--- a/sequence_overview.r	Tue Jun 07 04:45:50 2016 -0400
+++ b/sequence_overview.r	Tue Jun 07 08:39:08 2016 -0400
@@ -3,9 +3,10 @@
 args <- commandArgs(trailingOnly = TRUE)
 
 input.file = args[1]
-outputdir = args[2]
-gene.classes = unlist(strsplit(args[3], ","))
-hotspot.analysis.sum.file = args[4]
+input.file = args[2]
+outputdir = args[3]
+gene.classes = unlist(strsplit(args[4], ","))
+hotspot.analysis.sum.file = args[5]
 NToverview.file = paste(outputdir, "ntoverview.txt", sep="/")
 NTsum.file = paste(outputdir, "ntsum.txt", sep="/")
 main.html = "index.html"