# HG changeset patch
# User estrain
# Date 1540124368 14400
# Node ID c8158764b7a7d123d4cf5dcfec4ba17c300d767c
# Parent  454e2f1ccff42aac9b46a5f786c51c8fb27dd23d
Uploaded

diff -r 454e2f1ccff4 -r c8158764b7a7 makein.pl
--- /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`;