Prioritizing non-coding variants #84
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…ue for VipVaranScore. Tests are commented for testing of annotation. created new annotation class VipScoreAnnotator for the annotation of the VipVaranScore Removed travis.yml
// level 1: overlap with a region
// level 2: level 1 + score of ncER(>0.499) fathmm(>0.5) ReMM*(>0.5)
// level 3: level 2 + constraint region above or equal to 0.7
And moved logic for determining a good tool score to methods
Created Interface classes for VipScoreAnnotator and VipScoreAnnotatorFactory. Created factory class for VipScoreannotator. Modified the Classifier interface and factory to handle VipScoreAnnotator
… the test accordingly
// level 0: nothing
// level 1: overlap with a region or a constraint value above or equal to 0.7 or a score of ncER(>49.9) fathmm(>0.5) ReMM*(>0.5)
// level 2: score of ncER(>49.9) fathmm(>0.5) ReMM*(>0.5) and overlap with a region or a constraint value above or equal to 0.7
// level 3: level 2 + constraint region above or equal to 0.7
changed tests accordingly
Changed the example.vcf and example-classified.vcf to comply with the new expected input and output.
…d how it determines a score per variant
…he new functionality
…also taken into account, updated the tests accordingly
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Internship project from @JonathanKlimp on prioritizing non-coding variants (report can be downloaded here)