#' Read lengths
 #'
 #' Read lengths as defined by runParameters.xml
 #'
 #' @usage
 #' \S4method{readlengths}{BCL2FastQparams}(object)
 #'
 #' @docType methods
 #' @name readlengths
 #' @rdname readlengths
 #' @aliases readlengths readlengths,BCL2FastQparams-method, readlengths.bcl2fastqparams
 #'
 #' @author 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)
 #' readlength <- readlengths(bcl2fastqparams)
 #' @param object A BCL2FastQparams object
 #' @return Read lengths as defined runParamaeters.xml
 #' @export
 readlengths.bcl2fastqparams <-  function (object)
 {
   dplyr::select(object@RunParameters$runParams,Read1,Read2) %>% mutate_all(as.numeric)
 }
 
 setGeneric("readlengths", function(object="BCL2FastQparams") standardGeneric("readlengths"))
 
 #' @rdname readlengths
 #' @export
 setMethod("readlengths", signature(object="BCL2FastQparams"), readlengths.bcl2fastqparams)
 
 #' Index lengths
 #'
 #' Index lengths as defined by runParameters.xml
 #'
 #' @usage
 #' \S4method{indexlengths}{BCL2FastQparams}(object)
 #'
 #' @docType methods
 #' @name indexlengths
 #' @rdname indexlengths
 #' @aliases indexlengths indexlengths,BCL2FastQparams-method, indexlengths.bcl2fastqparams
 #'
 #' @author 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)
 #' indexlength <- indexlengths(bcl2fastqparams)
 #' @param object A BCL2FastQparams object
 #' @return Index lengths as defined runParameters.xml.
 #' @export
 indexlengths.bcl2fastqparams <-  function (object)
 {
   dplyr::select(object@RunParameters$runParams,IndexRead1,IndexRead2)  %>% mutate_all(as.numeric)
 }
 
 setGeneric("indexlengths", function(object="BCL2FastQparams") standardGeneric("indexlengths"))
 
 #' @rdname indexlengths
 #' @export
 setMethod("indexlengths", signature(object="BCL2FastQparams"), indexlengths.bcl2fastqparams)
 
 
 readPattern <- function(bcl2fastqparams){
   c(readlengths(bcl2fastqparams)[1],indexlengths(bcl2fastqparams)[1],
     indexlengths(bcl2fastqparams)[2],readlengths(bcl2fastqparams)[2])
 }