Updates, bug(?) fixes

I've made some changes to fix problems with getting reads from
intervals. The whole GTFuse thing is sort of fragile when looking at
many intervals. I think that some of my problems were coming from using
/tmp as a temp directory (I had 300 bam files randomly deleted at some
point) so I'm not doing that anymore.
More updates
Bug fix
Bug fixes
Updates, debugging code

I'm in the processing of a debugging what can only be the last bug I
will ever deal with. For some reason the daemon processes don't end when
they should when I try to get a large amount of intervals. I'm working
on fixing that.
Merge commit 'c452b2b66d203fef7a2f1b2e1a0e61027a7d4cea' into gtfuse

Conflicts:
	cdpybio/cghub.py