hi,
the docs for tophat specify that -g and --max-multihits should set the same value: "max_hits". it appears that only the -g option is used. i see the verbose arg it's expecting is "--max-gene-family" which is not documented.
btw python's optparse module [ http://docs.python.org/library/optparse.html ] is in the stdlib and is simpler than the getopt bindings.
the docs for tophat specify that -g and --max-multihits should set the same value: "max_hits". it appears that only the -g option is used. i see the verbose arg it's expecting is "--max-gene-family" which is not documented.
btw python's optparse module [ http://docs.python.org/library/optparse.html ] is in the stdlib and is simpler than the getopt bindings.
Comment