Provide defaults for various control variables

`na.strings` has a default value of "NA" as stated in
https://kbroman.org/qtl2/assets/vignettes/input_files.html#CSV_files
quote:

> Missing value codes will be specified in the control file (as
> na.strings, with default value "NA") and will apply across all
> files, so a missing value code for one file cannot be an allowed
> value in another file.

for `comment.char`

> The CSV files can include a header with a set of comment lines
> initiated by a value specified in the control file as comment.char
> (with default value "#").

for `sep`:

The default separator is expected to be the comma, as stated in
https://kbroman.org/qtl2/assets/vignettes/input_files.html#field-separator
quote:

> If the data files use a separator other than a comma ...

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