Nanocem

fix some bugs of argparse and subsample

Add the support for rna004 direct RNA sequencing data.

1. adjust the base_shift for rna004 and tested on our sample
2. update some function of index

We have released a stable version of 0.0.5.8 and the changes are as below.

1. Changed the base shift method and its description [here](https://nanocem.readthedocs.io/en/latest/adaption/#base-shift-only-for-f5c), and the option **-- base_shift** had been updated.
2. Fixed the bugs when visualizing the features on the reverse strand.
3. Updated the [docs](https://nanocem.readthedocs.io/en/latest/)