X-Git-Url: https://git.donarmstrong.com/?p=rsem.git;a=blobdiff_plain;f=bam2readdepth.cpp;h=d252e2e0f74a4fc84c5078bb1dbbeba54f48ec60;hp=c7f0adbcecc96bfaab0a24b5fa4764d27cd2e268;hb=8bc3c21a5168b1dd6e36a95c018013e6a7641fee;hpb=946f9a6adb2a82048c8453d44693cd3838d32939

diff --git a/bam2readdepth.cpp b/bam2readdepth.cpp
index c7f0adb..d252e2e 100644
--- a/bam2readdepth.cpp
+++ b/bam2readdepth.cpp
@@ -1,13 +1,27 @@
-#include <iostream>
+#include <cstdio>
+#include <cstring>
+#include <cstdlib>
+#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");
-        std::exit(1);
-	}
-    ReadDepthWriter depth_writer(std::cout);
-    build_wiggles(argv[1], depth_writer);
-
-	return 0;
+  if (argc != 3) {
+    printf("Usage: rsem-bam2readdepth sorted_bam_input readdepth_output\n");
+    exit(-1);
+  }
+
+  ofstream fout(argv[2]);
+  general_assert(fout.is_open(), "Cannot write to " + cstrtos(argv[2]) + "!");
+
+  ReadDepthWriter depth_writer(fout);
+  
+  build_wiggles(argv[1], depth_writer);
+
+  fout.close();
+
+  return 0;
 }