interOpsReport: Function to parse InterOps files and generate summary reports

Description Usage Arguments Details Value Author(s) Examples

View source: R/processInterOps_Functions.R

Description

Parses the InterOps binary files produced by Illumina's Real Time Analysis sofware and used by Illumina's SAV sofware. InterOp binary files contain information on phasing/prephsing, yield,read numbers and basecalling quality score distributions per cycle. This interOpsReport functions parses and summarises the InterOps files, TileMetrics.bin and QMetrics.bin, and the Stats directory XML files, ConversionStats.xml and DemultiplexingStats.xml.

Usage

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interOpsReport(bcl2fastqparams, verbose = TRUE)

Arguments

bcl2fastqparams

A BCL2FastQparams object.

verbose

TRUE or FALSE . TRUE reports progress through file parsing.

Details

The interOpsReport function returns a list of machine and run information, basecalling quality information and demultiplexing information. The three named elements are descibed below.

Value

A named list of length 3 containing machine and run information, basecalling quality information and demultiplexing information.

Author(s)

Thomas Carroll.

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 <- BCL2FastQparams(runXML,config,runDir=getwd(),verbose=FALSE)

# myRes_BCAGJ8ANXX <- interOpsReport(bcl2fastqparams,verbose=TRUE) 

ThomasCarroll/basecallQC documentation built on May 10, 2017, 4:50 p.m.