#include "psublast/psublast.h"
#include <string.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> <len>"

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;
  char *counts;
  int   Length;
  int   i, start, end, from, to;

  if (argc!=4) fatalf(Usage, argv[0]);

  Length = atoi(argv[3]);
  counts = (char *)malloc(Length*sizeof(char))-1;
  memset(counts+1,0,Length);

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

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

      for (i=from; i<=to; i++) counts[i] = 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);

      for (i=from; i<=to; i++) counts[i] = 2;
  }
  fclose(fp);

  for (i=1; i<=Length; i++) {
      if (i==1 || (counts[i-1]!=1 && counts[i]==1))
          start = i;
      if (i==Length || (counts[i-1]==1 && counts[i]!=1)) {
          end = i-1;
          printf(">SBO %d %d\n", start, end);
      }
  }

  free(counts+1);

  exit(0);
}


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;
}



--------------------------------------------------------------------
#!/usr/local/bin/perl

my $CUTOFF = 0.9;

my $prevfrom = -1;
my $prevto = -1;

# Read-in a sorted aligns file
# SBO 1834191 1834421 >Contig_1_10.15 227 423 r 0.578723 0.680000

while (<>) {
   chomp;

   /^>SBO\s+(\d+)\s+(\d+)\s+(\S+)\s+(\d+)\s+(\d+)\s+(\S)\s(\S+)\s+(\S+)$/
        or die "Illegal line. $_";

   my ($from,$to,$other,$from_other,$to_other,$ori,$pctid,$max100) =
      ($1,$2,$3,$4,$5,$6,$7,$8);

   next if ($max100<$CUTOFF);

   if ($from > $prevto) {
      print ">SBO $prevfrom $prevto\n";
      $prevfrom = $from;
      $prevto = $to;
   } else {
      if ($to>$prevto) {
          $prevto = $to;
      }
   }
}