Sets up the output thread, feeds the given header to the output data set, and returns four functions:
One for potential additional output mapping of alignments (output-filter, can be NIL, which defaults to #'IDENTITY),
one for invoking the function that filters chunks (wrap-thread, can be NIL, which defaults to #'FUNCALL),
one for receiving chunks of alignments in filter threads (receive-chunk),
and one for finalizing alignments in the main thread (finalize).
The function wrap-thread is called once per thread, receives the main function for processing chunks as a thunk,
and has to eventually call that thunk. The purpose of wrap-thread is to enable setting up additional resources
to be used in output-filter and/or receive-chunk.
When the (already effective) :sorting-order is :coordinate or :queryname, sort the received chunks before
writing to output. Sorting is not supported for files, but by default only for in-memory representations.
The parameter original-sq should be used to query the reference sequence dictionary,
because the one in header may have already been filtered and modified.

Specialize this generic function for new kinds of output sources.