Documentation for prepare-for-rsem.

[IanSudbery]

Is this something you propose to solve/implement, or is this a request?
I'll do it.

Is your feature request related to a problem? Please describe.
The prepare-for-rsem script is currently not documented. Also, the name is a big confusing, as it will actaully prepare BAM files for consumption by a number of different tools.

Describe the solution you'd like
for the prepare-for-rsem function to appear on the read the docs. Possibly as prepare-for-em, with prepare-for-rsem being a synonym.