#include<stdio.h>
#include<stdlib.h>
#include<unistd.h>
#include<string.h>
#include"reconstruction.h"

int main( int argc, char **argv ) {

  ALLELE_DATA **add;
  int N=0, M=0, nchr=0, c, diploid=0;
  char filename[256], *species=NULL, *alleledir=NULL, *balleledir=NULL;
  double r=50e6;
  species = strdup("mouse");
     
  while ((c = getopt (argc, argv, "a:b:dm:n:s:r:")) != -1)
    switch (c) {	
    case 'a':
      alleledir = optarg;
      break;
    case 'b':
      balleledir = optarg;
      break;
    case 'd':
      diploid=1;
      break;
    case 'm':
      sscanf(optarg,"%d", &M);
      break;
    case 'n':
      sscanf(optarg,"%d", &N);
      break;
    case 'r':
      sscanf(optarg, "%lf", &r );
      break;
    case 's':
      species = optarg;
      break;
    }

  char **chroms = TheChromosomes( species, &nchr );
  printf( "species %s\n", species);
  printf( "bp_per_recomb %g\n", r );
  printf( "M sims %d\n", M);
  printf( "N av ssites per sim %d\n", N );
  printf( "diploid %d\n", diploid);

  if ( ( alleledir || balleledir ) && nchr > 0 && N > 0 && M > 0 && r > 0.0 ) {
      
    int s, chr, nseq=0;
    ALLELE_DATA ** add=NULL;
    if ( alleledir ) 
      add = ReadGenomeAlleleData( alleledir, NULL, 0, nchr, chroms ) ;
    else if ( balleledir )
      add = ReadAllBinaryAlleleData(balleledir, 0, nchr, chroms );
    
    int i;
    for( i=0;i<M;i++) {
      char filename[256];
      sprintf(filename, "simulate.%d", i+1);
      Simulate( nchr, add, diploid, r, N, filename );
    }
    return(0);
  }
  return(1);
}