fix a bug in ligation count (22454dc5) · Commits · Chaos / chaos.juicer

hic_local.sh

+9 −9

Original line number	Diff line number	Diff line
		@@ -37,14 +37,14 @@ do
		linecount_file=${split_prefix}_linecount.txt

		if [ ! -e $res_file ];then
		# num1=$(\
		# paste \
		# <(gunzip -c $read1_file) \
		# <(gunzip -c $read2_file) \| \
		# $awk_cmd '!((NR+2)%4)' \| \
		# grep -cE $ligation \
		# )
		num1=$(paste <(gunzip -c $read1_file) <(gunzip -c $read2_file) \| awk '!((NR+2)%4)' \| grep -cE $ligation)
		num1=$(\
		paste \
		<(gunzip -c $read1_file) \
		<(gunzip -c $read2_file) \| \
		$awk_cmd '!((NR+2)%4)' \| \
		grep -cE $ligation \
		)

		echo -ne "$num1" > $res_file
		fi