Join pair ends from one file

Turns out that JGI's sequencing platform automatically creates a single file with the forward, reverse and indexes, so users will need to parse outside of this script to be able to join the reads. 

This PR adds the possibility of passing 1 single file and creates the files to create the forward, reverse and if set the barcodes files before the joining step. 

Additionally, from the regular code reviewers it will be a good idea if @mikerobeson takes a look too before merging. 
I know but that's what happens when you use other script as an example ...