paf2gaps: Report gaps between PAF alignments.
In daewoooo/SVbyEye: Visualization of genomic structural variants

paf2gaps

R Documentation

Report gaps between PAF alignments.

Description

This function takes loaded PAF alignments using readPaf function and then reports all gaps in subsequent target and query alignments and classify them as either deletions ('D') or insertions ('I').

Usage

paf2gaps(paf.table, min.gap.diff = NULL)

Arguments

`paf.table`	A `data.frame` or `tibble` containing a single or multiple PAF record(s) with 12 mandatory columns along with CIGAR string defined in 'cg' column.
`min.gap.diff`	A user defined minimum gap size difference in target and query coordinates (and vice versa) to be retained.

Value

A tibble of PAF alignment gaps.

Author(s)

David Porubsky

Examples

## Get PAF to process ##
paf.file <- system.file("extdata", "test1.paf", package = "SVbyEye")
## Read in PAF
paf.table <- readPaf(paf.file = paf.file, include.paf.tags = TRUE, restrict.paf.tags = "cg")
## Report gaps between PAF alignments
paf2gaps(paf.table = paf.table)

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