fix a bug in ligation counting (822fd046) · Commits · Chaos / chaos.juicer

hic_info.sh

+1 −1

Original line number	Diff line number	Diff line
		@@ -4,7 +4,7 @@ slice_size=2000000
		genome_version=hg19
		enzyme=DpnII
		libraries=(DMSO_DHT)
		juicer_dir=~/local/chaos.tools
		juicer_dir=~/local/chaos.juicer
		bwa_cmd=~/conda/envs/basic_software/bin/bwa
		samtools_cmd=~/conda/envs/basic_software/bin/samtools
		awk_cmd=~/conda/envs/basic_software/bin/awk

+8 −8

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_cmd '!((NR+2)%4)' \| \
		# grep -cE $ligation \
		# )
		num1=$(paste <(gunzip -c $read1_file) <(gunzip -c $read2_file) \| awk '!((NR+2)%4)' \| grep -cE $ligation)
		echo -ne "$num1" > $res_file
		fi