Refactored wiggle code and added rsem-bam2readdepth program

[rsem.git] / wiggle.h

diff --git a/wiggle.h b/wiggle.h
new file mode 100644 (file)
index 0000000..09cc4f9
--- /dev/null
+++ b/wiggle.h
@@ -0,0 +1,41 @@
+#include <cstdio>
+#include <string>
+#include <vector>
+#include <ostream>
+
+struct Wiggle {
+    std::string name;
+    std::vector<float> read_depth;
+};
+
+class WiggleProcessor {
+public:
+    virtual ~WiggleProcessor() {}
+    virtual void process(const Wiggle& wiggle) = 0;
+};
+
+class UCSCWiggleTrackWriter : public WiggleProcessor {
+public:
+    UCSCWiggleTrackWriter(const std::string& output_filename,
+                          const std::string& track_name);
+        
+    ~UCSCWiggleTrackWriter();
+
+    void process(const Wiggle& wiggle);
+
+private:
+    FILE *fo;
+};
+
+class ReadDepthWriter : public WiggleProcessor {
+public:
+    ReadDepthWriter(std::ostream& stream);
+
+    void process(const Wiggle& wiggle);
+
+private:
+    std::ostream& stream_;
+};
+
+void build_wiggles(const std::string& bam_filename,
+                   WiggleProcessor& processor);