Move HDF5Utils out of copynumber package and expand unit tests.

[samuelklee]

The new annotation-based filtering tools make use of the utility methods in the HDF5Utils class for writing intervals, matrices, etc. to HDF5. This class currently lives in the copynumber package, so perhaps it should be moved somewhere more general. It would be nice to expand the unit tests as well. Currently, there is only a single, disabled test that checks for the ability to read/write very large, chunked matrices; this test inherently requires a relatively large amount of memory (>Xmx4G) to run, which is why it's disabled.