From: athreyab <athreyab@localhost>
Date: Sat, 19 May 2012 17:23:55 +0000 (+0000)
Subject: remove first \1
X-Git-Url: http://gitweb.planteome.org/?a=commitdiff_plain;h=01bb1e04d2e9f7ab83daf60699baa43e125aa81b;p=old-jaiswallab-svn%2F.git

remove first \1

svn path=/; revision=331
---

diff --git a/Personnel/athreyab/illumina_parse/create_pairs b/Personnel/athreyab/illumina_parse/create_pairs
index e2fa2b4..79cd154 100755
--- a/Personnel/athreyab/illumina_parse/create_pairs
+++ b/Personnel/athreyab/illumina_parse/create_pairs
@@ -28,7 +28,7 @@ function process_file(){
 				then
 					out=""
 				else
-					ns="${line//[^C]}"
+					ns="${line//[^N]}"
 					perl float_compare.pl "${#line}" "${#ns}" "${max_rate}"
 					r=$?
 					if [ $r -eq 1 ]
@@ -37,6 +37,7 @@ function process_file(){
 						echo $out >> "$output_folder/file_$i";
 						out=""
 					else
+						echo -e "$out||$line was removed\n"
 						out=""
 					fi
 				fi
diff --git a/Personnel/athreyab/illumina_parse/illumina_parse.pl b/Personnel/athreyab/illumina_parse/illumina_parse.pl
index d876a78..848fa1e 100755
--- a/Personnel/athreyab/illumina_parse/illumina_parse.pl
+++ b/Personnel/athreyab/illumina_parse/illumina_parse.pl
@@ -90,12 +90,14 @@ sub process_folders{
                                         next;
 				}
 				if(index($h1, ' 1:N') != -1){
-					$temp = $slash_string."1:N";
+					#$temp = $slash_string."1:N";
+					$temp = ":N";
 					$h1 =~ s/ 1:N/$temp/;
 					$h1 = $h1.$slash_string."1";
 				}
 				elsif(index($h1, ' 2:N') != -1){
-					$temp = $slash_string."2:N";
+					#$temp = $slash_string."2:N";
+					$temp = ":N";
 					$h1 =~ s/ 2:N/$temp/;
 					$h1 = $h1.$slash_string."2";
 				}