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bigdatagenomics / bdg-formats

Open source formats for scalable genomic processing systems using Avro. Apache 2 licensed.
Apache License 2.0
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Rename start/end fields in NucleotideContigFragment #138

Closed fnothaft closed 7 years ago

fnothaft commented 7 years ago

All other "top level" records use start/end.

heuermh commented 7 years ago

Do you mean fragmentStartPosition → fragmentStart and fragmentEndPosition → fragmentEnd?

fnothaft commented 7 years ago

Nope, I meant fragmentStartPosition → start and fragmentEndPosition → end

heuermh commented 7 years ago

All the other fields start with fragment (which I dislike), so these should match for now. I would like to replace NucleotideContigFragment with Sequence and Slice post bdg-formats version 0.11.0.

fnothaft commented 7 years ago

If we make this change, then we can support generated predicates on NucleotideContigFragment in https://github.com/bigdatagenomics/adam/pull/1540. Additionally, this is a small change that would harmonize the schemas. Anyways, it doesn't logically make sense to say "X improves Y but doesn't totally fix it, so let's not do X". Do you want me to drop the fragment prefixes from the other fields as well?

heuermh commented 7 years ago

Just made that suggestion in https://github.com/bigdatagenomics/bdg-formats/pull/139#issuecomment-303464145. I'll also propose similar changes to Slice in a sec

heuermh commented 7 years ago

See #140

fnothaft commented 7 years ago

140 sounds OK to me, but is realistically unrelated to #138, since we're not dropping NucleotideContigFragment in the immediate future.