naiveGetAllNNBySampAndStop: solves the All 1NN
In Ahhgust/MMDIT: Mitochondrial mixture project

(much) more efficient solutions exist (cover trees) O(n log n) for n individuals and a constant genome length the solution provided is O(n^2) by the same count. This version of the code finds the NN for each amplicon (not for the whole mito)

1	naiveGetAllNNBySampAndStop(amps, ignoreIndels = FALSE)

`amps`	the output from getAmps
`ignoreIndels`	(whether or not indels were used to constitute the strings...)

This looks at each individual in amps and finds the 2NN of that individual and the associated distances and the selects the 2nd individual. in theory this could give you the same individual as you queried (ties are broken arbitrarily). If you care about that... write your own :) I just want the distances!

Ahhgust/MMDIT documentation built on Jan. 27, 2021, 11:48 a.m.