Add variation of Jukes-Cantor distance - #61
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Add variation of Jukes-Cantor distance. The Jukes-Cantor equation remains unchanged, but the definition of which base pairs are considered different is modified. In this function, the fraction of nucleotides that are different incorporates not only the mismatches from the alignment matrix but also the base pairs that are left unaligned.
Add documentation for new function and update documentation of existing functions from the family "Alignment statistics" and "Similarity indexes".
charles-plessy
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Aug 27, 2026
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Can I ask you two minor changes?
| #' d <- JC69_distance_allseq(gb, exampleSubstitutionMatrix) | ||
| #' | ||
| #' @export | ||
| JC69_distance_allseq <- function(gb, m, adjust_p=FALSE) { |
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Can you add the usual guard for object length 0 ?
if(length(gb) == 0) return(numeric(0))
| # Gets the smallest sequence length. | ||
| totBps <- min(sum(seqlengths(gb)),sum(seqlengths(gb$query))) | ||
| if(is.na(totBps)){ | ||
| totBps <- min(sum(guessSeqLengths(gb)),sum(guessSeqLengths(gb$query))) |
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guessSeqLengths always returns seqlengths when available, so you can run totBps <- min(sum(guessSeqLengths(gb)),sum(guessSeqLengths(gb$query))) straight. Maybe I could have called the function safeSeqLengths but it is probably too late to rename it.
Add safeguard for gb object Remove redundant code
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Thanks Charles for your comments! I have updated the code with the proposed changes. |
charles-plessy
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Aug 27, 2026
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This pull request adds a variation of the Jukes-Cantor distance that takes into account unaligned base pairs in the computation.
It also updates the documentation of existing functions from the family "Alignment statistics" and "Similarity indexes".