levenAll: Wrapper for .C Levenshtein function

In sherrillmix/levenR: Simple Levenshtein Alignment and Distance Calculation

Wrapper for .C Levenshtein function

Description

Align and calculate distance betweeen two strings based on Levenshtein distance with ends-free or homopolymer alignments possible (probably not called directly)

Usage

levenAll(
  string1,
  string2,
  homoLimit = 0,
  prepend = NULL,
  append = NULL,
  revComp = FALSE,
  align = FALSE,
  nThreads = 1
)

Arguments

string1	A single string or vector of strings
string2	Another single string or vector of strings
homoLimit	deletions or insertions in homopolymers > homoLimit cost 0
prepend	1 or 2 for ends-free on front of string 1 or 2
append	1 or 2 for ends-free on back of string 1 or 2
revComp	Should the reverse compliment of string1 also be tested and the best of identity or reverse compliment returned?
align	Should an alignment be calculated
nThreads	If threads >1, run nThreads threads in parallel

Value

Either a distance or if align==TRUE a list with distance and alignment

Author(s)

Scott Sherrill-Mix [e-mail]

References

http://en.wikipedia.org/wiki/Levenshtein_distance

sherrillmix/levenR documentation built on Oct. 25, 2023, 11:42 a.m.