Command-line changes to parameter values

In order to simplify batch runs and make it easier to run simulations involving structure, we have added command-line flags that update the values of certain parameters, over-riding the values set in mainparams. These are as follows:

-m (mainparams) Read a different parameter input file instead of mainparams.

-e (extraparams) Read a different parameter input file instead of extraparams.

-s (stratparams) Read a different parameter input file instead of stratparams. (For use with the accompanying program, STRAT, for association mapping.)

-K (MAXPOPS) Change the number of populations.

-L (NUMLOCI) Change the number of loci.

-N (NUMINDS) Change the number of individuals.

-i (input file) Read data from a different input file.

-o (output file) Print results to a different output file.

Thus, to over-ride one of the preset parameter values, we invoke structure and then use the relevant flag, followed by the new parameter value. The flag and new value are separated by a space. The flags can be used in any order. For example, to change the number of assumed populations to 5, and direct the output to a file called output5, we could call structure as follows: ./structure -K 5 -o output5