Comments (6)
@fnothaft @jpdna I believe this one is a blocker for the next point release (0.10.1 or 0.11.0, however we decide) as I can't finish the implementation in bigdatagenomics/adam#1288 without a decision on this.
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Add new reference value fields
I like the approach in your 6. above of adding new explicitly named ref
prefixed fields.
If the decision was made to do that, then what further problems still remain?
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Option 6 only helps for the specific case of Number=R VCF INFO attribute values that map to fields. We'd still need something for generic Number=R VCF INFO values in VariantAnnotation.attributes
(1-4).
Then after many years dealing with corporate DBAs and other such naming standard b.s., I no longer abbreviate in field, method, or class names, so it'd be reference*
. :)
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How about we have a rule that for all Number=R attribute map "fields" that the the String that is the the value must itself by a comma delimited list with exactly two fields (post splitting), ref and alt
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I'd go for that if we also went with option 5 for AD,ADF,ADR. Added to description above.
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Yeah I see why you'd want option 5 over 6 then for consistency, that's be fine with me.
We could also make attributes a map of array where often the array would be length one (rather than have comma delimited strings in some cases), but I am not sure if I like the potential overhead of that nesting. Anyway, that attributes map representation decision would be easy to change in future though if we changed mind.
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Related Issues (20)
- Release version 0.12.0 HOT 1
- Javadoc errors in generated code cause release to fail
- Alignment record quality vs Read qualityScores
- Add barcodes field to ReadGroup HOT 3
- Add record definition for VariantContext HOT 1
- Snapshot version should be 0.14.0-SNAPSHOT
- Add record definition for VCF header HOT 1
- Jenkins build status icon link is broken HOT 1
- Migrate CI build to Travis or Github Actions
- Changelog is missing versions 0.14.0 and 0.15.0
- Update release script to update changelog
- Add impact, strand, ref/alt protein sequence, ref/alt coding sequence to TranscriptEffect
- Add sample to Sequence, Slice, and Read
- Add proteinId field to Feature
- Update pom.xml url to Github repository
- Update Avro dependency version to 1.11.1
- Fix avro-maven-plugin version 1.11.1 warnings HOT 1
- Migrate CI from Travis to Github Actions
- Documentation comment vs multiline comment warnings HOT 1
- Update avro dependency version to 1.12.0
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