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lines changed

‎.requirements.txt

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@@ -3,7 +3,7 @@ jsonschema
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referencing
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ipython
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pyyaml
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ga4gh.gks.metaschema==0.3.0b5
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ga4gh.gks.metaschema==0.3.0b6
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sphinx ~= 7.2
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sphinx-rtd-theme ~= 1.2
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jupyterlab

‎notebooks/referencing.ipynb

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‎schema/Makefile

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@@ -1,40 +1,5 @@
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.SECONDARY:
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.DELETE_ON_ERROR:
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BUILD_DIR := build
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IMPORT_DIR := import
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vpath %tag $(BUILD_DIR)
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vpath %.classes $(BUILD_DIR)
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SOURCES := $(wildcard *-source.yaml)
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TAGS := $(SOURCES:-source.yaml=.tag)
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IMPORTS := $(wildcard $(IMPORT_DIR)/*-source.yaml)
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all: build-ordered ${TAGS} prune-tag
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build-ordered: | $(BUILD_DIR)
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$(BUILD_DIR):
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mkdir $(BUILD_DIR)
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%.tag: %.classes %.json-tag %.defs-tag
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touch $(BUILD_DIR)/$@
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%.classes: %-source.yaml
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source2classes.py $< >${BUILD_DIR}/$@
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%.json-tag: %-source.yaml ${IMPORTS}
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source2splitjs.py $<
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touch $(BUILD_DIR)/$@
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%.defs-tag: %-source.yaml ${IMPORTS}
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y2t.py $<
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touch $(BUILD_DIR)/$@
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prune-tag: ${TAGS}
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$(MAKE) -f prune.mk
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touch $(BUILD_DIR)/$@
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all:
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(cd vrs; make all)
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clean:
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rm $(BUILD_DIR)/*
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(cd vrs; make clean)

‎schema/gks-common

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@@ -0,0 +1 @@
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../submodules/gks-common/schema/gks-common

‎schema/import/gks-common

-1
This file was deleted.

‎schema/json/Variation.json

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This file was deleted.

‎schema/json/import/gks-common

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This file was deleted.

‎schema/vrs/Makefile

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@@ -0,0 +1,40 @@
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.SECONDARY:
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.DELETE_ON_ERROR:
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BUILD_DIR := build
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IMPORT_DIR := import
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vpath %tag $(BUILD_DIR)
8+
vpath %.classes $(BUILD_DIR)
9+
10+
SOURCES := $(wildcard *-source.yaml)
11+
TAGS := $(SOURCES:-source.yaml=.tag)
12+
IMPORTS := $(wildcard $(IMPORT_DIR)/*-source.yaml)
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all: build-ordered ${TAGS} prune-tag
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build-ordered: | $(BUILD_DIR)
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$(BUILD_DIR):
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mkdir $(BUILD_DIR)
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%.tag: %.classes %.json-tag %.defs-tag
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touch $(BUILD_DIR)/$@
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%.classes: %-source.yaml
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source2classes.py $< >${BUILD_DIR}/$@
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%.json-tag: %-source.yaml ${IMPORTS}
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source2splitjs.py $<
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touch $(BUILD_DIR)/$@
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%.defs-tag: %-source.yaml ${IMPORTS}
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y2t.py $<
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touch $(BUILD_DIR)/$@
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prune-tag: ${TAGS}
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$(MAKE) -f prune.mk
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touch $(BUILD_DIR)/$@
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clean:
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rm $(BUILD_DIR)/*

‎schema/def/Adjacency.rst renamed to ‎schema/vrs/def/Adjacency.rst

+2-2
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@@ -29,7 +29,7 @@ Some Adjacency attributes are inherited from :ref:`Variation`.
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- 0..1
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- A free-text description of the entity.
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* - extensions
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- `Extension <import/gks-common/core.json#/$defs/Extension>`_
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- `Extension <../gks-common/core.json#/$defs/Extension>`_
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- 0..m
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-
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* - type
@@ -45,7 +45,7 @@ Some Adjacency attributes are inherited from :ref:`Variation`.
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- 0..m
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-
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* - adjoinedSequences
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- `IRI.json <import/gks-common/IRI.json>`_ | :ref:`Location`
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- `IRI.json <../gks-common/$defs/IRI.json>`_ | :ref:`Location`
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- 1..2
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- The terminal sequence or pair of adjoined sequences that defines in the adjacency.
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* - linker

‎schema/def/Allele.rst renamed to ‎schema/vrs/def/Allele.rst

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@@ -29,7 +29,7 @@ Some Allele attributes are inherited from :ref:`Variation`.
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- 0..1
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- A free-text description of the entity.
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* - extensions
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- `Extension <import/gks-common/core.json#/$defs/Extension>`_
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- `Extension <../gks-common/core.json#/$defs/Extension>`_
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- 0..m
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-
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* - type
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- 0..m
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-
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* - location
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- `IRI.json <import/gks-common/IRI.json>`_ | :ref:`Location`
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- `IRI.json <../gks-common/$defs/IRI.json>`_ | :ref:`Location`
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- 1..1
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- The location of the Allele
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* - state

‎schema/def/CopyNumber.rst renamed to ‎schema/vrs/def/CopyNumber.rst

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@@ -29,7 +29,7 @@ Some CopyNumber attributes are inherited from :ref:`Variation`.
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- 0..1
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- A free-text description of the entity.
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* - extensions
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- `Extension <import/gks-common/core.json#/$defs/Extension>`_
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- `Extension <../gks-common/core.json#/$defs/Extension>`_
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- 0..m
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-
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* - type
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- 0..m
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-
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* - location
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- `IRI.json <import/gks-common/IRI.json>`_ | :ref:`Location`
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- `IRI.json <../gks-common/$defs/IRI.json>`_ | :ref:`Location`
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- 1..1
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- A location for which the number of systemic copies is described.

‎schema/def/CopyNumberChange.rst renamed to ‎schema/vrs/def/CopyNumberChange.rst

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@@ -29,7 +29,7 @@ Some CopyNumberChange attributes are inherited from :ref:`CopyNumber`.
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- 0..1
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- A free-text description of the entity.
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* - extensions
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- `Extension <import/gks-common/core.json#/$defs/Extension>`_
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- `Extension <../gks-common/core.json#/$defs/Extension>`_
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- 0..m
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-
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* - type
@@ -45,7 +45,7 @@ Some CopyNumberChange attributes are inherited from :ref:`CopyNumber`.
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- 0..m
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-
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* - location
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- `IRI.json <import/gks-common/IRI.json>`_ | :ref:`Location`
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- `IRI.json <../gks-common/$defs/IRI.json>`_ | :ref:`Location`
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- 1..1
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- A location for which the number of systemic copies is described.
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* - copyChange

‎schema/def/CopyNumberCount.rst renamed to ‎schema/vrs/def/CopyNumberCount.rst

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@@ -29,7 +29,7 @@ Some CopyNumberCount attributes are inherited from :ref:`CopyNumber`.
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- 0..1
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- A free-text description of the entity.
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* - extensions
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- `Extension <import/gks-common/core.json#/$defs/Extension>`_
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- `Extension <../gks-common/core.json#/$defs/Extension>`_
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- 0..m
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-
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* - type
@@ -45,7 +45,7 @@ Some CopyNumberCount attributes are inherited from :ref:`CopyNumber`.
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- 0..m
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-
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* - location
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- `IRI.json <import/gks-common/IRI.json>`_ | :ref:`Location`
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- `IRI.json <../gks-common/$defs/IRI.json>`_ | :ref:`Location`
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- 1..1
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- A location for which the number of systemic copies is described.
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* - copies

‎schema/def/Expression.rst renamed to ‎schema/vrs/def/Expression.rst

File renamed without changes.

‎schema/def/Ga4ghIdentifiableObject.rst renamed to ‎schema/vrs/def/Ga4ghIdentifiableObject.rst

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@@ -29,7 +29,7 @@ Some Ga4ghIdentifiableObject attributes are inherited from :ref:`gks.core:Entity
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- 0..1
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- A free-text description of the entity.
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* - extensions
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- `Extension <import/gks-common/core.json#/$defs/Extension>`_
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- `Extension <../gks-common/core.json#/$defs/Extension>`_
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- 0..m
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-
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* - type

‎schema/def/Haplotype.rst renamed to ‎schema/vrs/def/Haplotype.rst

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@@ -29,7 +29,7 @@ Some Haplotype attributes are inherited from :ref:`Variation`.
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- 0..1
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- A free-text description of the entity.
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* - extensions
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- `Extension <import/gks-common/core.json#/$defs/Extension>`_
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- `Extension <../gks-common/core.json#/$defs/Extension>`_
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- 0..m
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-
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* - type
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- 0..m
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-
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* - members
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- :ref:`Adjacency` | :ref:`Allele` | `IRI.json <import/gks-common/IRI.json>`_
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- :ref:`Adjacency` | :ref:`Allele` | `IRI.json <../gks-common/$defs/IRI.json>`_
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- 2..m
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- A list of :ref:`Alleles <Allele>` and :ref:`Adjacencies <Adjacency>` that comprise a Haplotype. Members must share the same reference sequence as adjacent members. Alleles should not have overlapping or adjacent coordinates with neighboring Alleles. Neighboring alleles should be ordered by ascending coordinates, unless represented on a DNA inversion (following an Adjacency with end-defined adjoinedSequences), in which case they should be ordered in descending coordinates. Sequence references MUST be consistent for all members between and including the end of one Adjacency and the beginning of another.

‎schema/def/LengthExpression.rst renamed to ‎schema/vrs/def/LengthExpression.rst

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@@ -29,7 +29,7 @@ Some LengthExpression attributes are inherited from :ref:`SequenceExpression`.
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- 0..1
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- A free-text description of the entity.
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* - extensions
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- `Extension <import/gks-common/core.json#/$defs/Extension>`_
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- `Extension <../gks-common/core.json#/$defs/Extension>`_
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- 0..m
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-
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* - type

‎schema/def/LiteralSequenceExpression.rst renamed to ‎schema/vrs/def/LiteralSequenceExpression.rst

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@@ -29,7 +29,7 @@ Some LiteralSequenceExpression attributes are inherited from :ref:`SequenceExpre
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- 0..1
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- A free-text description of the entity.
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* - extensions
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- `Extension <import/gks-common/core.json#/$defs/Extension>`_
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- `Extension <../gks-common/core.json#/$defs/Extension>`_
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- 0..m
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-
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* - type

‎schema/def/Location.rst renamed to ‎schema/vrs/def/Location.rst

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‎schema/def/MolecularVariation.rst renamed to ‎schema/vrs/def/MolecularVariation.rst

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‎schema/def/Range.rst renamed to ‎schema/vrs/def/Range.rst

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‎schema/def/ReferenceLengthExpression.rst renamed to ‎schema/vrs/def/ReferenceLengthExpression.rst

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@@ -29,7 +29,7 @@ Some ReferenceLengthExpression attributes are inherited from :ref:`SequenceExpre
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- 0..1
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- A free-text description of the entity.
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* - extensions
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- `Extension <import/gks-common/core.json#/$defs/Extension>`_
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- `Extension <../gks-common/core.json#/$defs/Extension>`_
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- 0..m
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-
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* - type

‎schema/def/Residue.rst renamed to ‎schema/vrs/def/Residue.rst

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‎schema/def/SequenceExpression.rst renamed to ‎schema/vrs/def/SequenceExpression.rst

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@@ -29,7 +29,7 @@ Some SequenceExpression attributes are inherited from :ref:`gks.core:Entity`.
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- 0..1
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- A free-text description of the entity.
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* - extensions
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- `Extension <import/gks-common/core.json#/$defs/Extension>`_
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- `Extension <../gks-common/core.json#/$defs/Extension>`_
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- 0..m
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-
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* - type

‎schema/def/SequenceLocation.rst renamed to ‎schema/vrs/def/SequenceLocation.rst

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@@ -29,7 +29,7 @@ Some SequenceLocation attributes are inherited from :ref:`Ga4ghIdentifiableObjec
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- 0..1
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- A free-text description of the entity.
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* - extensions
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- `Extension <import/gks-common/core.json#/$defs/Extension>`_
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- `Extension <../gks-common/core.json#/$defs/Extension>`_
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- 0..m
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-
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* - type
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- 0..1
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- A sha512t24u digest created using the VRS Computed Identifier algorithm.
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* - sequenceReference
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- `IRI.json <import/gks-common/IRI.json>`_ | :ref:`SequenceReference`
44+
- `IRI.json <../gks-common/$defs/IRI.json>`_ | :ref:`SequenceReference`
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- 0..1
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- A :ref:`SequenceReference`.
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* - start

‎schema/def/SequenceReference.rst renamed to ‎schema/vrs/def/SequenceReference.rst

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@@ -29,7 +29,7 @@ Some SequenceReference attributes are inherited from :ref:`gks.core:Entity`.
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- 0..1
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- A free-text description of the entity.
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* - extensions
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- `Extension <import/gks-common/core.json#/$defs/Extension>`_
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- `Extension <../gks-common/core.json#/$defs/Extension>`_
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- 0..m
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-
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* - type

‎schema/def/SequenceString.rst renamed to ‎schema/vrs/def/SequenceString.rst

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‎schema/def/SystemicVariation.rst renamed to ‎schema/vrs/def/SystemicVariation.rst

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‎schema/def/ValueObject.rst renamed to ‎schema/vrs/def/ValueObject.rst

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‎schema/def/Variation.rst renamed to ‎schema/vrs/def/Variation.rst

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- 0..1
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- A free-text description of the entity.
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* - extensions
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- `Extension <import/gks-common/core.json#/$defs/Extension>`_
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- `Extension <../gks-common/core.json#/$defs/Extension>`_
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- 0..m
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-
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* - type

‎schema/json/Adjacency.json renamed to ‎schema/vrs/json/Adjacency

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11
{
22
"$schema": "https://json-schema.org/draft/2020-12/schema",
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"$id": "https://w3id.org/ga4gh/schema/vrs/2.x/json/Adjacency",
34
"title": "Adjacency",
45
"type": "object",
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"maturity": "draft",
@@ -29,7 +30,7 @@
2930
"type": "array",
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"ordered": true,
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"items": {
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"$ref": "import/gks-common/Extension.json"
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"$ref": "/ga4gh/schema/gks-common/1.x/json/Extension"
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}
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},
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"type": {
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4748
"type": "array",
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"ordered": false,
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"items": {
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"$ref": "Expression.json"
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"$ref": "/ga4gh/schema/vrs/2.x/json/Expression"
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}
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},
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"adjoinedSequences": {
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5758
"items": {
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"oneOf": [
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{
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"$ref": "SequenceLocation.json"
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"$ref": "/ga4gh/schema/vrs/2.x/json/SequenceLocation"
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},
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{
63-
"$ref": "import/gks-common/IRI.json"
64+
"$ref": "/ga4gh/schema/gks-common/1.x/json/IRI"
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}
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]
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},
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7273
"description": "The sequence found between adjoined sequences.",
7374
"oneOf": [
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{
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"$ref": "LengthExpression.json"
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"$ref": "/ga4gh/schema/vrs/2.x/json/LengthExpression"
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},
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{
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"$ref": "LiteralSequenceExpression.json"
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"$ref": "/ga4gh/schema/vrs/2.x/json/LiteralSequenceExpression"
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},
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{
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"$ref": "ReferenceLengthExpression.json"
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"$ref": "/ga4gh/schema/vrs/2.x/json/ReferenceLengthExpression"
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}
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]
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}

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