feat: output read orientation fractions to json

[balajtimate]

Description

• Add json output of the fractions of read orientation (number of mapped reads, fraction of SF, SR and final orientation) per input sample
• Clean up debug logging

Type of change

• New feature (non-breaking change which adds functionality)

Checklist

Please carefully read these items and tick them off if the statements are true
or do not apply.

• I have performed a self-review of my own code
• My code follows the existing coding style, lints and generates no new
  warnings
• I have added type annotations to all function/method signatures, and I
  have added type annotations for any local variables that are non-trivial,
  potentially ambiguous or might otherwise benefit from explicit typing.
• I have commented my code in hard-to-understand areas
• I have added ["Google-style docstrings"] to all new modules, classes,
  methods/functions or updated previously existing ones
• I have added tests that prove my fix is effective or that my feature
  works
• New and existing unit tests pass locally with my changes and I have not
  reduced the code coverage relative to the previous state
• I have updated any sections of the app's documentation that are affected
  by the proposed changes

If for some reason you are unable to tick off all boxes, please leave a
comment explaining the issue you are facing so that we can work on it
together.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 100.00%. Comparing base (d3cbe0e) to head (6828a24).
Report is 1 commits behind head on dev.

Additional details and impacted files

@@            Coverage Diff            @@
##               dev      #169   +/-   ##
=========================================
  Coverage   100.00%   100.00%           
=========================================
  Files           13        13           
  Lines         1142      1164   +22     
=========================================
+ Hits          1142      1164   +22     

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[uniqueg]

Some minor issues. In addition to the ones mentioned in line, I'm wondering if there aren't some docs that need to be updated? Example outputs maybe?

[balajtimate]

No docs update needed right now. I'll rewrite the full documentation on RtD, there it will be included.

[uniqueg]

No docs update needed right now. I'll rewrite the full documentation on RtD, there it will be included.

Oh, never mind. Had only a brief look and thought that you'd ended up including the stats in the main output after all. But seeing now that you're just writing it into a separate file, as discussed 👍