#' Generate basecallQC report
#'
#' Creates a summary report from basecalling and demultiplexing metrics.
#'
#' @usage
#' \S4method{reportBCL}{basecallQC}(object,reportOut,reportOutDir,output,reportRMDfile,FQQC)
#' @docType methods
#' @name reportBCL
#' @rdname reportBCL
#' @aliases reportBCL reportBCL,baseCallQC-method
#' @author Thomas Carroll
#'
#' @param object A basecall QC object as returned from basecallQC() function
#' @param reportOut Name of report file
#' @param reportOutDir Directory for the report file
#' @param output Whether the report contains frozen or sortable tables. Options are "static" and "html"
#' @param reportRMDfile RMD to be used for reporting. (Default uses standard report template)
#' @param FQQC TRUE or FALSE, whether to run ShortRead fastq QC on any fastQ in output directory.
#' @return An HTML report is written to file.
#' @import stringr XML RColorBrewer methods raster ShortRead prettydoc
#' @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)
#' sampleSheet <- dir(fileLocations,pattern="*\\.csv",full.names=TRUE)
#' outDir <- file.path(fileLocations,"Runs/161105_D00467_0205_AC9L0AANXX/C9L0AANXX/")
#' bcl2fastqparams <- BCL2FastQparams(runXML,config,runDir=getwd(),outDir,verbose=FALSE)
#' bclQC <- basecallQC(bcl2fastqparams,RunMetaData=NULL,sampleSheet)
#' reportBCL(bclQC,"TestReport.html",output="html")
#' @export
reportBCL.basecallQC <- function(object,reportOut="report.html",reportOutDir=getwd(),
                      output="static",reportRMDfile=NULL,FQQC=FALSE){
  BCLQCreport <- object
  doFQQC <- FQQC
  fileLocations <- system.file("extdata",package="basecallQC")
  if(is.null(reportRMDfile)){
    reportRMD <- file.path(fileLocations,"reportRMDs","basecallqcreport.Rmd")
  }
  if(!file.exists(reportRMD)) stop()
  render(reportRMD,
         output_file = reportOut,output_dir=reportOutDir,params=list(title=paste0("basecallQC")))
}

setGeneric("reportBCL", function(object="basecallQC",reportOut="character",reportOutDir="character",
                                 output="character",reportRMDfile=NULL,FQQC=FALSE) standardGeneric("reportBCL"))

#' @rdname reportBCL
#' @export
setMethod("reportBCL", signature(object="basecallQC"), reportBCL.basecallQC)