# HG changeset patch
# User davidvanzessen
# Date 1399549842 14400
# Node ID afddfd016ba6614328ca17aeaab509ec46e92616
# Parent  4f50fd2821a63486721a99c08e1fae56566031c6
Uploaded

diff -r 4f50fd2821a6 -r afddfd016ba6 r_wrapper.sh
--- a/r_wrapper.sh	Thu May 08 04:23:45 2014 -0400
+++ b/r_wrapper.sh	Thu May 08 07:50:42 2014 -0400
@@ -32,8 +32,9 @@
 			break
 		fi
 		file=$name"_"$barcode
-		cat $file.fastq | perl -e '$i=0;while(< >){if(/^\@/&&$i==0){s/^\@/\>/;print;}elsif($i==1){print;$i=-3}$i++;}' > $file.fasta
-		cat $file.fastq
+		cat $file.fastq | awk 'NR%4==1{printf ">%s\n", substr($0,2)}NR%4==2{print}' > $file.fasta
+		#cat $file.fastq | perl -e '$i=0;while(< >){if(/^\@/&&$i==0){s/^\@/\>/;print;}elsif($i==1){print;$i=-3}$i++;}' > $file.fasta
+		#cat $file.fastq
 		echo "<tr><td>$barcode</td><td>$count</td><td><a href='$file.fastq'>$file.fastq</a></td><td><a href='$file.fasta'>$file.fasta</a></td></tr>" >> $output
 done < output.txt
 echo "</tbody></body></html>" >> $output