force_align: Perform forced alignment with increased gap open penalty
In ssw: Striped Smith-Waterman Algorithm for Sequence Alignment using SIMD

force_align

R Documentation

Perform forced alignment with increased gap open penalty

Description

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


# 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)

ssw documentation built on Sept. 18, 2024, 9:07 a.m.