rbamtools (version 2.16.17)

bamCount: bamCount: Counting of CIGAR-OP items

Description

The bamCount function takes a bamReader object, a set of reference coordinates and the 'complex' argument and returns an integer vector.

Usage

bamCount(object,coords)

Arguments

object

An instance of bamReader. Must be opened and contain initialized index.

coords

Integer vector of length 3: coords=c(refid, start, stop)

Details

The method returns integer vector of length 10. Entries 1 to 9 contain the number of CIGAR-OP items found in the given range. The 10th entry is the total number of aligns in the range. The returned vector is named. The names of the vector are "M", "I","N","S","H","P","=","X" and nAligns. The first 9 names are the abbreviations for CIGAR-OP items which are defined in the SAM file format reference.

Examples

# NOT RUN {
bam <- system.file("extdata", "accepted_hits.bam", package="rbamtools")
reader<-bamReader(bam,idx=TRUE)
coords<-getRefCoords(reader,"chr1")
count<-bamCount(reader,coords)
count
bamClose(reader)
# }