerr << (*refIter).RefName << endl;\r
  60                 cerr << (*refIter).RefLength << endl;\r
  61                 cerr << "Has alignments? : " << ( ((*refIter).RefHasAlignments) ? "yes" : "no" ) << endl;\r
  62         }\r
  63         cerr << endl;\r
  64 \r
  65         alignmentsRead = 0;\r
  66         while ( bReader.GetNextAlignment(bAlignment) && (alignmentsRead <= 10) ) {\r
  67                 cerr << "Alignment " << alignmentsRead << endl;\r
  68                 cerr << bAlignment.Name << endl;\r
  69                 cerr << "Aligned to ref " << bAlignment.RefID << " at position " << bAlignment.Position << endl;\r
  70                 ++alignmentsRead;\r
  71         }\r
  72 \r
  73         cerr << "Jumping in BAM file" << endl;\r
  74         if ( bReader.Jump(1, 5000) ) {\r
  75                 cerr << "Jumping seems ok - getting first 10 alignments that start at or after chr2:5000" << endl;\r
  76 \r
  77                 alignmentsRead = 0;\r
  78                 while ( bReader.GetNextAlignment(bAlignment) && (alignmentsRead <= 10) ) {\r
  79                         if ( bAlignment.Position >= 5000 ) { \r
  80                                 cerr << "Alignment " << alignmentsRead << endl;\r
  81                                 cerr << bAlignment.Name << endl;\r
  82                                 cerr << "Aligned to ref " << bAlignment.RefID << " at position " << bAlignment.Position << endl;\r
  83                                 ++alignmentsRead;\r
  84                         }\r
  85                 }\r
  86         }\r
  87 \r
  88         cerr << "Rewinding BAM file" << endl;\r
  89         if ( bReader.Rewind() ) {\r
  90                 cerr << "Rewind seems to be ok - getting first 10 alignments" << endl;\r
  91                 \r
  92                 alignmentsRead = 0;\r
  93                 while ( bReader.GetNextAlignment(bAlignment) && (alignmentsRead <= 10) ) {\r
  94                         cerr << "Alignment " << alignmentsRead << endl;\r
  95                         cerr << bAlignment.Name << endl;\r
  96                         cerr << "Aligned to ref " << bAlignment.RefID << " at position " << bAlignment.Position << endl;\r
  97                         ++alignmentsRead;\r
  98                 }\r
  99         }\r
 100 \r
 101         cerr << "Closing BAM file..." << endl << endl;\r
 102         bReader.Close();\r
 103 \r
 104         cerr << "Exiting..." << endl << endl;\r
 105         return 0;\r
 106 }\r