rbamtools (version 2.4.0)

bamGapList-class: Class "bamGapList"

Description

The bamGapList class represents a list of Alignment gap (N-items in Cigar-data) sites . For each gap-site, left and right start and end positions as well as the gap-length are reported. Numbers of aligns supporting this site, number of left-sided start positions (

Objects from the Class

Objects can be created by calls of the form siteList(reader,coords)).

Examples

library(rbamtools)
bam<-system.file("extdata", "accepted_hits.bam", package="rbamtools")
reader<-bamReader(bam,idx=TRUE)
bsl<-bamGapList(reader)
bsl
size(bsl)
nAligns(bsl)
nGapAligns(bsl)
summary(bsl)
dfr<-as.data.frame(bsl)
head(dfr)
bamClose(reader)