Added failing test
Added debugging hooks to aid in poor man's profiler
Started implementing numeric bam file keys so we don't need long file strings in each bin/region/normalization record.  Unit tests all pass, but clearly not done. Next thing I have to add more unit tests so that they detect the current broken state.
WIP
Bin normalization now completes with file keys
Added more tests and starting to adding support for true variable length file names
variable length file names now supported, so there is no fixed limit on file names anymore
matrix.gff fixed
Moved batch function into constructor
Removed no longer used function
Removed unnecessary logic
Fixed tab file generation
Fixed tab file generation so format exactly matches before hdf5 schema change
Can now explicitly provide region format (gff/bed)

Default is still to automatically determine format from file name extension, but this is overridden if format specified.

Resolves #16 .  I chose to do this on this branch so as not to have to deal with conflicts later.
Merge pull request #22 from BradnerLab/long-file-names

Long file names and specifying region format now supported