interOpsReport {basecallQC} | R Documentation

## Function to parse InterOps files and generate summary reports

### 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

    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.

- "machineReport" A data.frame containing information machine and software parameters

- "sequencingReport" A data.frame of mean cluster density, percentage clusters passing filter, phasing and prephasing percentages, number of reads total/passing filter and percent of reads with mean quality score > Q30 grouped by lane and read

- "demuxReport" A data.frame of demultiplexing results containing yield, number of reads, percentage of reads with quality scores greater than >Q30 and the percent of total reads per lane. Results are summarised per lane for samples, underdetermined indexes and all indexes (identifed and unidentified).

### Value

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

### Author(s)

Thomas Carroll.

### Examples

    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)

[Package basecallQC version 1.16.0 Index]