parseCigarString: Function to parse CIGAR string into a set interval ranges.

In daewoooo/SVbyEye: Visualization of genomic structural variants

Function to parse CIGAR string into a set interval ranges.

Description

Function to parse CIGAR string into a set interval ranges.

Usage

parseCigarString(cigar.str = NULL, coordinate.space = "reference")

Arguments

cigar.str	A character string containing alignment represented as a CIGAR string.
coordinate.space	A used defined coordinate space given CIGAR should be parsed against, either 'reference' or 'query'.

Value

A IRangesList object.

Author(s)

David Porubsky

Examples

## Get PAF to process
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")
## Parse CIGAR in reference (target) space
parseCigarString(cigar.str = paf.table$cg)
## Parse CIGAR in query space
parseCigarString(cigar.str = paf.table$cg, coordinate.space = "query")

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