--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mirdeep2/mapper_wrapper.pl	Mon Sep 19 19:04:41 2011 -0400
@@ -0,0 +1,13 @@
+#!/usr/bin/perl
+
+$bowtie_index_name = $ARGV[0];
+$output_arf = $ARGV[1];
+$bowtie_files_path = $ARGV[2];
+$options = join (" ", @ARGV[3..$#ARGV]);
+
+$basename = `basename $bowtie_index_name`;
+chomp $basename;
+
+system ("mapper.pl $options -p $bowtie_files_path/$basename -t $output_arf 2> /dev/null");
+
+if (-s $output_arf == 0) {die "No reads aligned to the reference.";}