#'Provides Coverage by the CpG density. CpG Density is defined as the number
 #'of CpGs observed in certain base pair long region.

 #'@param bs bsseq object

 #'@param organism scientific name of the organism of interest,

 #'e.g. Mmusculus or Hsapiens

 #'@param windowLength Length of the window to calculate the density

 #'Default value for window length is 1000 basepairs.

 #'@return Data frame with sample name and coverage in repeat masker regions
 #'@examples

 #'library(BSgenome.Hsapiens.NCBI.GRCh38)

 #'directory <- system.file("extdata/bismark_data",package='scmeth')
 #'bs <- HDF5Array::loadHDF5SummarizedExperiment(directory)

 #'cpgDensity(bs,Hsapiens,1000)

 #'@import BSgenome

 #'@importFrom bsseq getCoverage

 #'@export

 cpgDensity <- function(bs,organism,windowLength=1000){

     cov <- bsseq::getCoverage(bs)

     gr <- GenomicRanges::granges(bs)

     #GenomeInfoDb::seqlevelsStyle(gr) <- GenomeInfoDb::seqlevelsStyle(organism)[1]
     cpgd <- Repitools::cpgDensityCalc(gr, organism, window = windowLength)

     maxcpgd <- max(cpgd)
     cpgdCov <- sapply(seq_len(ncol(cov)), function(i) {

         cv = as.vector(cov[,i])

         cpgdCell <- cpgd[cv>0 ]

         tab <- table(cpgdCell)
         x <- rep(0, maxcpgd)
         x[as.numeric(names(tab))] <- tab
         x

     })
 

     rownames(cpgdCov) <- seq_len(maxcpgd)

     return(cpgdCov)

 }