Implementation of Freebayes tumor/normal calling

Like the previous work, this pull request is a work-in-progress and pushed just to gather review and adjustments on the way.

I'm not fond of the way I'm building the freebayes command line... suggestions?

NOTE: the calling is not plugged in yet in the pipeline!

It also includes a minor refactoring of ``get_paired_bams`` and ``is_paired_analysis`` to generalize things across the pipeline (once this PR is in, I'll make a separate one to port existing users). Brad, let me know if it is what you intended.