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figure out why some annotations don't implement Annotation and decide if they should #2493

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lbergelson opened this issue Mar 20, 2017 · 2 comments
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figure out why some annotations don't implement Annotation and decide if they should #2493

lbergelson opened this issue Mar 20, 2017 · 2 comments
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@jamesemery
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Annotations Engine refactoring
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Engine-4.0

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@lbergelson
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Some annotation base classes don't implement the Annotation marker interface. (i.e. VariantAnnotation) This was the case in gatk3 as well, but it's unclear why. It may be a historical artifact rather than a design decision, in which case it should be corrected. If it's important to have the marker interface then all the annotations should implement them. If it isn't, then we should probably remove it or move abstract functions into the interface.
@droazen droazen added this to the 4.0 release milestone Mar 20, 2017
@droazen droazen assigned jamesemery and unassigned lbergelson Jul 17, 2017
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droazen commented Jul 17, 2017

Adding to annotation epic #3274

@jamesemery jamesemery mentioned this issue Dec 20, 2017
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This has been handled by other annotation pull requests like #3851

lbergelson pushed a commit that referenced this issue Feb 26, 2018
@jamesemery @lbergelson
Port of GATK3 Variant Annotator Tool (#3803)
8d929ed 
* Beta port of GATK3 version of VariantAnnotator with the necessary changes to the annotation engine and client annotations to support annotating variants independent of the haplotype caller.
* The annotations closely match the GATK3 output, including replicating existing bugs in some cases
* closes #51 
* close #2493
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