Incompatibility with new version of R

[pashadag]

When running with a new version of R, you get
“Fatal error: you must specify '--save', '--no-save' or '--vanilla'

The fix for this is to change the way Rscript is called, at every instance. For example, the line that calls "doc_walker" must be changed to

execCommand("cat $win_file.1 | $exec_folder/doc_walker $scov_file $exp_file full | $exec_folder/gcContent $ref_folder/fasta_files_folder/$chr.fa | $Rfolder/Rscript --slave --file=$exec_folder/annot1_win.R \"--args $win_file.2\" ", $par);