get_readpairs: Parse BAM file for improper read pairs near a set of GRanges

In cancer-genomics/trellis: Somatic structural variant analysis

Parse BAM file for improper read pairs near a set of GRanges

Description

All reads aligned to the intervals given by queryRanges(object) are identified by the low-level function .scan_all_readpairs. This function reads alignments by readGAlignments and then makes pairs of the alignments by makeGAlignmentPairs2. The latter function is an adaption of the function makeGAlignmentPairs implemented in the GenomeAlignments package but allows for the read pairs to be improper.

Usage

get_readpairs(object, bam.file, flags = scanBamFlag())

Arguments

object	Typically an AmpliconGraph, though the only requirement is that the method queryRanges is defined
bam.file	character-vector providing valid complete path to a bam file
flags	length-two integer vector as given by scanBamFlags

Value

A GAlignmentPairs object

cancer-genomics/trellis documentation built on Feb. 2, 2023, 7:04 p.m.