#include"reconstruction.h"
#include<unistd.h>
#include<string.h>
     
void ProcessSeqCalls( char *dir, char *suffix, ALLELE_DATA **add, int nchr, int *nseq, int penalty, FILE *outfp ) {
  glob_t globbuf;
  char pattern[256];
  struct dirent **d;
  sprintf(pattern, "%s/*%s", dir, suffix );
  printf("pattern %s\n", pattern);
  glob( pattern, 0, NULL, &globbuf );
  int n = globbuf.gl_pathc;
  int chr;
  //      if ( n > 21 ) n =21;  
  if (n < 0)
    fprintf(stderr, "ERROR no files to process in %s\n", dir );
  else {
    int k=0,i;
    for(i=0;i<n;i++) {
      printf("%s\n", globbuf.gl_pathv[k]);
      SEQ_CALL *seq_call = ReadSeqCall(  globbuf.gl_pathv[k], add, nchr ); 
      for(chr=1;chr<=nchr;chr++) {
	ReconstructMosaicDiploid( seq_call, penalty, chr, fp );
      }
      FreeSeqCall(seq_call);
    }
  }
}


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

  ALLELE_DATA **add;
  int index;
  int c;
  int diploid=1;
  int penalty=100;
  char *alleledir = NULL;
  char *outdir = NULL;
  char *calldir = NULL;
  char *maskfile = NULL;
  char *zfile = NULL;
  char *Penalty = NULL;
  char *opterr = 0;
     
  while ((c = getopt (argc, argv, "da:m:c:o:p:z:")) != -1)
    switch (c) {	
    case 'd':
      diploid=1;
      break;
    case 'a':
      alleledir = optarg;
      break;
    case 'c':
      calldir = optarg;
      break;
    case 'm':
      maskfile = optarg;
      break;
    case 'o':
      outdir = optarg;
      break;
    case 'p':
      Penalty = optarg;
      break;
    case 'z':
      zfile = optarg;
      break;
    }
  if ( Penalty )
    sscanf( Penalty, "%d" , &penalty);
  if ( outdir == NULL )
    outdir = strdup("./");
  if ( zfile == NULL )
    zfile = strdup("mosaic.txt"); // outputfile of mosaic
  printf("calldir %s\n", calldir );
  printf("penalty = %d\n", penalty); 	

  if ( alleledir && calldir ) {
    int s, chr, nchr=5, nseq=0;
    ALLELE_DATA ** add = ReadGenomeAlleleData( alleledir, maskfile, &nchr ) ;
    FILE *fp = fopen(zfile,"w");
    ProcessSeqCalls( calldir , "", add, nchr, &nseq, penalty, fp );
  }
}