wiggle.h

   1 #include <cstdio>
   2 #include <string>
   3 #include <vector>
   4 #include <ostream>
   5
   6 struct Wiggle {
   7     std::string name;
   8     std::vector<float> read_depth;
   9     size_t length;
  10 };
  11
  12 class WiggleProcessor {
  13 public:
  14     virtual ~WiggleProcessor() {}
  15     virtual void process(const Wiggle& wiggle) = 0;
  16 };
  17
  18 class UCSCWiggleTrackWriter : public WiggleProcessor {
  19 public:
  20     UCSCWiggleTrackWriter(const std::string& output_filename,
  21                           const std::string& track_name);
  22
  23     ~UCSCWiggleTrackWriter();
  24
  25     void process(const Wiggle& wiggle);
  26
  27 private:
  28     FILE *fo;
  29 };
  30
  31 class ReadDepthWriter : public WiggleProcessor {
  32 public:
  33     ReadDepthWriter(std::ostream& stream);
  34
  35     void process(const Wiggle& wiggle);
  36
  37 private:
  38     std::ostream& stream_;
  39 };
  40
  41 void build_wiggles(const std::string& bam_filename,
  42                    WiggleProcessor& processor);