Improved handling of range coordinates #205
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This PR follows #204 by @wasade . It uniformly makes the internal data structure BED-like (0-based, exclusive end), and makes all parsers (BLAST, SAM, PAF) match this standard. The output coverage format is now BED by default. The user can use parameter
--outcov-fmtto control this behavior. Acceptable values arebed,gff,0e,1e,0i, and1i. Additionally, because the left shift operation is removed, the algorithms are slightly more performant.