Bug fix party!

**NOT READY FOR MERGE**

Fixes #1467 #1615 #1656. Addresses part of #1696.

@gregcaporaso and I pair-programmed most of this.
Phil Hugenholtz said by email that this is the right information to include, and asks that we add the following (I adapted this slightly from him email to fit this context):

Lane mask was originally available in ARB. For more information on ARB, see:
http://www.ncbi.nlm.nih.gov/pubmed/14985472