gridss setupreference errors if no bam file provided

[lkhilton]

In version 2.12 the gridss.sh script includes a check to make sure at least one input bam file is provided. This then requires me to provide an input bam file even though setupreference doesn't require a bam file. This wasn't a problem in previous versions. It would be nice to add a condition to only test for the bam file if any of do_preprocess, do_call, or do_assemble are true.

gridss/scripts/gridss

Lines 243 to 247 in d1d1f85

	if [[ "$@" == "" ]] ; then
	echo "$USAGE_MESSAGE" 1>&2
	echo "At least one input bam must be specified." 1>&2
	exit $EX_NOINPUT
	fi