Filter reads with given number of 'N'

[GoogleCodeExporter]

Previously PerM can only discard any reads with 'N' or encode reads all 'N' as 
'a'. In version 3.5, user can specify --includeReadsWN 3
For example to allow reads with 3 or less 'N' to be included while discard 
reads with more than 3 'N'. The 'N' in the kepted reads, however will still 
encoded as 'A' internally. 

Original issue reported on code.google.com by Chen.Yan...@gmail.com on 25 May 2011 at 8:03