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update submodule
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larrybabb committed Sep 7, 2024
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Showing 18 changed files with 30 additions and 27 deletions.
3 changes: 3 additions & 0 deletions .readthedocs.yaml
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Expand Up @@ -5,6 +5,9 @@ build:
tools:
python: "3.11"

submodules:
include: all

sphinx:
configuration: docs/source/conf.py

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4 changes: 2 additions & 2 deletions schema/vrs/def/Adjacency.rst
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Expand Up @@ -33,7 +33,7 @@ Some Adjacency attributes are inherited from :ref:`Variation`.
- 0..m
- Alternative name(s) for the Entity.
* - extensions
- :ref:`Extension`
- `Extension </ga4gh/schema/gks-common/1.x/data-types/json/Extension>`_
- 0..m
- A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.
* - digest
Expand All @@ -49,7 +49,7 @@ Some Adjacency attributes are inherited from :ref:`Variation`.
- 1..1
- MUST be "Adjacency".
* - adjoinedSequences
- :ref:`IRI` | :ref:`Location`
- `IRI </ga4gh/schema/gks-common/1.x/data-types/json/IRI>`_ | :ref:`Location`
- 2..2
- The terminal sequence or pair of adjoined sequences that defines in the adjacency.
* - linker
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4 changes: 2 additions & 2 deletions schema/vrs/def/Allele.rst
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Expand Up @@ -33,7 +33,7 @@ Some Allele attributes are inherited from :ref:`Variation`.
- 0..m
- Alternative name(s) for the Entity.
* - extensions
- :ref:`Extension`
- `Extension </ga4gh/schema/gks-common/1.x/data-types/json/Extension>`_
- 0..m
- A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.
* - digest
Expand All @@ -49,7 +49,7 @@ Some Allele attributes are inherited from :ref:`Variation`.
- 1..1
- MUST be "Allele"
* - location
- :ref:`IRI` | :ref:`Location`
- `IRI </ga4gh/schema/gks-common/1.x/data-types/json/IRI>`_ | :ref:`Location`
- 1..1
- The location of the Allele
* - state
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4 changes: 2 additions & 2 deletions schema/vrs/def/CisPhasedBlock.rst
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Expand Up @@ -33,7 +33,7 @@ Some CisPhasedBlock attributes are inherited from :ref:`Variation`.
- 0..m
- Alternative name(s) for the Entity.
* - extensions
- :ref:`Extension`
- `Extension </ga4gh/schema/gks-common/1.x/data-types/json/Extension>`_
- 0..m
- A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.
* - digest
Expand All @@ -49,7 +49,7 @@ Some CisPhasedBlock attributes are inherited from :ref:`Variation`.
- 1..1
- MUST be "CisPhasedBlock"
* - members
- :ref:`Allele` | :ref:`IRI`
- :ref:`Allele` | `IRI </ga4gh/schema/gks-common/1.x/data-types/json/IRI>`_
- 2..m
- A list of :ref:`Alleles <Allele>` that are found in-cis on a shared molecule.
* - sequenceReference
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4 changes: 2 additions & 2 deletions schema/vrs/def/CopyNumber.rst
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Expand Up @@ -37,7 +37,7 @@ Some CopyNumber attributes are inherited from :ref:`Variation`.
- 0..m
- Alternative name(s) for the Entity.
* - extensions
- :ref:`Extension`
- `Extension </ga4gh/schema/gks-common/1.x/data-types/json/Extension>`_
- 0..m
- A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.
* - digest
Expand All @@ -49,6 +49,6 @@ Some CopyNumber attributes are inherited from :ref:`Variation`.
- 0..m
-
* - location
- :ref:`IRI` | :ref:`Location`
- `IRI </ga4gh/schema/gks-common/1.x/data-types/json/IRI>`_ | :ref:`Location`
- 1..1
- A location for which the number of systemic copies is described.
6 changes: 3 additions & 3 deletions schema/vrs/def/CopyNumberChange.rst
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Expand Up @@ -33,7 +33,7 @@ Some CopyNumberChange attributes are inherited from :ref:`CopyNumber`.
- 0..m
- Alternative name(s) for the Entity.
* - extensions
- :ref:`Extension`
- `Extension </ga4gh/schema/gks-common/1.x/data-types/json/Extension>`_
- 0..m
- A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.
* - digest
Expand All @@ -45,14 +45,14 @@ Some CopyNumberChange attributes are inherited from :ref:`CopyNumber`.
- 0..m
-
* - location
- :ref:`IRI` | :ref:`Location`
- `IRI </ga4gh/schema/gks-common/1.x/data-types/json/IRI>`_ | :ref:`Location`
- 1..1
- A location for which the number of systemic copies is described.
* - type
- string
- 1..1
- MUST be "CopyNumberChange"
* - copyChange
- :ref:`Coding`
- `Coding <../data-types/data-types-source.json#/$defs/Coding>`_
- 1..1
- MUST be a `Coding` representing one of "EFO:0030069" (complete genomic loss), "EFO:0020073" (high-level loss), "EFO:0030068" (low-level loss), "EFO:0030067" (loss), "EFO:0030064" (regional base ploidy), "EFO:0030070" (gain), "EFO:0030071" (low-level gain), "EFO:0030072" (high-level gain).
4 changes: 2 additions & 2 deletions schema/vrs/def/CopyNumberCount.rst
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Expand Up @@ -33,7 +33,7 @@ Some CopyNumberCount attributes are inherited from :ref:`CopyNumber`.
- 0..m
- Alternative name(s) for the Entity.
* - extensions
- :ref:`Extension`
- `Extension </ga4gh/schema/gks-common/1.x/data-types/json/Extension>`_
- 0..m
- A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.
* - digest
Expand All @@ -45,7 +45,7 @@ Some CopyNumberCount attributes are inherited from :ref:`CopyNumber`.
- 0..m
-
* - location
- :ref:`IRI` | :ref:`Location`
- `IRI </ga4gh/schema/gks-common/1.x/data-types/json/IRI>`_ | :ref:`Location`
- 1..1
- A location for which the number of systemic copies is described.
* - type
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4 changes: 2 additions & 2 deletions schema/vrs/def/DerivativeMolecule.rst
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Expand Up @@ -33,7 +33,7 @@ Some DerivativeMolecule attributes are inherited from :ref:`Variation`.
- 0..m
- Alternative name(s) for the Entity.
* - extensions
- :ref:`Extension`
- `Extension </ga4gh/schema/gks-common/1.x/data-types/json/Extension>`_
- 0..m
- A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.
* - digest
Expand All @@ -49,7 +49,7 @@ Some DerivativeMolecule attributes are inherited from :ref:`Variation`.
- 1..1
- MUST be "DerivativeMolecule".
* - components
- :ref:`IRI` | :ref:`TraversalBlock`
- `IRI </ga4gh/schema/gks-common/1.x/data-types/json/IRI>`_ | :ref:`TraversalBlock`
- 2..m
- The molecular components that constitute the derivative molecule.
* - circular
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2 changes: 1 addition & 1 deletion schema/vrs/def/Ga4ghIdentifiableObject.rst
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Expand Up @@ -37,7 +37,7 @@ Some Ga4ghIdentifiableObject attributes are inherited from :ref:`gks.core-im:Ent
- 0..m
- Alternative name(s) for the Entity.
* - extensions
- :ref:`Extension`
- `Extension </ga4gh/schema/gks-common/1.x/data-types/json/Extension>`_
- 0..m
- A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.
* - digest
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2 changes: 1 addition & 1 deletion schema/vrs/def/LengthExpression.rst
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Expand Up @@ -33,7 +33,7 @@ Some LengthExpression attributes are inherited from :ref:`SequenceExpression`.
- 0..m
- Alternative name(s) for the Entity.
* - extensions
- :ref:`Extension`
- `Extension </ga4gh/schema/gks-common/1.x/data-types/json/Extension>`_
- 0..m
- A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.
* - type
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2 changes: 1 addition & 1 deletion schema/vrs/def/LiteralSequenceExpression.rst
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Expand Up @@ -33,7 +33,7 @@ Some LiteralSequenceExpression attributes are inherited from :ref:`SequenceExpre
- 0..m
- Alternative name(s) for the Entity.
* - extensions
- :ref:`Extension`
- `Extension </ga4gh/schema/gks-common/1.x/data-types/json/Extension>`_
- 0..m
- A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.
* - type
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2 changes: 1 addition & 1 deletion schema/vrs/def/ReferenceLengthExpression.rst
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Expand Up @@ -33,7 +33,7 @@ Some ReferenceLengthExpression attributes are inherited from :ref:`SequenceExpre
- 0..m
- Alternative name(s) for the Entity.
* - extensions
- :ref:`Extension`
- `Extension </ga4gh/schema/gks-common/1.x/data-types/json/Extension>`_
- 0..m
- A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.
* - type
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2 changes: 1 addition & 1 deletion schema/vrs/def/SequenceExpression.rst
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Expand Up @@ -33,7 +33,7 @@ Some SequenceExpression attributes are inherited from :ref:`gks.core-im:Entity`.
- 0..m
- Alternative name(s) for the Entity.
* - extensions
- :ref:`Extension`
- `Extension </ga4gh/schema/gks-common/1.x/data-types/json/Extension>`_
- 0..m
- A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.
* - type
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4 changes: 2 additions & 2 deletions schema/vrs/def/SequenceLocation.rst
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Expand Up @@ -33,7 +33,7 @@ Some SequenceLocation attributes are inherited from :ref:`Ga4ghIdentifiableObjec
- 0..m
- Alternative name(s) for the Entity.
* - extensions
- :ref:`Extension`
- `Extension </ga4gh/schema/gks-common/1.x/data-types/json/Extension>`_
- 0..m
- A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.
* - digest
Expand All @@ -45,7 +45,7 @@ Some SequenceLocation attributes are inherited from :ref:`Ga4ghIdentifiableObjec
- 1..1
- MUST be "SequenceLocation"
* - sequenceReference
- :ref:`IRI` | :ref:`SequenceReference`
- `IRI </ga4gh/schema/gks-common/1.x/data-types/json/IRI>`_ | :ref:`SequenceReference`
- 0..1
- A reference to a :ref:`Sequence` on which the location is defined.
* - start
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2 changes: 1 addition & 1 deletion schema/vrs/def/SequenceReference.rst
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Expand Up @@ -33,7 +33,7 @@ Some SequenceReference attributes are inherited from :ref:`gks.core-im:Entity`.
- 0..m
- Alternative name(s) for the Entity.
* - extensions
- :ref:`Extension`
- `Extension </ga4gh/schema/gks-common/1.x/data-types/json/Extension>`_
- 0..m
- A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.
* - type
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4 changes: 2 additions & 2 deletions schema/vrs/def/Terminus.rst
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Expand Up @@ -33,7 +33,7 @@ Some Terminus attributes are inherited from :ref:`Variation`.
- 0..m
- Alternative name(s) for the Entity.
* - extensions
- :ref:`Extension`
- `Extension </ga4gh/schema/gks-common/1.x/data-types/json/Extension>`_
- 0..m
- A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.
* - digest
Expand All @@ -49,6 +49,6 @@ Some Terminus attributes are inherited from :ref:`Variation`.
- 1..1
- MUST be "Terminus".
* - location
- :ref:`IRI` | :ref:`Location`
- `IRI </ga4gh/schema/gks-common/1.x/data-types/json/IRI>`_ | :ref:`Location`
- 1..1
- The location of the terminus.
2 changes: 1 addition & 1 deletion schema/vrs/def/TraversalBlock.rst
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Expand Up @@ -33,7 +33,7 @@ Some TraversalBlock attributes are inherited from :ref:`gks.core-im:Entity`.
- 0..m
- Alternative name(s) for the Entity.
* - extensions
- :ref:`Extension`
- `Extension </ga4gh/schema/gks-common/1.x/data-types/json/Extension>`_
- 0..m
- A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.
* - type
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2 changes: 1 addition & 1 deletion schema/vrs/def/Variation.rst
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Expand Up @@ -37,7 +37,7 @@ Some Variation attributes are inherited from :ref:`Ga4ghIdentifiableObject`.
- 0..m
- Alternative name(s) for the Entity.
* - extensions
- :ref:`Extension`
- `Extension </ga4gh/schema/gks-common/1.x/data-types/json/Extension>`_
- 0..m
- A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.
* - digest
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