Addition the new logging method and fix spacing/margins for argparse help doc

[florianzwagemaker]

Task IDs:

• CU-2hyrfrj
• CU-2hyrf2u
• CU-2hyrgeu

Includes the following:

• Updated dependencies to newer versions for the following packages:
  • pysam lenient version 0.19.*
  • pandas >=1.3
  • mappy pinned 2.24
  • parmap lenient version 1.5.*
• Removed tqdm dependency
• Removed bedtools dependency
• Added rich as a dependency
• Added a new logging method using rich as a handler and output various logmessages and stats to stdout
• Added new wrapper classes to fix spacing and margins in the argparse help document (respect proper line endings for example)