#include"reconstruction.h"
#include<unistd.h>
#include<string.h>
#include<stdlib.h>
#include<stdio.h>
     
int main( int argc, char **argv ) {

  ALLELE_DATA **add;
  char *alleledir = NULL;
  char *mosaicfile = NULL;
  char *outdir = NULL;
  int c;
  int format = 1; // fix this 
  while ((c = getopt (argc, argv, "a:m:d:")) != -1)
    switch (c) {	
    case 'a':
      alleledir = optarg;
      break;
    case 'd':
      outdir = optarg;
      break;
    case 'm':
      mosaicfile = optarg;
      break;
    }
  if ( outdir == NULL ) outdir = strdup("./");

  if ( alleledir && mosaicfile ) {
    int nchr=5, i;
    ALLELE_DATA **ad=(ALLELE_DATA**)calloc(nchr+1,sizeof(ALLELE_DATA*));
    MOSAIC *mosaic;

    for(i=1;i<=nchr;i++) {
      FILE *fp;
      char filename[256];
      sprintf(filename, "%s/chr%d.alleles.txt", alleledir, i);
      printf("%s\n", filename);
      fp = fopen( filename, "r");
      if ( fp != NULL ) {
	ad[i] = ReadAlleleData( filename, format );
	sprintf(filename, "chr%d.alleles.Data", i);
	WriteBinaryAlleleData( ad[i], filename );
	fclose(fp);
      }
      else {
	fprintf(stderr, "ERROR could not open %s\n", filename);
	exit(1);
      }
    }
    mosaic = ReadMosaic( mosaicfile, ad[1]->col, ad[1]->Ncol );
    ImputeFromMosaic( mosaic, ad, nchr, outdir );

    return(0);
  }
  return(1);
}