
PARAMETERS FOR THE PROGRAM STRAT.  The program will also read details about
the input data file from the file "mainparams".  


"(int)" means that this takes an integer value.
"(d)"   means that this is a double (ie, a Real number such as 3.14).
"(B)"   means that this variable is Boolean 
        (ie insert 1 for True, and 0 for False).


#define NUMSIMSTATS  1000  // (int) number of simulated test stats per locus
#define PHENOTYPECOL   2   // (int) which column in the input file contains phenotype data

#define POOLFREQ      10   // (int) pool alleles that have fewer than this many copies
#define LOCUSxONLY     0   // (int) Estimate a p-value for this locus only.  The loci 
                                    are numbered {1...L} according to their order in the
                                    input file.  Setting this to 0 turns this option off
                                    -- ie, p-values are estimated for all loci.
#define EMERROR     0.001  // (double) stop EM when change is less than this (>0)
#define MISSINGPHENO  -9   // (int) value used to designate missing phenotype data.
                                    These individuals are ignored by STRAT.



Command line options:

-m mainparams
-e extraparams
-s stratparams
-K MAXPOPS 
-L NUMLOCI
-N NUMINDS
-i input genotype file
-o Structure output file (with _q suffix)
-S STRAT output file 
-r number of simulated test stats per locus
-c column of input file that contains the phenotype data
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