Use read and write method of GeneData to save in h5 format.

[sjteresi]

The names of the files are the "chromosome + _GeneData.h5" Take a look at the current_chromosome and current_gene_data and complete_genedata variables in density.py

[sjteresi]

Update: @teresi it is 6/23/2020 at 4:30 pm and I have updated the usage.

Graphs.py will be broken now, but I will fix at a later date. As that is not as important right now.

The code saves its cache inside the filtered_input_data folder

[sjteresi]

@teresi I have updated the code:

• Had to fix the boolean command line arguments, turns out the old notation wasn't actually being interpreted correctly and was always interpreting it as True.

• Moved the verification code to its own module.

• Accurately save the H5 files for TransposonData and GeneData on a chromosome-by-chromosome basis.

• Added verification code for the H5 files and clarified within the code with a #NOTE the names of the H5 files being saved. I also moved them into /filtered_input_data/h5_cache. At my note in Process() you should be able to use the filename variable created there to grab the H5 files later down the road.