test: add validation tests for intronic positions#676
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add ga4gh inherent
* SequenceOffsetLocation, RelativeSequenceLocation, RelativeAllele
validation/models.yaml
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| id: NM_001385641.1 | ||
| type: SequenceReference | ||
| refgetAccession: SQ.cXRaN1IhgR6Mg9U-qafH2Be6IuQgB6Ox | ||
| anchor: 610 |
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Shouldn't this be 609, rather than 610?
Basing this on thinking through this simplified example
validation/models.yaml
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| id: NM_001385641.1 | ||
| type: SequenceReference | ||
| refgetAccession: SQ.cXRaN1IhgR6Mg9U-qafH2Be6IuQgB6Ox | ||
| anchor: 1059 |
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Should this be 1057?
validation/models.yaml
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| relativeState: | ||
| type: LiteralSequenceExpression | ||
| sequence: A | ||
| baseState: | ||
| type: LiteralSequenceExpression | ||
| sequence: A |
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Only thing we did not review together @ahwagner @larrybabb
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@ahwagner... baseState v relativeState? is this only different when the transcript is in the opposite direction? So if the LiteralSequenceExpression is A in the baseState it would be T in the relativeState?
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Yeah, I see this in the PR as "mappedState". I'm on the fence about it, okay either way, I think I do prefer "mappedState". We should definitely keep the class as "relativeAllele" and definitely keep the "relativeLocation" slot on the relative allele.
larrybabb
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larrybabb
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I left a comment for @ahwagner because I'm not 100% confident of the purpose of both base/relative State fields. I believe the relativeState would always be the complement of the baseState when the mapped sequence is in the opposite direction of the base sequence.
!!! think we should consider changing the name of relativeState to mappedState. It seems like baseState clearly aligns with the relativeLocation.baseSequenceLocation so I would think that mappedState would align similarly with the relativeLocation.mappedSequenceLocation
validation/models.yaml
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| relativeState: | ||
| type: LiteralSequenceExpression | ||
| sequence: A | ||
| baseState: | ||
| type: LiteralSequenceExpression | ||
| sequence: A |
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@ahwagner... baseState v relativeState? is this only different when the transcript is in the opposite direction? So if the LiteralSequenceExpression is A in the baseState it would be T in the relativeState?
| offsetStart: -1 | ||
| offsetEnd: 0 | ||
| out: | ||
| ga4gh_digest: null |
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We need to review digest behavior for RelativeLocation and RelativeAllele objects
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