pafAlignmentToBins: Function to break PAF alignment into matching bases between...

In daewoooo/SVbyEye: Visualization of genomic structural variants

Function to break PAF alignment into matching bases between query and target sequence. In addition, locations of inserted bases in query and target sequence can be reported as well.

Description

Function to break PAF alignment into matching bases between query and target sequence. In addition, locations of inserted bases in query and target sequence can be reported as well.

Usage

pafAlignmentToBins(paf.aln = NULL, binsize = 10000)

Arguments

paf.aln	A data.frame or tibble containing a single PAF record with 12 mandatory columns along with CIGAR string defined in 'cg' column.
binsize	A size of a bin in base pairs to split a PAF alignment into.

Value

A tibble object storing binned PAF alignments.

Author(s)

David Porubsky

Examples

## Get PAF to bin ##
paf.file <- system.file("extdata", "test3.paf", package = "SVbyEye")
## Read in PAF
paf.table <- readPaf(paf.file = paf.file, include.paf.tags = TRUE, restrict.paf.tags = "cg")
## Split a single PAF alignment into user defined bins
pafAlignmentToBins(paf.aln = paf.table[1, ], binsize = 100)

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