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Refactor SequenceDictionary to use Contig instead of SequenceRecord #997

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heuermh opened this issue Apr 12, 2016 · 1 comment
Closed

Refactor SequenceDictionary to use Contig instead of SequenceRecord #997

heuermh opened this issue Apr 12, 2016 · 1 comment

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@heuermh
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@heuermh heuermh commented Apr 12, 2016

In discussion with @tdanford around RDD[Feature]s we thought it might be worthwhile to refactor SequenceDictionary to use Contig from bdg-formats instead of SequenceRecord.

I also suggested renaming Contig to Reference and adding a new schema class ReferenceSet, per GA4GH (https://github.com/ga4gh/schemas/blob/master/src/main/resources/avro/references.avdl#L17 and https://github.com/ga4gh/schemas/blob/master/src/main/resources/avro/references.avdl#L79, respectively). I'm not suggesting using those schema classes wholesale, just the names. I'm not that keen on the name ReferenceSet either, but calling it Assembly was problematic.

@fnothaft
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@fnothaft fnothaft commented Mar 2, 2017

Closing this, as bigdatagenomics/bdg-formats#43 seems like a better solution.

@fnothaft fnothaft closed this Mar 2, 2017
@heuermh heuermh added this to Completed in Release 0.23.0 Mar 8, 2017
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