The tiling doesn't work in some cases where inferred chromosome length is smaller than win.size-step.size. This may fix that

tileMethylCounts3.R

setGeneric("tileMethylCounts3", 
           function(object,win.size=1000,step.size=1000,cov.bases=0)
             standardGeneric("tileMethylCounts3") )

#' @aliases tileMethylCounts,methylRaw-method
#' @rdname tileMethylCounts-methods
setMethod("tileMethylCounts3", signature(object="methylRaw"),
  function(object,win.size,step.size,cov.bases){
    
    g.meth =as(object,"GRanges")
    #chrs   =IRanges::levels(seqnames(g.meth))
    chrs   =as.character(unique(seqnames(g.meth)))
    #widths =seqlengths(g.meth) # this doesn't work with BioC 3.0
    widths =sapply(chrs,function(x,y) max(end(y[seqnames(y)==x,])),g.meth  )# lengths of max bp in each chr
    all.wins=GRanges()
    for(i in 1:length(chrs))
    {
      # get max length of feature covered chromosome
      max.length=max(IRanges::end(g.meth[seqnames(g.meth)==chrs[i],])) 
      
      #get sliding windows with covered CpGs
      numTiles=floor(  (max.length-(win.size-step.size) )/step.size )+1
      numTiles=ifelse(numTiles<1, 1,numTiles)
      temp.wins=GRanges(seqnames=rep(chrs[i],numTiles),
                        ranges=IRanges(start=1+0:(numTiles-1)*step.size,
                                       width=rep(win.size,numTiles)) )
      all.wins=suppressWarnings(c(all.wins,temp.wins))
    }
    regionCounts(object,all.wins,cov.bases,strand.aware=FALSE)
  }
)

#' @aliases tileMethylCounts,methylRawList-method
#' @rdname tileMethylCounts-methods
setMethod("tileMethylCounts3", signature(object="methylRawList"),
  function(object,win.size,step.size,cov.bases){
    
    new.list=lapply(object,tileMethylCounts3,win.size,step.size,cov.bases) 
    new("methylRawList", new.list,treatment=object@treatment)
    
})



#' @aliases tileMethylCounts,methylBase-method
#' @rdname tileMethylCounts-methods
setMethod("tileMethylCounts3", signature(object="methylBase"),
          function(object,win.size,step.size,cov.bases){
            
            g.meth =as(object,"GRanges")
            #chrs   =IRanges::levels(seqnames(g.meth))
            chrs   =as.character(unique(seqnames(g.meth)))
            
            #widths =seqlengths(g.meth)
            widths =sapply(chrs,function(x,y) max(end(y[seqnames(y)==x,])),g.meth  )# lengths of max bp in each chr
            
            all.wins=GRanges()
            for(i in 1:length(chrs))
            {
              # get max length of feature covered chromosome
              max.length=max(IRanges::end(g.meth[seqnames(g.meth)==chrs[i],])) 
              
              #get sliding windows with covered CpGs
              numTiles=floor(  (max.length-(win.size-step.size) )/step.size )+1
              numTiles=ifelse(numTiles<1, 1,numTiles)
              temp.wins=GRanges(seqnames=rep(chrs[i],numTiles),
                                ranges=IRanges(start=1+0:(numTiles-1)*step.size,
                                               width=rep(win.size,numTiles)) )
              all.wins=suppressWarnings(c(all.wins,temp.wins))
            }
            regionCounts(object,all.wins,cov.bases,strand.aware=FALSE)
          }
)