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Fix indent take 2
Reverting changes to exonerate_hits.py (Issue 27)
Fix issue 27: No check for strand when there is only one hit
More README formatting changes
Add citation information
Moved exonerate commands to DEBUG to not clutter logs.
credit to Elliot for logo
Even more consistent full length contig decisions
Merge branch 'develop' of github.com:mossmatters/HybSeqPipeline into … …develop