Added ligation regex quote check (fd760622) · Commits · Chaos / chaos.juicer

SLURM/scripts/juicer.sh

+5 −1

Changes for SLURM/scripts/juicer.sh: 5 added lines, 1 removed line.
Original line number	Diff line number	Diff line
		@@ -274,6 +274,10 @@ if [ ! -e "${refSeq}.bwt" ]; then
		exit 1;
		fi

		## Check if ligation is a unquoted regex, if so quote
		if [[ -n "$ligation" && $ligation =~ [\\|] && ! $ligation =~ [\"\'] ]];
		export ligation="'$ligation'"

		## Set ligation junction based on restriction enzyme
		if [ -z "$ligation" ]; then
		case $site in
		@@ -611,7 +615,7 @@ SPLITEND`
		$userstring

		date
		export usegzip=${usegzip}; export name=${name}; export name1=${name1}; export name2=${name2}; export ext=${ext}; export ligation="${ligation}"; ${juiceDir}/scripts/countligations.sh
		export usegzip=${usegzip}; export name=${name}; export name1=${name1}; export name2=${name2}; export ext=${ext}; export ligation=${ligation}; ${juiceDir}/scripts/countligations.sh
		date
		CNTLIG`
		dependcount="$jid"