ROBUSTNESS: Add explicit 'stringsAsFactors' arguments [read.table]

[HenrikBengtsson]

$ (cd aroma.seq; grep -A 1 -F "read.table" -- R/*.R;)
R/CnvKitCopyNumberRatioFile.R:## Doesn't work, because 'flavor' is passed along all the way to read.table(),
R/CnvKitCopyNumberRatioFile.R-## which gives an error on 'unused argument (flavor = "PSCBS")'.   See also
--
R/FastaReferenceIndexFile.R:  data <- read.table(pathname, sep="\t", colClasses=colClasses)
R/FastaReferenceIndexFile.R-  ## Column names as in GATK (suggested in thread 'How can I prepare a