[WIP] Hdf5 io

[alexey0308]

@simon-anders asked to provide an HDF5 interface to the matrices, saved in the middle steps.

In this PR I'm updating the io to use hdf5 instead of npz.
The current way is to save all in a single file, where hdf5 groups correspond to the chromosomes.
I do not change the function interfaces for now, i.e. it still uses a directory as input, hence the output file name
is hardcoded.

@simon-anders @LKremer please comment here in case you have alternative better ideas, since it was discussed only between me and Simon so far.

• ADD ExitStack in the dump COO function to avoid unclosed files in case of exception.
• ADD Calculate nnz element number during dump coo function and return it
• ADD streamed saving and reading for large data sets:
  A duck-typed object is used to represent the sparse matrix from HDF5 file.
  prepare function got an additional argument to choose between in memory or streamed transformation COO->CSR in HDF5.