Add align-to-reference rollover mode to AssemblePairs

[Jason Vander Heiden]

It's confusing that we are requiring users to feed the failed output from one mode into another mode, and then merge. We should add a mode that automatically does this by doing:

1. De novo (align) assemble first.
2. Attempt reference assembly if de novo fails.

Also, it bugs me that failed files output results after operations in the --rc flag. It should output unmanipulated input records.

[Jason Vander Heiden]

Finished in addd2e1, but it needs more testing.

[Jason Vander Heiden]

Seems fine.