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feat: add "recombinant" qc metric #1700

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50 changes: 50 additions & 0 deletions packages/nextclade-schemas/input-pathogen-json.schema.json
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Original file line number Diff line number Diff line change
Expand Up @@ -83,6 +83,11 @@
}
],
"scoreWeight": 75.0
},
"recombinants": {
"enabled": true,
"mutationsThreshold": 20,
"scoreWeight": 100.0
}
},
"phenotypeData": [
Expand Down Expand Up @@ -444,6 +449,11 @@
}
],
"scoreWeight": 75.0
},
"recombinants": {
"enabled": true,
"mutationsThreshold": 20,
"scoreWeight": 100.0
}
}
],
Expand Down Expand Up @@ -524,6 +534,18 @@
"$ref": "#/definitions/QcRulesConfigStopCodons"
}
]
},
"recombinants": {
"default": {
"enabled": false,
"mutationsThreshold": 0,
"scoreWeight": 0.0
},
"allOf": [
{
"$ref": "#/definitions/QcRulesConfigRecombinants"
}
]
}
}
},
Expand Down Expand Up @@ -820,6 +842,34 @@
}
}
},
"QcRulesConfigRecombinants": {
"description": "Configuration for QC rule \"recombinants\"",
"examples": [
{
"enabled": true,
"mutationsThreshold": 20,
"scoreWeight": 100.0
}
],
"type": "object",
"properties": {
"enabled": {
"default": false,
"type": "boolean"
},
"mutationsThreshold": {
"default": 0,
"type": "integer",
"format": "uint",
"minimum": 0.0
},
"scoreWeight": {
"default": 0.0,
"type": "number",
"format": "double"
}
}
},
"NextcladeGeneralParamsOptional": {
"type": "object",
"properties": {
Expand Down
35 changes: 35 additions & 0 deletions packages/nextclade-schemas/input-pathogen-json.schema.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -60,6 +60,10 @@ examples:
- cdsName: ORF3a
codon: 238
scoreWeight: 75.0
recombinants:
enabled: true
mutationsThreshold: 20
scoreWeight: 100.0
phenotypeData:
- name: receptor_binding
nameFriendly: Receptor Binding
Expand Down Expand Up @@ -276,6 +280,10 @@ definitions:
- cdsName: ORF3a
codon: 238
scoreWeight: 75.0
recombinants:
enabled: true
mutationsThreshold: 20
scoreWeight: 100.0
type: object
properties:
missingData:
Expand Down Expand Up @@ -324,6 +332,13 @@ definitions:
scoreWeight: 75.0
allOf:
- $ref: '#/definitions/QcRulesConfigStopCodons'
recombinants:
default:
enabled: false
mutationsThreshold: 0
scoreWeight: 0.0
allOf:
- $ref: '#/definitions/QcRulesConfigRecombinants'
QcRulesConfigMissingData:
description: Configuration for QC rule "missing data"
examples:
Expand Down Expand Up @@ -529,6 +544,26 @@ definitions:
type: integer
format: uint
minimum: 0.0
QcRulesConfigRecombinants:
description: Configuration for QC rule "recombinants"
examples:
- enabled: true
mutationsThreshold: 20
scoreWeight: 100.0
type: object
properties:
enabled:
default: false
type: boolean
mutationsThreshold:
default: 0
type: integer
format: uint
minimum: 0.0
scoreWeight:
default: 0.0
type: number
format: double
NextcladeGeneralParamsOptional:
type: object
properties:
Expand Down
50 changes: 50 additions & 0 deletions packages/nextclade-schemas/nextclade-auspice-extensions.schema.json
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Original file line number Diff line number Diff line change
Expand Up @@ -362,6 +362,11 @@
}
],
"scoreWeight": 75.0
},
"recombinants": {
"enabled": true,
"mutationsThreshold": 20,
"scoreWeight": 100.0
}
},
"phenotypeData": [
Expand Down Expand Up @@ -723,6 +728,11 @@
}
],
"scoreWeight": 75.0
},
"recombinants": {
"enabled": true,
"mutationsThreshold": 20,
"scoreWeight": 100.0
}
}
],
Expand Down Expand Up @@ -803,6 +813,18 @@
"$ref": "#/definitions/QcRulesConfigStopCodons"
}
]
},
"recombinants": {
"default": {
"enabled": false,
"mutationsThreshold": 0,
"scoreWeight": 0.0
},
"allOf": [
{
"$ref": "#/definitions/QcRulesConfigRecombinants"
}
]
}
}
},
Expand Down Expand Up @@ -1079,6 +1101,34 @@
}
}
},
"QcRulesConfigRecombinants": {
"description": "Configuration for QC rule \"recombinants\"",
"examples": [
{
"enabled": true,
"mutationsThreshold": 20,
"scoreWeight": 100.0
}
],
"type": "object",
"properties": {
"enabled": {
"default": false,
"type": "boolean"
},
"mutationsThreshold": {
"default": 0,
"type": "integer",
"format": "uint",
"minimum": 0.0
},
"scoreWeight": {
"default": 0.0,
"type": "number",
"format": "double"
}
}
},
"NextcladeGeneralParamsOptional": {
"type": "object",
"properties": {
Expand Down
35 changes: 35 additions & 0 deletions packages/nextclade-schemas/nextclade-auspice-extensions.schema.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -237,6 +237,10 @@ definitions:
- cdsName: ORF3a
codon: 238
scoreWeight: 75.0
recombinants:
enabled: true
mutationsThreshold: 20
scoreWeight: 100.0
phenotypeData:
- name: receptor_binding
nameFriendly: Receptor Binding
Expand Down Expand Up @@ -452,6 +456,10 @@ definitions:
- cdsName: ORF3a
codon: 238
scoreWeight: 75.0
recombinants:
enabled: true
mutationsThreshold: 20
scoreWeight: 100.0
type: object
properties:
missingData:
Expand Down Expand Up @@ -500,6 +508,13 @@ definitions:
scoreWeight: 75.0
allOf:
- $ref: '#/definitions/QcRulesConfigStopCodons'
recombinants:
default:
enabled: false
mutationsThreshold: 0
scoreWeight: 0.0
allOf:
- $ref: '#/definitions/QcRulesConfigRecombinants'
QcRulesConfigMissingData:
description: Configuration for QC rule "missing data"
examples:
Expand Down Expand Up @@ -688,6 +703,26 @@ definitions:
type: integer
format: uint
minimum: 0.0
QcRulesConfigRecombinants:
description: Configuration for QC rule "recombinants"
examples:
- enabled: true
mutationsThreshold: 20
scoreWeight: 100.0
type: object
properties:
enabled:
default: false
type: boolean
mutationsThreshold:
default: 0
type: integer
format: uint
minimum: 0.0
scoreWeight:
default: 0.0
type: number
format: double
NextcladeGeneralParamsOptional:
type: object
properties:
Expand Down
50 changes: 50 additions & 0 deletions packages/nextclade-schemas/output-json.schema.json
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Original file line number Diff line number Diff line change
Expand Up @@ -1699,6 +1699,16 @@
}
]
},
"recombinants": {
"anyOf": [
{
"$ref": "#/definitions/QcResultRecombinants"
},
{
"type": "null"
}
]
},
"overallScore": {
"type": "number",
"format": "double"
Expand Down Expand Up @@ -1988,6 +1998,46 @@
}
}
},
"QcResultRecombinants": {
"type": "object",
"required": [
"excessMutations",
"mutationsThreshold",
"score",
"status",
"totalPrivateMutations",
"totalReversionSubstitutions"
],
"properties": {
"score": {
"type": "number",
"format": "double"
},
"status": {
"$ref": "#/definitions/QcStatus"
},
"totalPrivateMutations": {
"type": "integer",
"format": "uint",
"minimum": 0.0
},
"totalReversionSubstitutions": {
"type": "integer",
"format": "uint",
"minimum": 0.0
},
"mutationsThreshold": {
"type": "integer",
"format": "uint",
"minimum": 0.0
},
"excessMutations": {
"type": "integer",
"format": "uint",
"minimum": 0.0
}
}
},
"PhenotypeValue": {
"description": "Result for a single phenotype value",
"type": "object",
Expand Down
35 changes: 35 additions & 0 deletions packages/nextclade-schemas/output-json.schema.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -1177,6 +1177,10 @@ definitions:
anyOf:
- $ref: '#/definitions/QcResultStopCodons'
- type: 'null'
recombinants:
anyOf:
- $ref: '#/definitions/QcResultRecombinants'
- type: 'null'
overallScore:
type: number
format: double
Expand Down Expand Up @@ -1390,6 +1394,37 @@ definitions:
type: integer
format: uint
minimum: 0.0
QcResultRecombinants:
type: object
required:
- excessMutations
- mutationsThreshold
- score
- status
- totalPrivateMutations
- totalReversionSubstitutions
properties:
score:
type: number
format: double
status:
$ref: '#/definitions/QcStatus'
totalPrivateMutations:
type: integer
format: uint
minimum: 0.0
totalReversionSubstitutions:
type: integer
format: uint
minimum: 0.0
mutationsThreshold:
type: integer
format: uint
minimum: 0.0
excessMutations:
type: integer
format: uint
minimum: 0.0
PhenotypeValue:
description: Result for a single phenotype value
type: object
Expand Down
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