fix: add processed sample paths to mapping

[balajtimate]

Description

Add the paths to the processed subset of samples to the mapping function in get_library_type.py, so that STAR makes use of them instead of the original (unprocessed) samples, when aligning to determinate the mate relationship.

Fixes #149

Type of change

• Bug fix (non-breaking change which fixes an issue)

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 ✅

Comparison is base (8443c05) 100.00% compared to head (4c33968) 100.00%.

Additional details and impacted files

@@            Coverage Diff            @@
##               dev      #150   +/-   ##
=========================================
  Coverage   100.00%   100.00%           
=========================================
  Files           13        13           
  Lines         1108      1109    +1     
=========================================
+ Hits          1108      1109    +1     

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[uniqueg]

Hmm, coverage test is failing. Maybe you need to update the unit tests (or add one)?

[uniqueg]

Please check the unit tests

[balajtimate]

I'm not sure why, the detailed coverage run says 100% (also for the PR). Can it be rerun?

[uniqueg]

Really weird. And no, I don't know how to rerun it without rerunning all the tests. Well, I think I'll just merge it then. If it persists, we can still investigate