get_readpairs2: Extract reads from a bam file

View source: R/alignment-utils.R

get_readpairs2R Documentation

Extract reads from a bam file

Description

Parses a BAM file for read pairs near intervals specified by a GRanges object and returns the read pairs in a GAlignmentPairs object.

Usage

get_readpairs2(g, bam.file, flags = scanBamFlag())

Arguments

g

A GRanges object

bam.file

A character vector of the path to a bam file

flags

A length-two integer vector as given by scanBamFlags

Value

A GAlignmentPairs object

See Also

get_readpairs


cancer-genomics/trellis documentation built on Aug. 20, 2024, 5:48 p.m.