Perform forced alignment with increased gap open penalty — force_align • ssw

Perform forced alignment with increased gap open penalty

Usage

force_align(
  read,
  reference,
  force_overhang = FALSE,
  match_score = 2L,
  mismatch_penalty = 2L
)

Arguments

read: A character string of the read.
reference: A character string of the reference.
force_overhang: Logical. If TRUE, ensures only one end of the alignment overhangs. Default is FALSE.
match_score: An integer for scoring matches, ranging from 0 to 255. Default is 2.
mismatch_penalty: An integer for mismatch penalties, ranging from 0 to 255. Default is 2.

Value

A list of class ssw containing the input sequences, the ssw aligner object, and the alignment results.

Examples

if (FALSE) { # is_installed_ssw_py()
# Results are truncated
a <- force_align("ACTG", "TTTTCTGCCCCCACG")
a

# Format the results
b <- a |> formatter()
b

# Print the formatted results directly
a |> formatter(print = TRUE)
}