readPaf: Read PAF from an input file

In daewoooo/SVbyEye: Visualization of genomic structural variants

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.

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 March 31, 2024, 8:58 a.m.