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Support lowercase bases? #9

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luizirber opened this issue Jun 16, 2021 · 1 comment
Open

Support lowercase bases? #9

luizirber opened this issue Jun 16, 2021 · 1 comment
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enhancement New feature or request

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@luizirber
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luizirber commented Jun 16, 2021 •
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This error in rust-mdbg is triggered because lowercase bases are passed to nthash. Possible solutions:

  1. users of the crate need to provide uppercase (non-repeat masked) nucleotides. This will probably trigger another allocation, so potentially slower.
  2. accept lowercase bases in nthash. One solution is modifying H_LOOKUP and RC_LOOKUP to also have the lowercase variants.
    • should this also have some sort of "strict mode" that doesn't accept lowercase bases, declared in the constructor?
@luizirber luizirber added the enhancement New feature or request label Jun 16, 2021
@luizirber luizirber mentioned this issue Jun 16, 2021
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@RagnarGrootKoerkamp
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Similarly, it may be nice to accept [0,1,2,3] values for convenience as well, for when data is already packed.

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@luizirber @RagnarGrootKoerkamp