as_bam: convert 'GAlignments' object to 'data.table'

In openanalytics/gread: Fast Reading and Processing of Common Gene Annotation and Next Generation Sequencing Format Files

Description

For internal use only. Converts a GAlignments object to bam object.

Usage

as_bam(x)

Arguments

x	A GAlignments object.

Value

An object of class bam that inherits from data.table.

Examples

## Not run: 
For internal use only
library(GenomicAlignments)
path <- system.file("tests", package="gread")
bam_file <- file.path(path, "sample.bam")

# with no metadata
bam <- GenomicAlignments::readGAlignments(bam_file)
gread:::as_bam(bam)

# with some metadata
bam <- as(as_granges(read_format(bam_file)), "GAlignments")
gread:::as_bam(bam)

## End(Not run)

openanalytics/gread documentation built on May 24, 2019, 2:29 p.m.