From e7946e8f2742cb657d3b21bd6d5e1b77a2d5363b Mon Sep 17 00:00:00 2001
From: athreyab <athreyab@localhost>
Date: Tue, 1 May 2012 02:36:13 +0000
Subject: [PATCH] pair/singleton script update

svn path=/; revision=327
---
 .../athreyab/illumina_parse/create_pairs      | 28 ++++++++++++-------
 1 file changed, 18 insertions(+), 10 deletions(-)

diff --git a/Personnel/athreyab/illumina_parse/create_pairs b/Personnel/athreyab/illumina_parse/create_pairs
index 8626f03..e2fa2b4 100755
--- a/Personnel/athreyab/illumina_parse/create_pairs
+++ b/Personnel/athreyab/illumina_parse/create_pairs
@@ -1,10 +1,17 @@
 #!/bin/bash
 
-function process_file{
-	array=("$@")
-	for i in "${array[@]}"
+function process_file(){
+	file_name="$1"
+	index=0
+	i=0
+        while read line ; do
+                array[$index]="$line"
+                index=$(($index+1))
+	done < "$file_name"
+	
+	while [ $i -lt $index ]
 	do	
-		echo "processing file ${array[i]}"
+		echo "processing file ${array[$i]}"
 		while read line ; do
 			if [ $line_index == 0 ]
 			then
@@ -42,7 +49,7 @@ function process_file{
 			then		
 				line_index=0
 			fi
-		done < "${array[i]}"
+		done < "${array[$i]}"
 	done
 }
 
@@ -101,17 +108,18 @@ else
 
 	# delete temp files as we dont' need them anymore. We already
 	# have that information in array1 and array2
-	rm -f array1.txt
-	rm -f array2.txt
-
 	i=0
 	line_index=0
 	out=""
 	remove_entry=0
 	
 	# loop through each files in array1, filter them and put in a file
-	process_file "${array1[@]}"
-	process_file "${array2[@]}"
+	process_file "array1.txt"
+	process_file "array2.txt"
+	rm -f array1.txt
+	rm -f array2.txt
+
+
 fi
 
 
-- 
2.34.1