src/toolkit/bamtools_resolve.h

   1 // ***************************************************************************
   2 // bamtools_resolve.h (c) 2011 Derek Barnett
   3 // Marth Lab, Department of Biology, Boston College
   4 // All rights reserved.
   5 // ---------------------------------------------------------------------------
   6 // Last modified: 19 April 2011
   7 // ---------------------------------------------------------------------------
   8 // Resolves paired-end reads (marking the IsProperPair flag as needed) in a
   9 // BAM file.
  10 // ***************************************************************************
  11
  12 #ifndef BAMTOOLS_RESOLVE_H
  13 #define BAMTOOLS_RESOLVE_H
  14
  15 #include "bamtools_tool.h"
  16
  17 namespace BamTools {
  18
  19 class ResolveTool : public AbstractTool {
  20
  21     public:
  22         ResolveTool(void);
  23         ~ResolveTool(void);
  24
  25     public:
  26         int Help(void);
  27         int Run(int argc, char* argv[]);
  28
  29     private:
  30         struct ResolveSettings;
  31         ResolveSettings* m_settings;
  32
  33         struct ResolveToolPrivate;
  34         ResolveToolPrivate* m_impl;
  35 };
  36
  37 } // namespace BamTools
  38
  39 #endif // BAMTOOLS_RESOLVE_H