#include "psublast/psublast.h"

typedef struct region {
    int b, e;
    int flag;
    struct region *link;
} region_list_t, *region_list_ptr;

typedef struct line {
    char orf[100];
    int len;
    int b, e;
} hit_t, *hit_ptr;

#define Usage    "%s <plusfile> <minusfile>"

#define   MAX_NUM_MATCHES   100000

static hit_t Matches[MAX_NUM_MATCHES];
static int numMatches = 0;

static region_list_ptr new_region(int b, int e, region_list_ptr link);
static int insert_region(region_list_ptr *rlist, int b, int e, int flag);


int main(int argc, char *argv[])
{
  FILE *fp;
  char buf[1000], *tok, *orf;
  region_list *regions;

  if (argc!=2) fatalf(Usage, argv[0]);

  fp = ckopen(argv[1],"r");

  regions = NULL;

  while (fgets(buf,1000,fp)!=NULL)  {
      tok  = strtok(buf, " ");
      orf  = strsave(tok);
      tok  = strtok(NULL, " ");
      from = atoi(tok);
      tok  = strtok(NULL, " \n");
      to   = atoi(tok);

      insert_region(&regions, from, to, 1);
  }
  fclose(fp);
 
  fp = ckopen(argv[2],"r");

  while (fgets(buf,1000,fp)!=NULL)  {
      tok  = strtok(buf, " ");
      tok  = strtok(NULL, " ");
      from = atoi(tok);
      tok  = strtok(NULL, " \n");
      to   = atoi(tok);

      insert_region(&regions, from, to, -1);
  }
  fclose(fp);

  for (r=regions; r; r=r->link)
      if (r->flag == -1)
         printf(">SBO %d %d\n", r->b, r->e);

}


static region_list_ptr new_region(int b, int e, region_list_ptr link)
{
   region_list_ptr new = ckalloc(sizeof(region_list_t));
   new->b = b;
   new->e = e;
   new->link = link;

   return new;
}