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Improved handling of range coordinates #205

Merged
merged 16 commits into from
Sep 28, 2024
Merged

Improved handling of range coordinates #205

merged 16 commits into from
Sep 28, 2024

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qiyunzhu
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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-fmt to control this behavior. Acceptable values are bed, gff, 0e, 1e, 0i, and 1i. Additionally, because the left shift operation is removed, the algorithms are slightly more performant.

@qiyunzhu qiyunzhu merged commit ddea40a into main Sep 28, 2024
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