get_annotation_input now will not process any file with a _ character in name, rather than checking for specific words in file name (more flexible). Also fixed bug where wrong parameter name was being used for operation (was not causing incorrect output as it was accessing a global variable rather than the local one).
Simplified get_annotation_input which accepts the raw_leiden_data and mutalyzer_output files as parameters rather than figuring them out automatically.
added documentation for get_annotation_input