src/toolkit/bamtools_resolve.h

   1 // ***************************************************************************
   2 // bamtools_resolve.h (c) 2011 Derek Barnett
   3 // Marth Lab, Department of Biology, Boston College
   4 // ---------------------------------------------------------------------------
   5 // Last modified: 23 June 2011
   6 // ---------------------------------------------------------------------------
   7 // Resolves paired-end reads (marking the IsProperPair flag as needed).
   8 // ***************************************************************************
   9
  10 #ifndef BAMTOOLS_RESOLVE_H
  11 #define BAMTOOLS_RESOLVE_H
  12
  13 #include "bamtools_tool.h"
  14
  15 namespace BamTools {
  16
  17 class ResolveTool : public AbstractTool {
  18
  19     public:
  20         ResolveTool(void);
  21         ~ResolveTool(void);
  22
  23     public:
  24         int Help(void);
  25         int Run(int argc, char* argv[]);
  26
  27     private:
  28         struct ResolveSettings;
  29         ResolveSettings* m_settings;
  30
  31         struct ResolveToolPrivate;
  32         ResolveToolPrivate* m_impl;
  33
  34         struct ReadNamesFileReader;
  35         struct ReadNamesFileWriter;
  36         struct StatsFileReader;
  37         struct StatsFileWriter;
  38 };
  39
  40 } // namespace BamTools
  41
  42 #endif // BAMTOOLS_RESOLVE_H