Allow for both linear and circular plasmids, as well as regions #62
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…ough regions with caveats: assume embedded into circular genome, and that they are all oriented 'correctly', as two regions that are the same, but one is the reverse of the other, will have DCJ distance 1 under current assumptions)
…compare orientations of longest block on ref and query. If they're different, reverse the fake marker on the query sequence. If the longest blocks on ref and query are not the same, then the orientation is ambiguous and change nothing about the fake marker.
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(although regions with caveats: assume embedded into circular genome, and that they are all oriented 'correctly', as two regions that are the same, but one is the reverse of the other, will have DCJ distance 1 under current assumptions)
addresses issues #44 and #6