parallelBamSummarise: summarise mapping observations from a BAM file using parallel...

In sagrudd/nanopoRe: Accessory Methods for the Analysis of Oxford Nanopore Technologies DNA Sequence Data

Description

This method will parse a BAM file and summarise the mapping observations in a way that can be used for preparation of figures and confidence plots by the nanopoRe package. This method is multithreaded and REQUIRES access to the reference genome.

Usage

parallelBamSummarise(bamFile, force = FALSE, blockSize=10000L,
    mc.cores = min(parallel::detectCores() - 1, 24))

Arguments

bamFile	is the location to the BAM file to parse
force	logical value describing whether the analysis should be force recalculated
blockSize	describes the size of BAM chunk to parse
mc.cores	number of threads to use for the process

Value

data.frame of per read summary observations

Examples

demoBam <- system.file("extdata",
    "Ecoli_zymo_R10_filt_subs.bam",
    package = "nanopoRe")
referenceGenome <- system.file("extdata",
    "Escherichia_coli_complete_genome.fasta",
    package = "nanopoRe")
setReferenceGenome(referenceGenome)
loadReferenceGenome()
bamSummary <- parallelBamSummarise(
    demoBam, force=FALSE, blockSize=10000L, mc.cores=2)

sagrudd/nanopoRe documentation built on June 7, 2020, 10:20 p.m.