Join paired ends

PR for joining paired-ends. Even though I am still cleaning up the code, I figure it is short and simple enough to start getting feedback. 

Code located here:
https://github.com/mikerobeson/qiime/blob/join_paired_ends/scripts/join_paired_ends.py
https://github.com/mikerobeson/qiime/blob/join_paired_ends/qiime/join_paired_ends.py

Top of my to do list:
1) Set up tests and test files.