readPaf: Read PAF from an input file
In daewoooo/SVbyEye: Visualization of genomic structural variants

readPaf

R Documentation

Read PAF from an input file

Description

This function takes an PAF output file from minimap2 and loads the file along with user defined set of additional alignment tags (see PAF specification).

Usage

readPaf(
  paf.file = NULL,
  include.paf.tags = TRUE,
  restrict.paf.tags = c("NM", "cg")
)

Arguments

`paf.file`	A path to a PAF file containing alignments to be loaded.
`include.paf.tags`	Set to `TRUE` if all additional PAF alignment tags should be included in the output.
`restrict.paf.tags`	Define a set of PAF tag ids (e.g. NM, cg) to be reported in the output.

Value

A tibble of loaded PAF alignments

Author(s)

David Porubsky

Examples

## Get PAF to read in ##
paf.file <- system.file("extdata", "test1.paf", package = "SVbyEye")
## Read in PAF
paf.table <- readPaf(paf.file = paf.file)
## Read in PAF including all tags
paf.table <- readPaf(paf.file = paf.file, include.paf.tags = TRUE)
## Read in PAF including CIGAR string only
paf.table <- readPaf(paf.file = paf.file, include.paf.tags = TRUE, restrict.paf.tags = "cg")

daewoooo/SVbyEye documentation built on Oct. 15, 2024, 6:12 a.m.