polish for scaffod.fa(contain Ns)

[DayTimeMouse]

Hi,

Thanks for developing this tool.

I have mentioned this issue #136.

I have already used no Ns scffolds.fa, and record Ns' positions and counts.
However, polished assembly size is not equal to scffolds.fa(no Ns), so I can't restore Ns to scffolds.fa(no Ns), due to postions may change.

What should I do?

Thanks in advance.