remove first \1

svn path=/; revision=331

diff --git a/Personnel/athreyab/illumina_parse/create_pairs b/Personnel/athreyab/illumina_parse/create_pairs
index e2fa2b40884ef0514d5e2829d3d6e161074d6b5b..79cd154f402dc0be1b8ceb2e87a863a189ccebca 100755 (executable)
--- 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 d876a789cdcb9ccacb8d5eebea2cd4d0b6beb747..848fa1e753dc1883982d05b99c1c1558897bce60 100755 (executable)
--- 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";
                                }