rbamtools (version 2.0.1)

bamSort: bamSort(bamAlign)

Description

Sorts a given BAM-file (by position or by name) into a second BAM-file.

Usage

bamSort(object,prefix,byName=FALSE,maxmem=100000000)

Arguments

object

An Instance of class bamReader

prefix

Character String

byName

Logical

maxmem

Approximate maximum memory usage

Value

• None

Details

BAM-files must be sorted before an index can be created. During this routine, some content of the source file is copied into the working memory, sorted and written into temporary files. Finally, the sorted files are merged into a single target. The name of the target is [prefix].bam. Number and size of temporary files depend on source file size and used working memory (maxmem). Small maxmem values result in large numbers of temporary files. The minimum maxmem value is 100000000. Smaller maxmem values cause an error.

Examples

library(rbamtools)
bam_file <- system.file("extdata", "accepted_hits.bam", package="rbamtools")
reader<-bamReader(bam_file)
isOpen(reader)
bamSort(reader,"sorted")
bamClose(reader)