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) Check for correct combination of parameters. That is, inform user that a parameter for 'SeqPrep' will not be used if the paired-end joining method is 'fastq-join', and vice versa. 
2) Set up tests and test files.