bamtools_pileup.h

   1 #ifndef BAMTOOLS_PILEUP_H
   2 #define BAMTOOLS_PILEUP_H
   3
   4 #include <iostream>
   5 #include <string>
   6
   7 namespace BamTools {
   8
   9 class BamMultiReader;
  10 class BamRegion;
  11
  12 class Pileup {
  13
  14     public:
  15         Pileup(BamMultiReader* reader, std::ostream* outStream);
  16         ~Pileup(void);
  17
  18     public:
  19         bool Run(void);
  20         void SetFastaFilename(const std::string& filename);
  21         void SetIsPrintingMapQualities(bool ok);
  22         void SetRegion(const BamRegion& region);
  23
  24     private:
  25         struct PileupPrivate;
  26         PileupPrivate* d;
  27 };
  28
  29 } // namespace BamTools
  30
  31 #endif // BAMTOOLS_PILEUP_H