mgymrek/lobstr-code — pull request #35 by mgymrek (2014-04-20 21:20:02+00:00)
Title: Alignment speedups

Dramatic alignment speedups using suggestions from Heng Li:

- don't allow mismatches in very short flanking regions (default, <30bp)
- stop alignment search after X (default: 1000) hits have been found)

to compensate for loss in sensitivity, still try to align something even if only aligned 1 flank