# Read the data table
my @table;
while (<>) {
   chomp;
   my ($start, $stop, $id, $id2) = split /\t/, $_;
   push @table, [ $start, $stop, $id1, $id2 ];
}

# Patch up the data
for (my $i=1; $i < $#table; ++$i) {
   # check surrounding items and patch the data, as needed
   . . .
}

# Print the new table
for my $ar (@table) {
   my ($start, $stop, $id, $id2) = @$ar;
   print .....
}