--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/makein.pl	Sun Oct 21 08:19:28 2018 -0400
@@ -0,0 +1,24 @@
+#!/usr/bin/perl
+
+###############################
+# 
+# ConFinder requires an input
+# directory containing files
+# with *.fastq or *.fq 
+#
+###############################
+
+$fold=shift(@ARGV);
+
+$dat = shift(@ARGV);
+$fq = shift(@ARGV);
+$fq=~s/\.gz//;
+
+# If we're here the file should be some type
+# of fastq data type, append .fq if it's 
+# missing 
+if(!(($fq=~/\.fastq$/)||($fq=~/\.fq$/))) {
+  $fq=$fq.".fq";
+}
+
+`ln -s $dat $fold/$fq\n`;