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feat: add CLI arg to pass organism #38

Merged
merged 2 commits into from
Oct 20, 2020
Merged

feat: add CLI arg to pass organism #38

merged 2 commits into from
Oct 20, 2020

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uniqueg
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@uniqueg uniqueg commented Oct 20, 2020

  • add optional CLI argument (default: hsapiens) to pass organism to application as either a short name or taxon identifier
  • add corresponding argument to htsinfer.infer_read_layout.infer() signature and docstring

Fixes #24

Type of change

Please delete options that are not relevant.

  • Bug fix (non-breaking change which fixes an issue)
  • New feature (non-breaking change which adds functionality)
  • Breaking change (fix or feature that would cause existing functionality
    to not work as expected)
  • Documentation update

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.

@uniqueg uniqueg merged commit 3a4e494 into dev Oct 20, 2020
@uniqueg uniqueg deleted the cli_arg_organism branch October 20, 2020 22:53
uniqueg added a commit to danielbatora/htsinfer that referenced this pull request Nov 11, 2020
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Add optional CLI parameter for organism to main app
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