# HG changeset patch
# User nikos
# Date 1423652735 18000
# Node ID 7a5780dc7b71d0514dd88d72bb92e185119a1bc3
# Parent  68af3d2260aa26c11175644fda7a13e56d295a9c
Fixed bug with "rm merged_temp2"

diff -r 68af3d2260aa -r 7a5780dc7b71 summarize_unique_barcodes.sh
--- a/summarize_unique_barcodes.sh	Mon Jan 26 07:13:03 2015 -0500
+++ b/summarize_unique_barcodes.sh	Wed Feb 11 06:05:35 2015 -0500
@@ -174,12 +174,14 @@
 if [ ! -s paired ]; then
     zcat merged_temp.gz | awk '{print $1, $2, "NA", $4, $5}' - > merged_temp2
     gzip -c merged_temp2 > merged_temp.gz
+    rm merged_temp2
 fi
 
 #Fix priming position
 if [ ! -z $priming_pos ]; then
     zcat merged_temp.gz | awk -v pos="${priming_pos}" '{print $1, $2, pos, $4, $5}' - > merged_temp2
     gzip -c merged_temp2 > merged_temp.gz
+    rm merged_temp2
 fi
 
 #File summary.txt columns: RNA_ID, Start, End, barcode sequence, sequenced_count[=number of sequenced fragments fulfilling previous requiremnts]
@@ -218,8 +220,8 @@
 
 #Produce k2n file
 if [ "$k2n" == "True" ]; then
-    Rscript $R_SCRIPT_PATH/k2n.R merged_temp.gz $output_dir/read_counts.txt ${max_observed_barcodes} $BAR_LEN $output_dir/k2n.txt
+    Rscript $R_SCRIPT_PATH/k2n.R merged_temp.gz $output_dir/unique_barcodes.txt $output_dir/k2n.txt
 fi
 
 #Remove temp files
-rm merged_temp2 merged_temp.gz positions_temp_sorted.gz paired
+rm merged_temp.gz positions_temp_sorted.gz paired