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Intel-HLS / GenomicsDB

GenomicsDB
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Pass through query JSON (backward compatibility) #172

Closed kgururaj closed 6 years ago

kgururaj commented 6 years ago

Keeping a GenomicsDBFeatureReader constructor which accepts a single query JSON from the user and passes it through to the C++ library (backward compatibility).

CI test for this constructor

francares commented 6 years ago

@kgururaj is someone using that? shouldn't we just tend to expose the protobuf classes instead of using file paths? In case someone creates a command line tool for example, this person can create the adapter on top of the Java or C++ GenomicsDB library. This adapter will read the content of the file from the specific path and deserialize into a protobuf object.

kgururaj commented 6 years ago

Yes, the ODA folks and Spark users. I agree we should phase out the JSON Java API gradually - the Protobuf classes are incomplete in my opinion and would require more work. Once we are confident of the Protobuf API we can remove the JSON API.