BCL2FastQparams: The Parameters for BCL2FastQparams object.

Description Usage Arguments Details Value Examples

Description

Parameter class and accessors for use with basecallQC

Parameter class and accessors

Usage

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BCL2FastQparams(runXML = NULL, config = NULL, runDir = NULL,
  outDir = NULL, verbose = TRUE)

Arguments

runXML

file path to runParameters.xml ,if not specified looks in top level of run directory.

config

file path to config.ini ,if not specified looks in top level of run directory.

runDir

file path to run directory.

outDir

file path to out directory.

verbose

TRUE or FALSE. Messages on or off. Warnings/errors persist

Details

The BCL2FastQparams object contains slots RunDir, OutDir and RunParameters

Value

A BCL2FastQparams object (See details).

Examples

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fileLocations <- system.file("extdata",package="basecallQC")
runXML <- dir(fileLocations,pattern="runParameters.xml",full.names=TRUE)
config <- dir(fileLocations,pattern="config.ini",full.names=TRUE)
BCL2FastQparams(runXML,config,runDir=getwd(),verbose=FALSE)

ThomasCarroll/basecallQC documentation built on May 9, 2019, 4:45 p.m.