refactor: refactor and create unit test for oligomapOutputToSam_nhfiltered.py

[deliaBlue]

Provide comprehensive unit tests for every function in the code by formalizing the generation of synthetic inputs and checking against expectation.
The unit tests must cover every single line of code.
Use pytest to write and run the unit tests, and use the pytest-cov extension to track the test coverage.
Add the unit test execution and coverage calculation to the CI pipeline.