BCL2FastQparams-class   The Parameters for BCL2FastQparams object.
baseCallMetrics         Gather basecalling metrics from a Run (using
                        Run's ConversionStats.xml file).
basecallQC-class        The basecallQC object and constructor.
createBCLcommand        Function to create command for Illumina
                        basecalling/demultiplexing using bcl2fastq
                        versions >= 2.1.7.
createBasemasks         Function to create basemasks for basecalling
                        from Illumina samplesheet (for bcl2Fastq
                        versions >= 2.1.7).
demultiplexMetrics      Gather demultiplexing metrics from a Run (using
                        Run's DemultiplexingStats.xml file).
demuxBarplot            Barplot of Illumina demultiplexing statistics.
demuxBoxplot            Boxplot of Illumina demultiplexing statistics.
indexlengths            Index lengths
interOpsReport          Function to parse InterOps files and generate
                        summary reports
makeFQTable             Generate an HTML table linking to per sample
                        summary fastq QC statistics from ShortRead
passFilterBar           Barplot of Illumina basecalling statistics for
                        reads passing filter.
passFilterBoxplot       Boxplot of Illumina basecalling statistics for
                        reads passing filter.
passFilterTilePlot      Tile plot of Illumina basecalling statistics
                        for reads passing filter.
readlengths             Read lengths
reportBCL               Generate basecallQC report
summaryConvStatsTable   Creates an HTML table of per sample summary
                        statistics from basecalling results
summaryDemuxTable       Generate an HTML table of per sample summary
                        demultiplexing statistics
validateBCLSheet        Illumina sample sheet cleaning and updating for
                        bcl2Fastq versions >= 2.1.7
