a version of tileMethylCounts where the chromosome names obtained from GRanges out of unique seqnames, so there will be no chr names that do not have coverage. see the discussion here: https://groups.google.com/forum/#!topic/methylkit_discussion/75y6dbrbCWI

tileMethylCounts2.R

setGeneric("tileMethylCounts2", 
           function(object,win.size=1000,step.size=1000,cov.bases=0)
             standardGeneric("tileMethylCounts2") )

setMethod("tileMethylCounts2", signature(object="methylRaw"),
          function(object,win.size,step.size,cov.bases){
            
            g.meth =as(object,"GRanges")
            chrs   =as.character(unique(seqnames(g.meth)))
            widths =seqlengths(g.meth)
            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
              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("tileMethylCounts2", signature(object="methylRawList"),
          function(object,win.size,step.size,cov.bases){
            
            new.list=lapply(object,tileMethylCounts,win.size,step.size,cov.bases) 
            new("methylRawList", new.list,treatment=object@treatment)
            
          })



#' @aliases tileMethylCounts,methylBase-method
#' @rdname tileMethylCounts-methods
setMethod("tileMethylCounts2", signature(object="methylBase"),
          function(object,win.size,step.size,cov.bases){
            
            g.meth =as(object,"GRanges")
            chrs   =as.character(unique(seqnames(g.meth)))
            widths =seqlengths(g.meth)
            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
              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)
          }
)