New module for cghub

I'm building some infrastructure for using GTFuse from Annai Systems
right now.
More work toward GTFuse engine

I haven't tested the engine yet but I know it wasn't working before.
I've made it now so that it can theoretically be stopped I just need to
test it out.
More updates, made variant calling engine

I'd like to try this out a bit before continuing. It may be advanced
enough to start using now.
Bug fix

Can't have default parameter with self.
Updates, reads from intervals working

The engine to get reads is working now although I've left a few debu
statements in there for now. I'm going to work on getting the variant
calling engine working too.
More updates for getting reads, variant calling

I'm having trouble getting reads for a large number of intervals, but I
think I have a solution. If an interval fails, I just need to unmount
the bam, remove the cache info, and remount. I'm going to reorganize the
file some more.
More updates

I've refactored the code quite a bit to make GTFuseBam class. I'd like
to make another class for bam files that contain reads from a subset of
intervals.
More refactoring

I've made a class for bam file with reads from intervals. I've updated
the reads from intervals engine but haven't tested. I still need to
update the variant calling engine.
Small typo fixes
Major refactoring, added variant calling features

Still working on finishing. Adding ability for variant calling to be
stopped and started up again.
A few more updates/refactoring

Going to start testing new engine for downloading/variant calling.
More refactoring, bug fixes

I've fixed many bugs and played with the html. I am going to test now. I
know there are still problems with restarting a job whose engine was
stopped and deleted.
Removed left-over comments that blocked code
Bug fixes

The variant calling engine starts up and seems to be working ok. I had
to fix some of the html stuff.
Small bug fix for html
Formatting fixes
More refactoring, bug fixes

I know that resuming a job whose engine has been killed isn't working
but I think the variant calling starting from the beginning is working.
Bug fixes
Update/bug fix

I think samtools merge was unhappy because I was merging too many bam
files. I changed it around so I'm constantly merging on the fly.
Minor updates, bug fixes