still writes the various training files to disk, but now the user needs only input and use the prefix instead of keeping track of how the npz matrix is named
removes the --N parameter that was used for de-buging
makes a new json file that stores the k-mer size and ani_thresh, removes these parameters from run_YACHT.py as they must/should always match the ones used in make_training_data_from_sketches.py
Changes default coverage to 0.01
Fix integration test to reflect these changes
Note: these are breaking changes and not backward compatible due to script parameter changes and default setting changes
--Nparameter that was used for de-bugingrun_YACHT.pyas they must/should always match the ones used inmake_training_data_from_sketches.pyNote: these are breaking changes and not backward compatible due to script parameter changes and default setting changes