bamtools_count.h

   1 // ***************************************************************************
   2 // bamtools_count.h (c) 2010 Derek Barnett, Erik Garrison
   3 // Marth Lab, Department of Biology, Boston College
   4 // All rights reserved.
   5 // ---------------------------------------------------------------------------
   6 // Last modified: 1 June 2010
   7 // ---------------------------------------------------------------------------
   8 // Prints alignment count for BAM file
   9 //
  10 // ** Expand to multiple??
  11 //
  12 // ***************************************************************************
  13
  14 #ifndef BAMTOOLS_COUNT_H
  15 #define BAMTOOLS_COUNT_H
  16
  17 #include "bamtools_tool.h"
  18
  19 namespace BamTools {
  20
  21 class CountTool : public AbstractTool {
  22
  23     public:
  24         CountTool(void);
  25         ~CountTool(void);
  26
  27     public:
  28         int Help(void);
  29         int Run(int argc, char* argv[]);
  30
  31     private:
  32         struct CountSettings;
  33         CountSettings* m_settings;
  34 };
  35
  36 } // namespace BamTools
  37
  38 #endif // BAMTOOLS_COUNT_H