bamParseLengths: Parse reads in bam files by insert size.

Description Usage Arguments

Description

bam.parselengths separates reads from a paired-end bam file into separate files based on insert sizes using samtools view and the system awk.

Usage

1
bamParseLengths(bamFiles, breaks, threads = getOption("threads", 1L))

Arguments

bamFiles

A character vector of paths to bam files.

breaks

A numeric vector of read lengths used as break points to parse reads by length. For example, if breaks=c(0,100,200), reads will be parsed into reads of length 0-99 and 100-199. Length of vector must beat least 2.

threads

A positive integer specifying how many bams to process simultaneously.


dvera/travis documentation built on June 5, 2019, 5:12 a.m.