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poseidon-framework / poseidon-hs

A toolset to work with modular genotype databases in the Poseidon format
https://poseidon-framework.github.io/#/trident
MIT License
7 stars 2 forks source link

Added an option to validate all SNPs #233

Closed nevrome closed 1 year ago

nevrome commented 1 year ago

Just as suggested in #223.

nevrome commented 1 year ago

test/testDat/poseidonHSGoldenTestData/validate3 is empty, because validate writes nothing to stdout. It just writes to stderr (logging) and then returns an exit code. Call it lazy programming, but I kept the empty file around to detect any change to this behaviour :grimacing:. Same holds for validate1 and validate2. Would you prefer to test this more directly?

stschiff commented 1 year ago

No, that's OK... indeed the Golden tests are lazy but robust. All good.

codecov-commenter commented 1 year ago

Codecov Report

Base: 71.02% // Head: 71.03% // Increases project coverage by +0.00% :tada:

Coverage data is based on head (ce0f313) compared to base (1c0e6fd). Patch coverage: 71.42% of modified lines in pull request are covered.

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Additional details and impacted files ```diff @@ Coverage Diff @@ ## master #233 +/- ## ======================================= Coverage 71.02% 71.03% ======================================= Files 18 18 Lines 2226 2237 +11 Branches 244 246 +2 ======================================= + Hits 1581 1589 +8 - Misses 401 402 +1 - Partials 244 246 +2 ``` | [Impacted Files](https://codecov.io/gh/poseidon-framework/poseidon-hs/pull/233?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=poseidon-framework) | Coverage Δ | | |---|---|---| | [src/Poseidon/GenotypeData.hs](https://codecov.io/gh/poseidon-framework/poseidon-hs/pull/233?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=poseidon-framework#diff-c3JjL1Bvc2VpZG9uL0dlbm90eXBlRGF0YS5ocw==) | `55.30% <0.00%> (ø)` | | | [src/Poseidon/CLI/Validate.hs](https://codecov.io/gh/poseidon-framework/poseidon-hs/pull/233?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=poseidon-framework#diff-c3JjL1Bvc2VpZG9uL0NMSS9WYWxpZGF0ZS5ocw==) | `54.16% <66.66%> (-0.38%)` | :arrow_down: | | [src/Poseidon/Package.hs](https://codecov.io/gh/poseidon-framework/poseidon-hs/pull/233?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=poseidon-framework#diff-c3JjL1Bvc2VpZG9uL1BhY2thZ2UuaHM=) | `75.31% <80.00%> (+0.05%)` | :arrow_up: | Help us with your feedback. Take ten seconds to tell us [how you rate us](https://about.codecov.io/nps?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=poseidon-framework). Have a feature suggestion? [Share it here.](https://app.codecov.io/gh/feedback/?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=poseidon-framework)

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