9 extern bool no_fractional_weight; // if no_frac_weight == true, each alignment counts as weight 1
13 std::vector<double> read_depth;
17 class WiggleProcessor {
19 virtual ~WiggleProcessor() {}
20 virtual void process(const Wiggle& wiggle) = 0;
23 class UCSCWiggleTrackWriter : public WiggleProcessor {
25 UCSCWiggleTrackWriter(const std::string& output_filename,
26 const std::string& track_name);
28 ~UCSCWiggleTrackWriter();
30 void process(const Wiggle& wiggle);
36 class ReadDepthWriter : public WiggleProcessor {
38 ReadDepthWriter(std::ostream& stream);
40 void process(const Wiggle& wiggle);
43 std::ostream& stream_;
46 void build_wiggles(const std::string& bam_filename,
47 WiggleProcessor& processor);