heuristic option: unknown_sequences = (error|skip|as-is)

[yarikoptic]

In regards to

    if skipped_unknown:
        lgr.warning("Could not figure out where to stick %d sequences: %s" %
                    (len(skipped_unknown), skipped_unknown))

which is pretty much unknown_sequences="skip" for such an option, so we just skip those we cannot figure out ATM.
That could lead to a lengthy conversion which would still miss some critical data. so I think we should default to error and just make it easy to "overload" with a custom setting ....

until we come up with some centralized approach to heuristic options, it could be just

options = {
    'unknown_sequences': 'error'
}
for k, v in options.items():
     ek = 'REPROIN_' + k.upper()
     if ek in sys.environ:
          options[k] = sys.environ[ek]

thus allowing to override from environment.