Fix/argument handling 20240807 (#7) * version: -> 0.9.7 * fix: changed argument order in handle_args so that placement of positional arguments does not cause `argument not found` errors (s. #6) * fix: changed default db format from bed to hmmer * doc: removed misleading references to db format from readme * doc: corrected argument types of `annotation_db`, `bwa_index` to positional