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Autogen field names in projection package #941

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fnothaft opened this issue Feb 13, 2016 · 3 comments
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Autogen field names in projection package #941

fnothaft opened this issue Feb 13, 2016 · 3 comments
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@fnothaft
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@fnothaft fnothaft commented Feb 13, 2016

@jpdna has identified a bug whose root cause has to do with a default field being used when a field is projected out using Parquet's projection feature and our org.bdgenomics.adam.projection package. The TL;DR on the bug (@jpdna can you open an issue for this and link the issue to this issue?) is that the firstOfPair/secondOfPair fields changed to readInFragment but the AlignmentRecordField enum didn't get changed, so the projection didn't get fixed. To not have this problem come up in the future, we should autogenerate the enums from the avro schemas from bdg-formats.

@heuermh
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@heuermh heuermh commented Sep 6, 2016

Adding unit tests for projection field classes in #1144. I was hoping these could be a template for any auto-generated code, but unfortunately the tests don't fail unless the manually written assertions fail. There apparently isn't any runtime checking by Parquet.

@fnothaft
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@fnothaft fnothaft commented Mar 3, 2017

This can be resolved using the codegen from #1391.

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@fnothaft fnothaft commented May 12, 2017

I will take this once #1391 merges.

fnothaft added a commit to fnothaft/adam that referenced this issue May 24, 2017
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fnothaft added a commit to fnothaft/adam that referenced this issue Jul 11, 2017
fnothaft added a commit to fnothaft/adam that referenced this issue Jul 11, 2017
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@heuermh heuermh moved this from Triage to Completed in Release 0.23.0 Jan 4, 2018
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