From c869372c6043ff60ab6fb99d2be6491c99c45438 Mon Sep 17 00:00:00 2001
From: Tyghe Vallard <vallardt@gmail.com>
Date: Thu, 10 Dec 2015 14:24:25 -0500
Subject: [PATCH] added old perl code

---
 fixFastq.pl | 32 ++++++++++++++++++++++++++++++++
 1 file changed, 32 insertions(+)
 create mode 100755 fixFastq.pl

diff --git a/fixFastq.pl b/fixFastq.pl
new file mode 100755
index 0000000..13b620f
--- /dev/null
+++ b/fixFastq.pl
@@ -0,0 +1,32 @@
+#!/usr/bin/perl -w
+
+use strict;
+
+my ($in, $out, $a, $b, $c, $d, $l, $r, $n);
+
+if (!-d "output") {
+    `mkdir output`;
+}
+
+foreach $in (`ls *.fastq`) {
+    chomp $in;
+    $out = "output/new_" . $in;
+    open (OUT, ">$out") or die "cannot open $out: $!";
+
+    open (IN, "$in") or die "cannot open $in: $!";
+    while ($a = <IN>) {
+	$b = <IN>;
+	$c = <IN>;
+	$d = <IN>;
+
+	chomp $a;
+	($l, $r) = split(/\s+/, $a);
+	$n = substr($r,0,1);
+	print OUT $l, '#0/', "$n  \($a\)\n";
+
+	print OUT $b, $c, $d;
+    }
+    close IN;
+    close OUT;
+}
+