Update parse_mutations.R

[danerkestey]

In this optimized version, I minimized string operations and redundant conversions for parse_unique_mutations:

• Precomputed unique(muts) outside loop to avoid redundant calculations
• Avoid unnecessary conversions in the loop by directly extracting substrings and values
• Used a single loop to iterate over unique_muts compared to the nested loops
• Returned data frame with added parameter stringsAsFactors = FALSE to make sure char columns aren't converted to factors

[DBecker7]

This won't work - you've removed the call to provoc:::parse_mutation(), so no actual parsing is done. You can see a few test cases in tests/parse_mutations.R where something like ~27785A gets parsed into aa:orf7b:Y10*. The parse_mutation() function is the workhorse and contains all of the bioinformatic information required to determine the amino acid position within an open reading frame.

parse_mutations() should better handle the string operations, then pass them to parse_mutation(). The actual parse_mutation() function could be vectorized for speed improvements, but the amino acid information needs to remain.

Sorry, I believe it's my fault for not pointing you to the tests, and I now see that Baaijens does not have the mutations column (I thought it did). For the next steps, look at the output of parse_mutations(Baaijens$label) for the original function, and make sure the new version produces the same results.

[danerkestey]

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