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fix: do not use nan in htsinfer call #137

Merged
merged 1 commit into from
May 12, 2023
Merged

fix: do not use nan in htsinfer call #137

merged 1 commit into from
May 12, 2023

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ninsch3000
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Description

Don't keep default nan when reading samples table in htsinfer.smk, otherwise nan will be used instead of empty string in call to htsinfer.

Fixes #135

Type of change

Please delete options that are not relevant.

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

Conventional Commits guidelines

Changes to workflow inputs (sample table and/or configs)

  • major (add BREAKING CHANGE: in the beginning of the PR title)
    • more fields/properties are required
    • existing ones are dropped entirely
  • minor (add feat: in the beginning of the PR title)
    • optional fields/properties are added
    • required ones are made optional

Changes to workflow outputs

  • major (add BREAKING CHANGE: in the beginning of the PR title)
    • changes lead to removal/change of existing outputs (format or location)
  • minor (add feat: in the beginning of the PR title)
    • additional outputs are generated
    • content (but not format or location) of existing outputs changes

Everything else: patch
(add any other conventional commit in the beginning of the PR title)

Checklist:

  • My code changes follow the style of this project
  • I have performed a self-review of my own code
  • I have commented my code, particularly in hard-to-understand areas
  • My changes generate no new warnings
  • I have added tests that prove my fix is effective or that my feature works
  • New and existing tests pass locally with my changes
  • I have updated the project's documentation

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@balajtimate balajtimate left a comment

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Tested it with sample table with NaN entries and it fixed the issue.

@ninsch3000 ninsch3000 merged commit 7642eb9 into dev May 12, 2023
@ninsch3000 ninsch3000 deleted the fix_nan branch May 12, 2023 13:18
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fix: htsinfer.smk treats 'nan' values in sample table wrongly
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