Adding branch
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Adding in binary to realign blast hits.
Adding in realignment step for pairwise alignments.
Adding in half done tests for cactus_realign
Finished a set of tests for cactus_realign and got everything
compiling nice. Now need to get tests working.
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Now all tests are passing, but haven't yet evaluated how it effects
performance of cactus.
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Fixing small bug, everything seems to work.
All working, still needs a bit more tuning testing and evaluation to
see if can be made fast enough.
All working
Merge branch 'filterXDrops' into HEAD
Updating defaults for new "realign" mode