rbamtools (version 2.4.0)

bamReader: bamReader

Description

The bamReader function returns an object of class bamReader. The bamReader object represents a connection to an opened BAM-file. When an indexname is given or idx=TRUE, the function tries to load an existing BAM-index.

Usage

bamReader(filename,indexname,idx=FALSE,verbose=0)

Arguments

filename

Filename of BAM-file to be opened for reading.

indexname

Optional: Name of BAM-index file

idx

Logical

verbose

Numeric: Quantifies the extent of textual feedback (levels: 0,1,2).

Examples

bam<-system.file("extdata","accepted_hits.bam",package="rbamtools")
reader<-bamReader(bam)
align<-getNextAlign(reader)
name(align)
position(align)
bamClose(reader)
# Open reader and initialize BAM-index
reader<-bamReader(bam,idx=TRUE)
index.initialized(reader)