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Prioritizing non-coding variants#84

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dennishendriksen wants to merge 23 commits intomainmolgenis/vip-decision-tree:mainfrom feat/annotationmolgenis/vip-decision-tree:feat/annotationCopy head branch name to clipboard

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Commits on Dec 23, 2022

• Added functionality to ClassifierImpl. Class now annotates a test value for VipVaranScore.

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• Score is annotated based on:

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• removed unused classes for VIP-Varan score annotation

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• removed unused classes for VIP-Varan score annotation

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• removed unused classes for VIP-Varan score annotation

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Commits on Dec 27, 2022

• Renamed ClassifierImpl.java to AnnotateScore.

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• Renamed AnnotateScore to AnnotateScoreImpl.

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• Extracted class ScoreCalculator from AnnotateScoreImpl

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• Created tests for ScoreCalculator, and modified class to pass tests

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Commits on Dec 28, 2022

• Changed hardcoded index to get custom value to csq length - x

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Commits on Jan 6, 2023

• Update on the documentation

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Commits on Jan 10, 2023

• Removed unused commandline arguments. And there usages in different classes

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• Removed unused commandline arguments. And there usages in different classes

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• removed test for a good constraint value for a score of 2

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• removed test for a good constraint value for a score of 2 and changed the test accordingly

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• score calculation is now:

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• Removed unused test resources and tests from AppIT.

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• updated the README with explanation what this annotation tool does and how it determines a score per variant

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Commits on Jan 12, 2023

• update on AnnotateScoreImplTest. Change so that the test works with the new functionality

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Commits on Jan 18, 2023

• Update on score calculation. For the score calculation Gnomad is now also taken into account, updated the tests accordingly

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Commits on Jan 19, 2023

• Update on the comment on the score calculation

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Commits on Feb 3, 2023

• Update README.md

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• Update README.md

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