#include<stdio.h>
#include<reconstruction.h>

int main( int argc char **argv ) {

  char bdir[256];
  char sdir[256];
  char adir[256];
  char suffix[256];
  char maskfile[256];
  int nchr = 5, nseq=0;
  ALLELE_DATA **add = ReadGenomeAlleleData( adir, maskfile, &nchr );
  BINARY_DATA **bd = read_binary_genome( nchr, bdir );
  SEQ_CALL **sqq = ReadSeqCalls( sdir, suffix, add, nchr, &nseq );
}

  int check_mosaic( SEQ_CALL *sq, BINARY_DATA **bd ) {

    int chr, bp, m, idx=-1, last=-1;
    BINARY_DATA *b;
    int seq_idx=-1;
    for(seq_idx=0;seq_idx<bd[0]->nseq;seq_idx++){
      if ( !strcmp( bd[0]->id[seq_idx], sq->name ) ) break;
    }
    if ( seq_idx < bd[0]->nseq ) {
      for(m=0;m<sq->len;m++) {
	chr = sq->chr[m];
	bp = sq->bp[m];
	if ( chr != last ) {
	  idx = 0;
	  b = bd[chr];
	}
	while( idx < b->nsite && b->site[idx]<bp )
	  idx++;
	if ( b->site[idx] == bp ) {
	  int geno = b->mat[b->site[idx]][seq_idx];
}