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 };
  10
  11 class WiggleProcessor {
  12 public:
  13     virtual ~WiggleProcessor() {}
  14     virtual void process(const Wiggle& wiggle) = 0;
  15 };
  16
  17 class UCSCWiggleTrackWriter : public WiggleProcessor {
  18 public:
  19     UCSCWiggleTrackWriter(const std::string& output_filename,
  20                           const std::string& track_name);
  21
  22     ~UCSCWiggleTrackWriter();
  23
  24     void process(const Wiggle& wiggle);
  25
  26 private:
  27     FILE *fo;
  28 };
  29
  30 class ReadDepthWriter : public WiggleProcessor {
  31 public:
  32     ReadDepthWriter(std::ostream& stream);
  33
  34     void process(const Wiggle& wiggle);
  35
  36 private:
  37     std::ostream& stream_;
  38 };
  39
  40 void build_wiggles(const std::string& bam_filename,
  41                    WiggleProcessor& processor);