BioJulia / BioSequences.jl

Biological sequences for the julia language
http://biojulia.dev/BioSequences.jl
MIT License
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Decode nocheck #281

Closed jakobnissen closed 1 year ago

jakobnissen commented 1 year ago

Relax the requirement of Alphabet, such that it is no longer necessary to check for a valid encoding in decode. This implies that storing invalid data in a BioSequence is disallowed, but it speeds up getindex(::BioSequence), which is critical.

codecov[bot] commented 1 year ago

Codecov Report

All modified lines are covered by tests :white_check_mark:

Comparison is base (4839f27) 90.96% compared to head (2d089a3) 91.01%. Report is 1 commits behind head on master.

Additional details and impacted files ```diff @@ Coverage Diff @@ ## master #281 +/- ## ========================================== + Coverage 90.96% 91.01% +0.04% ========================================== Files 31 31 Lines 2402 2392 -10 ========================================== - Hits 2185 2177 -8 + Misses 217 215 -2 ``` | [Flag](https://app.codecov.io/gh/BioJulia/BioSequences.jl/pull/281/flags?src=pr&el=flags&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=BioJulia) | Coverage Δ | | |---|---|---| | [unittests](https://app.codecov.io/gh/BioJulia/BioSequences.jl/pull/281/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=BioJulia) | `91.01% <ø> (+0.04%)` | :arrow_up: | Flags with carried forward coverage won't be shown. [Click here](https://docs.codecov.io/docs/carryforward-flags?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=BioJulia#carryforward-flags-in-the-pull-request-comment) to find out more. | [Files](https://app.codecov.io/gh/BioJulia/BioSequences.jl/pull/281?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=BioJulia) | Coverage Δ | | |---|---|---| | [src/alphabet.jl](https://app.codecov.io/gh/BioJulia/BioSequences.jl/pull/281?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=BioJulia#diff-c3JjL2FscGhhYmV0Lmps) | `89.33% <ø> (+1.09%)` | :arrow_up: |

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