When multiple families were selected, the get_tf_family_file routine was not
correctly writing all the families to the local file (it only wrote the first
familiy).
Commented out the code in the process routine which threw an error if the
background peak position input method was set and a pre-computed peak set was
used. This background peak position input method is ALWAYS set to something
and so this error was being thrown every time a pre-computed background peak
set was selected.
The flag specifying whether TFBS hit details should be written was not being
handled properly.