mfpdesign: adding additional EcoFunPrimer arguments

[pommevilla]

MetaFunPrimer/src/mfpdesign

Lines 124 to 209 in d692c9e

	while getopts ":hi:o:-:" opt; do
	case ${opt} in
	h )
	usage
	echo "Exiting..."
	exit 1
	;;
	o )
	outdir=$OPTARG
	;;
	i )
	input_file=$OPTARG
	;;
	- )
	LONG_OPTARG="${OPTARG#*\s}"
	case ${OPTARG} in
	in )
	eval "input_file=\"\$$OPTIND\""
	if [ -z "input_file" ]; then
	die "Input file required for argument --in"
	fi
	if [ ! -f "input_file" ]; then
	die "Input file $input_file does not exist."
	fi
	shift
	;;
	out )
	eval "outdir=\"\$$OPTIND\""
	if [ -z "outdir" ]; then
	die "Output directory required for argument --out"
	fi
	if [ ! -f "input_file" ]; then
	die "Input file $input_file does not exist."
	fi
	shift
	;;
	assay_max )
	eval "assay_max=\"\$$OPTIND\""
	if [ -z "assay_max" ]; then
	die "Integer required for argument assay_max"
	fi
	shift
	;;
	min_product_length )
	eval "min_product_length=\"\$$OPTIND\""
	if [ -z "min_product_length" ]; then
	die "Integer required for argument min_product_length"
	fi
	shift
	;;
	max_product_length )
	eval "max_product_length=\"\$$OPTIND\""
	if [ -z "max_product_length" ]; then
	die "Integer required for argument max_product_length"
	fi
	shift
	;;
	min_oligo_length )
	eval "min_oligo_length=\"\$$OPTIND\""
	if [ -z "min_oligo_length" ]; then
	die "Integer required for argument min_oligo_length"
	fi
	shift
	;;
	max_oligo_length )
	eval "max_oligo_length=\"\$$OPTIND\""
	if [ -z "max_oligo_length" ]; then
	die "Integer required for argument max_oligo_length"
	fi
	shift
	;;
	help )
	usage
	exit 1
	;;
	* )
	die "Invalid option: $LONG_OPTARG"
	;;
	esac
	;;
	\? )
	die "Invalid option: $OPTARG"
	;;
	esac
	done

The following EcoFunPrimer arguments need to be added to mfpdesign (arguments to use indicated in parentheses):

• GCFilterMin, GCFilterMax (--gcmin, --gcmax)
• tempMin, tempMax (--tempmin, --tempmax)
• degeneracy (--degeneracy)