headerLine-class: Class '"headerLine"': Representation of header line segment...

In rbamtools: Read and Write BAM (Binary Alignment) Files

Description

headerLine represents the header Line segment of header section.

Objects from the Class

Objects can be created by calls of the form hl<-new("headerLine").

Slots

SO:

character

VN:

character

Methods

getHeaderText

signature(x = "bamRange"): Retrieve textual representation of header

getVal

signature(object = "bamRange"): Retrieving values for given item names.

setVal

signature(object = "bamRange"): Setting values for given item names.

as.list

signature(.Object = "bamRange"): Coercing of data into a list

Author(s)

Wolfgang Kaisers

Examples

bam<-system.file("extdata","accepted_hits.bam",package="rbamtools")
reader<-bamReader(bam)
header<-getHeader(reader)
htxt<-getHeaderText(header)
headLine<-headerLine(htxt)
getVal(headLine,"VN")
getVal(headLine,"SO")
setVal(headLine,"SO","unsorted")
l<-as.list(headLine)
txt<-getHeaderText(headLine)
bamClose(reader)

Example output

Loading required package: refGenome
Loading required package: doBy
Loading required package: RSQLite
[1] "1.0"
[1] "unsorted"

rbamtools documentation built on Nov. 11, 2019, 5:09 p.m.