Add new configuration entry for plugins #4611
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magicDGS
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@magicDGS One question for you, it seems like it would be better to use the existing method in a loop instead of factoring out another one, but maybe I am missing some detail. Looks good to me otherwise.
| for ( final String codecPackage : config.annotation_packages() ) { | ||
| finder.find(codecPackage, GenotypeAnnotation.class); | ||
| } | ||
| return finder.getConcreteClasses().stream().map(c -> (GenotypeAnnotation) ClassUtils.makeInstanceOf(c)) |
| final GATKConfig config = ConfigFactory.getInstance().getGATKConfig(); | ||
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| final ClassFinder finder = new ClassFinder(); | ||
| for ( final String codecPackage : config.annotation_packages() ) { |
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Why do this instead of calling ClassUtils.makeInstanceOfSubclasses on each package and merging the results?
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This code is all going to be removed soon by #4674. It might be best to wait for that, since it will reduce what this PR needs to do.
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Oh. Ok, lets wait for that then.
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How close is that PR to be accepted? I can divide this one into the ReadFilter config entry and wait for the annotator to be accepted to include the entry (or include it directly in #4674). What do you prefer?
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Closing because I've taken this over as #5573 |
Includes:
In addition, it changes the behavior of
VariantAnnotatorEngineto use the annotation packages from the configuration, and mimic what the plugin is doing. This closes #2155