add lsf_queue got Genome::Model::Event
should_use_alignment_pd if model's run_as =~ /^apipe/
add lsf_queue to AlignReads
pull queue param out of bsub_rusage (for events)
add lsf_queue to PrepareReferenceSequenceIndex event

The boundary between events and software results is not clear so this
mostly just makes more explicit what I believe was implicit.
use event's lsf_queue
pull AlignmentResult's LSF queue out of rusage
inject queue into rusage

To decide whether to use the production alignment queue we need
knowledge of the model so we have to inject the queue into the alignment
result.
Merge branch 'pinch' into AR-597

* pinch:
  inject queue into rusage
  pull AlignmentResult's LSF queue out of rusage
  use event's lsf_queue
  add lsf_queue to PrepareReferenceSequenceIndex event
  pull queue param out of bsub_rusage (for events)
  add lsf_queue to AlignReads
  should_use_alignment_pd if model's run_as =~ /^apipe/
  add lsf_queue got Genome::Model::Event