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.