speeds up add_peptide_positions by dropping Biostrings::match

CambridgeCentreForProteomics / camprotR

https://cambridgecentreforproteomics.github.io/camprotR/

MIT License

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speeds up add_peptide_positions by dropping Biostrings::match #53

Closed TomSmithCGAT closed 4 weeks ago

TomSmithCGAT commented 1 year ago

The speed (or lack of) of add_peptide_positions has been a pain for ages. This speeds it up about 4-fold by replacing Biostrings::matchPattern which appeared to be part of the issue from a quick profiling.

@csdaw - Any other ideas for optimisation?

TomSmithCGAT commented 1 year ago

Minor update to function outstanding (#54)