wiggle.h

   1 #ifndef WIGGLE_H_
   2 #define WIGGLE_H_
   3
   4 #include <cstdio>
   5 #include <string>
   6 #include <vector>
   7 #include <ostream>
   8
   9 extern bool no_fractional_weight; // if no_frac_weight == true, each alignment counts as weight 1
  10
  11 struct Wiggle {
  12     std::string name;
  13     std::vector<double> read_depth;
  14     size_t length;
  15 };
  16
  17 class WiggleProcessor {
  18 public:
  19     virtual ~WiggleProcessor() {}
  20     virtual void process(const Wiggle& wiggle) = 0;
  21 };
  22
  23 class UCSCWiggleTrackWriter : public WiggleProcessor {
  24 public:
  25     UCSCWiggleTrackWriter(const std::string& output_filename,
  26                           const std::string& track_name);
  27
  28     ~UCSCWiggleTrackWriter();
  29
  30     void process(const Wiggle& wiggle);
  31
  32 private:
  33     FILE *fo;
  34 };
  35
  36 class ReadDepthWriter : public WiggleProcessor {
  37 public:
  38     ReadDepthWriter(std::ostream& stream);
  39
  40     void process(const Wiggle& wiggle);
  41
  42 private:
  43     std::ostream& stream_;
  44 };
  45
  46 void build_wiggles(const std::string& bam_filename,
  47                    WiggleProcessor& processor);
  48
  49 #endif