text: FLASSO_RSCRIPT = """\
  #!/usr/bin/env Rscript
  
  # Calculate copy number segmentation by Fused Lasso.
  # Input: log2 coverage data in CNVkit's tabular format
  # Output: the CBS-style SEG data table
  
  %(rlibpath)s
  library('cghFLasso')
  
  tbl <- read.delim("%(probes_fname)s")
  
  write(paste("Segmenting", levels(tbl$chromosome)), stderr())
  fit <- cghFLasso(tbl$log2, FDR=%(threshold)g, chromosome=tbl$chromosome)
  
  # Reformat the output table as SEG
  outtable <- data.frame(sample="%(sample_id)s",
                         chromosome=tbl$chromosome,
                         start=tbl$start,
                         end=tbl$end,
                         nprobes=1,
                         value=fit$Esti.CopyN)
  
  write("Printing the segment table to standard output", stderr())
  write.table(outtable, '', sep='\t', row.names=FALSE)
  """
  