Mercurial > repos > nikos > rna_probing

changeset 12:52ff42c85994 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Fixed gzip bug.
author nikos
date Wed, 05 Nov 2014 11:44:47 -0500
parents f6265e05c55c
children 37d00e22959b
files summarize_unique_barcodes.sh
diffstat 1 files changed, 2 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- a/summarize_unique_barcodes.sh	Wed Nov 05 10:00:47 2014 -0500
+++ b/summarize_unique_barcodes.sh	Wed Nov 05 11:44:47 2014 -0500
@@ -173,13 +173,13 @@
 #If the experiment is single-end set NA values to the priming column.
 if [ ! -s paired ]; then
     zcat merged_temp.gz | awk '{print $1, $2, "NA", $4, $5}' - > merged_temp2
-    cat merged_temp2 | gzip > merged_temp.gz
+    gzip -c merged_temp2 > merged_temp.gz
 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
-    cat merged_temp2 | gzip > merged_temp.gz
+    gzip -c merged_temp2 > merged_temp.gz
 fi
 
 #File summary.txt columns: RNA_ID, Start, End, barcode sequence, sequenced_count[=number of sequenced fragments fulfilling previous requiremnts]