Added an option to ignore N bases in reads, which can lead to much cl…

[yfarjoun]

…eaner output when the input has many Ns in it.

Description

Please explain the changes you made here.

Checklist

• [x] Code compiles correctly
• [ ] All tests passing
• [ ] Extended the README / documentation, if necessary
• [ ] Added myself + history to the source file

[lindenb]

@yfarjoun thanks !