OPTIONS

The following options can be used with any of the programs in the QTL Cartographer suite. The current programs are Rmap, Rqtl, Rcross, Qstats, LRmapqtl, SRmapqtl, JZmapqtl, MImapqtl, MultiRegress, Eqtl, Prune, and Preplot.

-h

Prints out the current values of all program options, and information on what the program does. It then exits.

-V

Turns the verbosity mode off. The programs in the suite print out messages while running. This option turns off those messages. This is useful for batch files.

-A

Skips the interactive screen for setting options. All programs start up with a menu that allows setting of options. This turns the menu off. It is also very useful for batch files.

-R

The programs will read the default parameters from a file specified with this option. If a file called qtlcart.rc is in the current working directory, it will be opened by default and all parameter values read. If no such file exists, then default parameter values will be assumed, and the file will be created.

It is probably better to simply rename a resource file qtlcart.rc than to use this option.

-W

This option allows one to set the work directory. This directory must exist. All the input files must be in this directory and the output files will be placed there.

-s

This requires a long integer to act as the random number seed. By default, it is the value returned by the ANSI C function time(), which is usually the number of seconds since some arbitrary past date (often 1 January 1970). This number will also be used as a unique identifer on the first line of the output file.

This can be a useful option. It is recorded in the log file when any program is run. It is possible to recreate exactly what was done using the log file.

-e

This requires a filename for the log file. It will be appended to if it exists and created if not. The default is qtlcart.log.

-X

Give a filename stem. All output will start with this stem and have extensions indicating what is in them.