bamtools_pileup.h

   1 // ***************************************************************************
   2 // bamtools_pileup.h (c) 2010 Derek Barnett, Erik Garrison
   3 // Marth Lab, Department of Biology, Boston College
   4 // All rights reserved.
   5 // ---------------------------------------------------------------------------
   6 // Last modified: 13 July 2010
   7 // ---------------------------------------------------------------------------
   8 // Provides pileup conversion functionality.
   9 //
  10 // The 'assembly' aspect of pileup makes this more complicated than the
  11 // simpler one-to-one conversion methods for other formats.
  12 // ***************************************************************************
  13
  14 #ifndef BAMTOOLS_PILEUP_H
  15 #define BAMTOOLS_PILEUP_H
  16
  17 #include <iostream>
  18 #include <string>
  19
  20 namespace BamTools {
  21
  22 class BamMultiReader;
  23 class BamRegion;
  24
  25 class Pileup {
  26
  27     public:
  28         Pileup(BamMultiReader* reader, std::ostream* outStream);
  29         ~Pileup(void);
  30
  31     public:
  32         bool Run(void);
  33         void SetFastaFilename(const std::string& filename);
  34         void SetIsPrintingMapQualities(bool ok);
  35         void SetRegion(const BamRegion& region);
  36
  37     private:
  38         struct PileupPrivate;
  39         PileupPrivate* d;
  40 };
  41
  42 } // namespace BamTools
  43
  44 #endif // BAMTOOLS_PILEUP_H