#!/usr/bin/perl

open(FH, $ARGV[0]) || die("Cannot open:$!");

while (<FH>) {
   ($Query, $Score, $Start, $End, $one, $two) = split;

   if ( ! exists ( $hash{$Query} ) ) {
      $hash{$Query}[0] = $Score;
      $hash{$Query}[1] = $Start;
      $hash{$Query}[2] = $End;
      $hash{$Query}[3] = $one;
      $hash{$Query}[4] = $two;
   }
   else {
      if ( $hash{$Query}[1] > $Start ) {
           $hash{$Query}[0] = $Score;
           $hash{$Query}[1] = $Start;
           $hash{$Query}[2] = $End;
           $hash{$Query}[3] = $one;
           $hash{$Query}[4] = $two;
      }
   }
   if ( ! exists ( $hash2{$Query} ) ) {
      $hash2{$Query}[0] = $Score;
      $hash2{$Query}[1] = $Start;
      $hash2{$Query}[2] = $End;
      $hash{$Query}[3] = $one;
      $hash{$Query}[4] = $two;
   }
   else {
      if ( $hash2{$Query}[2] < $End ) {
           $hash2{$Query}[0] = $Score;
           $hash2{$Query}[1] = $Start;
           $hash2{$Query}[2] = $End;
           $hash{$Query}[3] = $one;
           $hash{$Query}[4] = $two;
      }
   }
}

foreach $Query ( keys (%hash) ) {
foreach $Query ( keys (%hash2) ) {
   print "$Query\t$hash{$Query}[0]\t$hash{$Query}[1]\t$hash2{$Query}[2]\t$hash{$Query}[3]\t$hash{$Query}[4]\n";
}
}
close(FH);
__DATA__
Books	6	159290954	159291342	+	 Author
Books	6	159294558	159294653	+	 Author
Books	6	159316253	159316398	+	 Author
Books	6	159330999	159331385	+	 Author
Books	6	159290971	159290997	+	 Author
Books	6	159316253	159316398	+	 Author
Books	6	159330999	159331289	+	 Author
Books	6	159316268	159316398	+	 Author
Books	6	159330999	159331245	+	 Author