rsem v1.1.21

[rsem.git] / bam2readdepth.cpp

diff --git a/bam2readdepth.cpp b/bam2readdepth.cpp
index 87fb178a60ad08c146cb6b23e3979e4237cdd480..d252e2e0f74a4fc84c5078bb1dbbeba54f48ec60 100644 (file)
--- a/bam2readdepth.cpp
+++ b/bam2readdepth.cpp
@@ -1,20 +1,27 @@
 #include <cstdio>
 #include <cstring>
 #include <cstdlib>
-#include <iostream>
+#include <fstream>
 
+#include "my_assert.h"
 #include "wiggle.h"
 
 using namespace std;
 
 int main(int argc, char* argv[]) {
-  if (argc != 2) {
-    printf("Usage: rsem-bam2readdepth sorted_bam_input\n");
+  if (argc != 3) {
+    printf("Usage: rsem-bam2readdepth sorted_bam_input readdepth_output\n");
     exit(-1);
   }
 
-    ReadDepthWriter depth_writer(std::cout);
-    build_wiggles(argv[1], depth_writer);
+  ofstream fout(argv[2]);
+  general_assert(fout.is_open(), "Cannot write to " + cstrtos(argv[2]) + "!");
 
-    return 0;
+  ReadDepthWriter depth_writer(fout);
+  
+  build_wiggles(argv[1], depth_writer);
+
+  fout.close();
+
+  return 0;
 }