ceScanOneStep function
This function run cne detection in one function.
ceScanOneStep(axt1, filter1=NULL, sizes1, assembly1, twoBit1,
              axt2, filter2=NULL, sizes2, assembly2, twoBit2,
              thresholds=c("49_50"), blatBinary="blat",
              blatCutoff1, blatCutoff2)

  The \code{axt} object or axt filenames with each assembly as referecne.
  The \code{GRanges} object or bed filenames.
  A \code{Seqinfo} object which contains the \code{seqnames} and
    \code{seqlengths} for each assembly.
  The assembly names.
  The file names of two bit files of two assemblies.
    A \code{character} object specifiying the scanning windows and
    minimal score.
    It can be specified in th form of "45_50" with scanning windows 50
    and minial score 45.
    More than one thresholds can be provided.
 A object of \code{character}. The path of blat binary.
 \item{blatCutoff1, blatCutoff2}{
  A object of \code{integer}.
  The CNEs with more than the cutoff hits on the reference genome are removed.

  An object \code{CNE} is returned.

  Ge Tan