rbamtools (version 2.0.1)

mapQuality: mapQuality: Reads the mapQuality value from bamAlign.

Description

The mapQuality is given by the alignment algorithm which produces the alignments.

Usage

mapQuality(object)

Arguments

object

An instance of class bamAlign.

Value

• Integer

Details

mapQuality gives measures for the probability that the map-Position is wrong. A value 255 indicates that the mapping quality is not available.

References

The SAM Format Specification. The SAM Format Specification Working Group. September 7, 2011. http://www.samtools.sourceforge.net/SAM1.pdf

Examples

bam_file <- system.file("extdata", "accepted_hits.bam", package="rbamtools")
reader<-bamReader(bam_file)
isOpen(reader)
align<-getNextAlign(reader)
mapQuality(align)
bamClose(reader)