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