nucmer2PAF: Read nucmer coordinates file in to PAF formatted table
In daewoooo/SVbyEye: Visualization of genomic structural variants

nucmer2PAF

R Documentation

Read nucmer coordinates file in to PAF formatted table

Description

This function takes alignments produced by nucmer (parameters: –mum –coords) and loads reported coordinates file (suffix .coords) into a PAF formatted table (see PAF specification).

Usage

nucmer2PAF(nucmer.coords = NULL)

Arguments

nucmer.coords

A path to a nucmer coordinates file containing alignments to be loaded.

Author(s)

David Porubsky

Examples

## Get nucmer coordinates to read in ##
nucmer.coords <- system.file("extdata", "HG00438_1_nucmer.coords", package = "SVbyEye")
## Read in nucmer coordinates
nucmer2PAF(nucmer.coords=nucmer.coords)

daewoooo/SVbyEye documentation built on March 31, 2024, 8:58 a.m.