@jbrowse/cli 5.0.0-beta.3 → 5.0.0-beta.7

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (11) hide show
  1. package/README.md +7 -0
  2. package/dist/commands/add-track-utils/track-config.js +3 -3
  3. package/dist/commands/make-pif/index.js +6 -1
  4. package/dist/commands/make-pif/pif-generator.js +34 -40
  5. package/dist/commands/validate/configManifest.generated.js +685 -75
  6. package/dist/commands/validate/configSchema.generated.js +17706 -0
  7. package/dist/commands/validate/index.js +8 -1
  8. package/dist/commands/validate/schemaValidate.js +300 -0
  9. package/dist/commands/validate/validateConfig.js +76 -278
  10. package/dist/version.js +1 -1
  11. package/package.json +5 -4
package/dist/commands/validate/configManifest.generated.js CHANGED
@@ -1702,7 +1702,7 @@ export const configManifest = {
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  },
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  {
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  "name": "displays",
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- "type": "(LinearBasicDisplayConfigurationSchema | LinearMultiRowFeatureDisplayConfigurationSchema | LinearAlignmentsDisplayConfigurationSchema | ChordVariantDisplayConfigurationSchema | DotplotDisplayConfigurationSchema | LinearSyntenyDisplayConfigurationSchema | LGVSyntenyDisplayConfigurationSchema | MultiWaySyntenyDisplayConfigurationSchema | LinearReferenceSequenceDisplayConfigurationSchema | LinearVariantDisplayConfigurationSchema | LinearMultiSampleVariantDisplayConfigurationSchema | LinearMultiSampleVariantMatrixDisplayConfigurationSchema | LDTrackDisplayConfigurationSchema | LinearWiggleDisplayConfigurationSchema | MultiLinearWiggleDisplayConfigurationSchema | LinearGCContentDisplayConfigurationSchema | LinearGCContentTrackDisplayConfigurationSchema | LinearMafDisplayConfigurationSchema | LinearHicDisplayConfigurationSchema | LinearArcDisplayConfigurationSchema | LinearPairedArcDisplayConfigurationSchema | LinearManhattanDisplayConfigurationSchema)[]"
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+ "type": "(LinearBasicDisplayConfigurationSchema | LinearMultiRowFeatureDisplayConfigurationSchema | LinearAlignmentsDisplayConfigurationSchema | ChordVariantDisplayConfigurationSchema | ChordSyntenyDisplayConfigurationSchema | DotplotDisplayConfigurationSchema | LinearSyntenyDisplayConfigurationSchema | LGVSyntenyDisplayConfigurationSchema | MultiWaySyntenyDisplayConfigurationSchema | LinearReferenceSequenceDisplayConfigurationSchema | LinearVariantDisplayConfigurationSchema | LinearMultiSampleVariantDisplayConfigurationSchema | LinearMultiSampleVariantMatrixDisplayConfigurationSchema | LDTrackDisplayConfigurationSchema | LinearWiggleDisplayConfigurationSchema | MultiLinearWiggleDisplayConfigurationSchema | LinearGCContentDisplayConfigurationSchema | LinearGCContentTrackDisplayConfigurationSchema | LinearMafDisplayConfigurationSchema | LinearHicDisplayConfigurationSchema | LinearArcDisplayConfigurationSchema | LinearPairedArcDisplayConfigurationSchema | LinearManhattanDisplayConfigurationSchema | LinearMarkDisplayConfigurationSchema)[]"
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  },
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  {
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  "name": "formatDetails",
@@ -1744,7 +1744,9 @@ export const configManifest = {
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  "displayTypes": [
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  "LinearBasicDisplay",
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  "LinearMultiRowFeatureDisplay",
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- "LinearArcDisplay"
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+ "LinearArcDisplay",
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+ "LinearManhattanDisplay",
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+ "LinearMarkDisplay"
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  ]
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  },
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  "AlignmentsTrack": {
@@ -1805,7 +1807,7 @@ export const configManifest = {
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  },
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  {
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  "name": "displays",
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- "type": "(LinearBasicDisplayConfigurationSchema | LinearMultiRowFeatureDisplayConfigurationSchema | LinearAlignmentsDisplayConfigurationSchema | ChordVariantDisplayConfigurationSchema | DotplotDisplayConfigurationSchema | LinearSyntenyDisplayConfigurationSchema | LGVSyntenyDisplayConfigurationSchema | MultiWaySyntenyDisplayConfigurationSchema | LinearReferenceSequenceDisplayConfigurationSchema | LinearVariantDisplayConfigurationSchema | LinearMultiSampleVariantDisplayConfigurationSchema | LinearMultiSampleVariantMatrixDisplayConfigurationSchema | LDTrackDisplayConfigurationSchema | LinearWiggleDisplayConfigurationSchema | MultiLinearWiggleDisplayConfigurationSchema | LinearGCContentDisplayConfigurationSchema | LinearGCContentTrackDisplayConfigurationSchema | LinearMafDisplayConfigurationSchema | LinearHicDisplayConfigurationSchema | LinearArcDisplayConfigurationSchema | LinearPairedArcDisplayConfigurationSchema | LinearManhattanDisplayConfigurationSchema)[]"
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+ "type": "(LinearBasicDisplayConfigurationSchema | LinearMultiRowFeatureDisplayConfigurationSchema | LinearAlignmentsDisplayConfigurationSchema | ChordVariantDisplayConfigurationSchema | ChordSyntenyDisplayConfigurationSchema | DotplotDisplayConfigurationSchema | LinearSyntenyDisplayConfigurationSchema | LGVSyntenyDisplayConfigurationSchema | MultiWaySyntenyDisplayConfigurationSchema | LinearReferenceSequenceDisplayConfigurationSchema | LinearVariantDisplayConfigurationSchema | LinearMultiSampleVariantDisplayConfigurationSchema | LinearMultiSampleVariantMatrixDisplayConfigurationSchema | LDTrackDisplayConfigurationSchema | LinearWiggleDisplayConfigurationSchema | MultiLinearWiggleDisplayConfigurationSchema | LinearGCContentDisplayConfigurationSchema | LinearGCContentTrackDisplayConfigurationSchema | LinearMafDisplayConfigurationSchema | LinearHicDisplayConfigurationSchema | LinearArcDisplayConfigurationSchema | LinearPairedArcDisplayConfigurationSchema | LinearManhattanDisplayConfigurationSchema | LinearMarkDisplayConfigurationSchema)[]"
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  },
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  {
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  "name": "formatDetails",
@@ -1845,7 +1847,8 @@ export const configManifest = {
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  }
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  ],
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  "displayTypes": [
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- "LinearAlignmentsDisplay"
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+ "LinearAlignmentsDisplay",
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+ "LinearMarkDisplay"
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  ]
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  },
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  "SyntenyTrack": {
@@ -1906,7 +1909,7 @@ export const configManifest = {
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  },
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  {
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  "name": "displays",
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- "type": "(LinearBasicDisplayConfigurationSchema | LinearMultiRowFeatureDisplayConfigurationSchema | LinearAlignmentsDisplayConfigurationSchema | ChordVariantDisplayConfigurationSchema | DotplotDisplayConfigurationSchema | LinearSyntenyDisplayConfigurationSchema | LGVSyntenyDisplayConfigurationSchema | MultiWaySyntenyDisplayConfigurationSchema | LinearReferenceSequenceDisplayConfigurationSchema | LinearVariantDisplayConfigurationSchema | LinearMultiSampleVariantDisplayConfigurationSchema | LinearMultiSampleVariantMatrixDisplayConfigurationSchema | LDTrackDisplayConfigurationSchema | LinearWiggleDisplayConfigurationSchema | MultiLinearWiggleDisplayConfigurationSchema | LinearGCContentDisplayConfigurationSchema | LinearGCContentTrackDisplayConfigurationSchema | LinearMafDisplayConfigurationSchema | LinearHicDisplayConfigurationSchema | LinearArcDisplayConfigurationSchema | LinearPairedArcDisplayConfigurationSchema | LinearManhattanDisplayConfigurationSchema)[]"
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+ "type": "(LinearBasicDisplayConfigurationSchema | LinearMultiRowFeatureDisplayConfigurationSchema | LinearAlignmentsDisplayConfigurationSchema | ChordVariantDisplayConfigurationSchema | ChordSyntenyDisplayConfigurationSchema | DotplotDisplayConfigurationSchema | LinearSyntenyDisplayConfigurationSchema | LGVSyntenyDisplayConfigurationSchema | MultiWaySyntenyDisplayConfigurationSchema | LinearReferenceSequenceDisplayConfigurationSchema | LinearVariantDisplayConfigurationSchema | LinearMultiSampleVariantDisplayConfigurationSchema | LinearMultiSampleVariantMatrixDisplayConfigurationSchema | LDTrackDisplayConfigurationSchema | LinearWiggleDisplayConfigurationSchema | MultiLinearWiggleDisplayConfigurationSchema | LinearGCContentDisplayConfigurationSchema | LinearGCContentTrackDisplayConfigurationSchema | LinearMafDisplayConfigurationSchema | LinearHicDisplayConfigurationSchema | LinearArcDisplayConfigurationSchema | LinearPairedArcDisplayConfigurationSchema | LinearManhattanDisplayConfigurationSchema | LinearMarkDisplayConfigurationSchema)[]"
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  },
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  {
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  "name": "formatDetails",
@@ -1946,6 +1949,7 @@ export const configManifest = {
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  }
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  ],
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  "displayTypes": [
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+ "ChordSyntenyDisplay",
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  "DotplotDisplay",
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  "LinearSyntenyDisplay",
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  "LGVSyntenyDisplay",
@@ -1968,7 +1972,7 @@ export const configManifest = {
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  },
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  {
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  "name": "displays",
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- "type": "(LinearBasicDisplayConfigurationSchema | LinearMultiRowFeatureDisplayConfigurationSchema | LinearAlignmentsDisplayConfigurationSchema | ChordVariantDisplayConfigurationSchema | DotplotDisplayConfigurationSchema | LinearSyntenyDisplayConfigurationSchema | LGVSyntenyDisplayConfigurationSchema | MultiWaySyntenyDisplayConfigurationSchema | LinearReferenceSequenceDisplayConfigurationSchema | LinearVariantDisplayConfigurationSchema | LinearMultiSampleVariantDisplayConfigurationSchema | LinearMultiSampleVariantMatrixDisplayConfigurationSchema | LDTrackDisplayConfigurationSchema | LinearWiggleDisplayConfigurationSchema | MultiLinearWiggleDisplayConfigurationSchema | LinearGCContentDisplayConfigurationSchema | LinearGCContentTrackDisplayConfigurationSchema | LinearMafDisplayConfigurationSchema | LinearHicDisplayConfigurationSchema | LinearArcDisplayConfigurationSchema | LinearPairedArcDisplayConfigurationSchema | LinearManhattanDisplayConfigurationSchema)[]"
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+ "type": "(LinearBasicDisplayConfigurationSchema | LinearMultiRowFeatureDisplayConfigurationSchema | LinearAlignmentsDisplayConfigurationSchema | ChordVariantDisplayConfigurationSchema | ChordSyntenyDisplayConfigurationSchema | DotplotDisplayConfigurationSchema | LinearSyntenyDisplayConfigurationSchema | LGVSyntenyDisplayConfigurationSchema | MultiWaySyntenyDisplayConfigurationSchema | LinearReferenceSequenceDisplayConfigurationSchema | LinearVariantDisplayConfigurationSchema | LinearMultiSampleVariantDisplayConfigurationSchema | LinearMultiSampleVariantMatrixDisplayConfigurationSchema | LDTrackDisplayConfigurationSchema | LinearWiggleDisplayConfigurationSchema | MultiLinearWiggleDisplayConfigurationSchema | LinearGCContentDisplayConfigurationSchema | LinearGCContentTrackDisplayConfigurationSchema | LinearMafDisplayConfigurationSchema | LinearHicDisplayConfigurationSchema | LinearArcDisplayConfigurationSchema | LinearPairedArcDisplayConfigurationSchema | LinearManhattanDisplayConfigurationSchema | LinearMarkDisplayConfigurationSchema)[]"
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  },
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  {
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  "name": "name",
@@ -2064,7 +2068,7 @@ export const configManifest = {
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  },
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  {
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  "name": "displays",
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- "type": "(LinearBasicDisplayConfigurationSchema | LinearMultiRowFeatureDisplayConfigurationSchema | LinearAlignmentsDisplayConfigurationSchema | ChordVariantDisplayConfigurationSchema | DotplotDisplayConfigurationSchema | LinearSyntenyDisplayConfigurationSchema | LGVSyntenyDisplayConfigurationSchema | MultiWaySyntenyDisplayConfigurationSchema | LinearReferenceSequenceDisplayConfigurationSchema | LinearVariantDisplayConfigurationSchema | LinearMultiSampleVariantDisplayConfigurationSchema | LinearMultiSampleVariantMatrixDisplayConfigurationSchema | LDTrackDisplayConfigurationSchema | LinearWiggleDisplayConfigurationSchema | MultiLinearWiggleDisplayConfigurationSchema | LinearGCContentDisplayConfigurationSchema | LinearGCContentTrackDisplayConfigurationSchema | LinearMafDisplayConfigurationSchema | LinearHicDisplayConfigurationSchema | LinearArcDisplayConfigurationSchema | LinearPairedArcDisplayConfigurationSchema | LinearManhattanDisplayConfigurationSchema)[]"
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+ "type": "(LinearBasicDisplayConfigurationSchema | LinearMultiRowFeatureDisplayConfigurationSchema | LinearAlignmentsDisplayConfigurationSchema | ChordVariantDisplayConfigurationSchema | ChordSyntenyDisplayConfigurationSchema | DotplotDisplayConfigurationSchema | LinearSyntenyDisplayConfigurationSchema | LGVSyntenyDisplayConfigurationSchema | MultiWaySyntenyDisplayConfigurationSchema | LinearReferenceSequenceDisplayConfigurationSchema | LinearVariantDisplayConfigurationSchema | LinearMultiSampleVariantDisplayConfigurationSchema | LinearMultiSampleVariantMatrixDisplayConfigurationSchema | LDTrackDisplayConfigurationSchema | LinearWiggleDisplayConfigurationSchema | MultiLinearWiggleDisplayConfigurationSchema | LinearGCContentDisplayConfigurationSchema | LinearGCContentTrackDisplayConfigurationSchema | LinearMafDisplayConfigurationSchema | LinearHicDisplayConfigurationSchema | LinearArcDisplayConfigurationSchema | LinearPairedArcDisplayConfigurationSchema | LinearManhattanDisplayConfigurationSchema | LinearMarkDisplayConfigurationSchema)[]"
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  },
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  {
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  "name": "formatDetails",
@@ -2108,7 +2112,8 @@ export const configManifest = {
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  "LinearVariantDisplay",
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  "LinearMultiSampleVariantDisplay",
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  "LinearMultiSampleVariantMatrixDisplay",
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- "LinearPairedArcDisplay"
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+ "LinearPairedArcDisplay",
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+ "LinearMarkDisplay"
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  ]
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  },
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  "LDTrack": {
@@ -2169,7 +2174,7 @@ export const configManifest = {
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  },
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  {
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  "name": "displays",
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- "type": "(LinearBasicDisplayConfigurationSchema | LinearMultiRowFeatureDisplayConfigurationSchema | LinearAlignmentsDisplayConfigurationSchema | ChordVariantDisplayConfigurationSchema | DotplotDisplayConfigurationSchema | LinearSyntenyDisplayConfigurationSchema | LGVSyntenyDisplayConfigurationSchema | MultiWaySyntenyDisplayConfigurationSchema | LinearReferenceSequenceDisplayConfigurationSchema | LinearVariantDisplayConfigurationSchema | LinearMultiSampleVariantDisplayConfigurationSchema | LinearMultiSampleVariantMatrixDisplayConfigurationSchema | LDTrackDisplayConfigurationSchema | LinearWiggleDisplayConfigurationSchema | MultiLinearWiggleDisplayConfigurationSchema | LinearGCContentDisplayConfigurationSchema | LinearGCContentTrackDisplayConfigurationSchema | LinearMafDisplayConfigurationSchema | LinearHicDisplayConfigurationSchema | LinearArcDisplayConfigurationSchema | LinearPairedArcDisplayConfigurationSchema | LinearManhattanDisplayConfigurationSchema)[]"
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+ "type": "(LinearBasicDisplayConfigurationSchema | LinearMultiRowFeatureDisplayConfigurationSchema | LinearAlignmentsDisplayConfigurationSchema | ChordVariantDisplayConfigurationSchema | ChordSyntenyDisplayConfigurationSchema | DotplotDisplayConfigurationSchema | LinearSyntenyDisplayConfigurationSchema | LGVSyntenyDisplayConfigurationSchema | MultiWaySyntenyDisplayConfigurationSchema | LinearReferenceSequenceDisplayConfigurationSchema | LinearVariantDisplayConfigurationSchema | LinearMultiSampleVariantDisplayConfigurationSchema | LinearMultiSampleVariantMatrixDisplayConfigurationSchema | LDTrackDisplayConfigurationSchema | LinearWiggleDisplayConfigurationSchema | MultiLinearWiggleDisplayConfigurationSchema | LinearGCContentDisplayConfigurationSchema | LinearGCContentTrackDisplayConfigurationSchema | LinearMafDisplayConfigurationSchema | LinearHicDisplayConfigurationSchema | LinearArcDisplayConfigurationSchema | LinearPairedArcDisplayConfigurationSchema | LinearManhattanDisplayConfigurationSchema | LinearMarkDisplayConfigurationSchema)[]"
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  },
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  {
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  "name": "formatDetails",
@@ -2270,7 +2275,7 @@ export const configManifest = {
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  },
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  {
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  "name": "displays",
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- "type": "(LinearBasicDisplayConfigurationSchema | LinearMultiRowFeatureDisplayConfigurationSchema | LinearAlignmentsDisplayConfigurationSchema | ChordVariantDisplayConfigurationSchema | DotplotDisplayConfigurationSchema | LinearSyntenyDisplayConfigurationSchema | LGVSyntenyDisplayConfigurationSchema | MultiWaySyntenyDisplayConfigurationSchema | LinearReferenceSequenceDisplayConfigurationSchema | LinearVariantDisplayConfigurationSchema | LinearMultiSampleVariantDisplayConfigurationSchema | LinearMultiSampleVariantMatrixDisplayConfigurationSchema | LDTrackDisplayConfigurationSchema | LinearWiggleDisplayConfigurationSchema | MultiLinearWiggleDisplayConfigurationSchema | LinearGCContentDisplayConfigurationSchema | LinearGCContentTrackDisplayConfigurationSchema | LinearMafDisplayConfigurationSchema | LinearHicDisplayConfigurationSchema | LinearArcDisplayConfigurationSchema | LinearPairedArcDisplayConfigurationSchema | LinearManhattanDisplayConfigurationSchema)[]"
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+ "type": "(LinearBasicDisplayConfigurationSchema | LinearMultiRowFeatureDisplayConfigurationSchema | LinearAlignmentsDisplayConfigurationSchema | ChordVariantDisplayConfigurationSchema | ChordSyntenyDisplayConfigurationSchema | DotplotDisplayConfigurationSchema | LinearSyntenyDisplayConfigurationSchema | LGVSyntenyDisplayConfigurationSchema | MultiWaySyntenyDisplayConfigurationSchema | LinearReferenceSequenceDisplayConfigurationSchema | LinearVariantDisplayConfigurationSchema | LinearMultiSampleVariantDisplayConfigurationSchema | LinearMultiSampleVariantMatrixDisplayConfigurationSchema | LDTrackDisplayConfigurationSchema | LinearWiggleDisplayConfigurationSchema | MultiLinearWiggleDisplayConfigurationSchema | LinearGCContentDisplayConfigurationSchema | LinearGCContentTrackDisplayConfigurationSchema | LinearMafDisplayConfigurationSchema | LinearHicDisplayConfigurationSchema | LinearArcDisplayConfigurationSchema | LinearPairedArcDisplayConfigurationSchema | LinearManhattanDisplayConfigurationSchema | LinearMarkDisplayConfigurationSchema)[]"
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  },
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  {
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  "name": "formatDetails",
@@ -2371,7 +2376,7 @@ export const configManifest = {
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  },
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  {
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  "name": "displays",
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- "type": "(LinearBasicDisplayConfigurationSchema | LinearMultiRowFeatureDisplayConfigurationSchema | LinearAlignmentsDisplayConfigurationSchema | ChordVariantDisplayConfigurationSchema | DotplotDisplayConfigurationSchema | LinearSyntenyDisplayConfigurationSchema | LGVSyntenyDisplayConfigurationSchema | MultiWaySyntenyDisplayConfigurationSchema | LinearReferenceSequenceDisplayConfigurationSchema | LinearVariantDisplayConfigurationSchema | LinearMultiSampleVariantDisplayConfigurationSchema | LinearMultiSampleVariantMatrixDisplayConfigurationSchema | LDTrackDisplayConfigurationSchema | LinearWiggleDisplayConfigurationSchema | MultiLinearWiggleDisplayConfigurationSchema | LinearGCContentDisplayConfigurationSchema | LinearGCContentTrackDisplayConfigurationSchema | LinearMafDisplayConfigurationSchema | LinearHicDisplayConfigurationSchema | LinearArcDisplayConfigurationSchema | LinearPairedArcDisplayConfigurationSchema | LinearManhattanDisplayConfigurationSchema)[]"
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+ "type": "(LinearBasicDisplayConfigurationSchema | LinearMultiRowFeatureDisplayConfigurationSchema | LinearAlignmentsDisplayConfigurationSchema | ChordVariantDisplayConfigurationSchema | ChordSyntenyDisplayConfigurationSchema | DotplotDisplayConfigurationSchema | LinearSyntenyDisplayConfigurationSchema | LGVSyntenyDisplayConfigurationSchema | MultiWaySyntenyDisplayConfigurationSchema | LinearReferenceSequenceDisplayConfigurationSchema | LinearVariantDisplayConfigurationSchema | LinearMultiSampleVariantDisplayConfigurationSchema | LinearMultiSampleVariantMatrixDisplayConfigurationSchema | LDTrackDisplayConfigurationSchema | LinearWiggleDisplayConfigurationSchema | MultiLinearWiggleDisplayConfigurationSchema | LinearGCContentDisplayConfigurationSchema | LinearGCContentTrackDisplayConfigurationSchema | LinearMafDisplayConfigurationSchema | LinearHicDisplayConfigurationSchema | LinearArcDisplayConfigurationSchema | LinearPairedArcDisplayConfigurationSchema | LinearManhattanDisplayConfigurationSchema | LinearMarkDisplayConfigurationSchema)[]"
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  },
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  {
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  "name": "formatDetails",
@@ -2472,7 +2477,7 @@ export const configManifest = {
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  },
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  {
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  "name": "displays",
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- "type": "(LinearBasicDisplayConfigurationSchema | LinearMultiRowFeatureDisplayConfigurationSchema | LinearAlignmentsDisplayConfigurationSchema | ChordVariantDisplayConfigurationSchema | DotplotDisplayConfigurationSchema | LinearSyntenyDisplayConfigurationSchema | LGVSyntenyDisplayConfigurationSchema | MultiWaySyntenyDisplayConfigurationSchema | LinearReferenceSequenceDisplayConfigurationSchema | LinearVariantDisplayConfigurationSchema | LinearMultiSampleVariantDisplayConfigurationSchema | LinearMultiSampleVariantMatrixDisplayConfigurationSchema | LDTrackDisplayConfigurationSchema | LinearWiggleDisplayConfigurationSchema | MultiLinearWiggleDisplayConfigurationSchema | LinearGCContentDisplayConfigurationSchema | LinearGCContentTrackDisplayConfigurationSchema | LinearMafDisplayConfigurationSchema | LinearHicDisplayConfigurationSchema | LinearArcDisplayConfigurationSchema | LinearPairedArcDisplayConfigurationSchema | LinearManhattanDisplayConfigurationSchema)[]"
2480
+ "type": "(LinearBasicDisplayConfigurationSchema | LinearMultiRowFeatureDisplayConfigurationSchema | LinearAlignmentsDisplayConfigurationSchema | ChordVariantDisplayConfigurationSchema | ChordSyntenyDisplayConfigurationSchema | DotplotDisplayConfigurationSchema | LinearSyntenyDisplayConfigurationSchema | LGVSyntenyDisplayConfigurationSchema | MultiWaySyntenyDisplayConfigurationSchema | LinearReferenceSequenceDisplayConfigurationSchema | LinearVariantDisplayConfigurationSchema | LinearMultiSampleVariantDisplayConfigurationSchema | LinearMultiSampleVariantMatrixDisplayConfigurationSchema | LDTrackDisplayConfigurationSchema | LinearWiggleDisplayConfigurationSchema | MultiLinearWiggleDisplayConfigurationSchema | LinearGCContentDisplayConfigurationSchema | LinearGCContentTrackDisplayConfigurationSchema | LinearMafDisplayConfigurationSchema | LinearHicDisplayConfigurationSchema | LinearArcDisplayConfigurationSchema | LinearPairedArcDisplayConfigurationSchema | LinearManhattanDisplayConfigurationSchema | LinearMarkDisplayConfigurationSchema)[]"
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  },
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  {
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  "name": "formatDetails",
@@ -2573,7 +2578,7 @@ export const configManifest = {
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  },
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  {
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  "name": "displays",
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- "type": "(LinearBasicDisplayConfigurationSchema | LinearMultiRowFeatureDisplayConfigurationSchema | LinearAlignmentsDisplayConfigurationSchema | ChordVariantDisplayConfigurationSchema | DotplotDisplayConfigurationSchema | LinearSyntenyDisplayConfigurationSchema | LGVSyntenyDisplayConfigurationSchema | MultiWaySyntenyDisplayConfigurationSchema | LinearReferenceSequenceDisplayConfigurationSchema | LinearVariantDisplayConfigurationSchema | LinearMultiSampleVariantDisplayConfigurationSchema | LinearMultiSampleVariantMatrixDisplayConfigurationSchema | LDTrackDisplayConfigurationSchema | LinearWiggleDisplayConfigurationSchema | MultiLinearWiggleDisplayConfigurationSchema | LinearGCContentDisplayConfigurationSchema | LinearGCContentTrackDisplayConfigurationSchema | LinearMafDisplayConfigurationSchema | LinearHicDisplayConfigurationSchema | LinearArcDisplayConfigurationSchema | LinearPairedArcDisplayConfigurationSchema | LinearManhattanDisplayConfigurationSchema)[]"
2581
+ "type": "(LinearBasicDisplayConfigurationSchema | LinearMultiRowFeatureDisplayConfigurationSchema | LinearAlignmentsDisplayConfigurationSchema | ChordVariantDisplayConfigurationSchema | ChordSyntenyDisplayConfigurationSchema | DotplotDisplayConfigurationSchema | LinearSyntenyDisplayConfigurationSchema | LGVSyntenyDisplayConfigurationSchema | MultiWaySyntenyDisplayConfigurationSchema | LinearReferenceSequenceDisplayConfigurationSchema | LinearVariantDisplayConfigurationSchema | LinearMultiSampleVariantDisplayConfigurationSchema | LinearMultiSampleVariantMatrixDisplayConfigurationSchema | LDTrackDisplayConfigurationSchema | LinearWiggleDisplayConfigurationSchema | MultiLinearWiggleDisplayConfigurationSchema | LinearGCContentDisplayConfigurationSchema | LinearGCContentTrackDisplayConfigurationSchema | LinearMafDisplayConfigurationSchema | LinearHicDisplayConfigurationSchema | LinearArcDisplayConfigurationSchema | LinearPairedArcDisplayConfigurationSchema | LinearManhattanDisplayConfigurationSchema | LinearMarkDisplayConfigurationSchema)[]"
2577
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  },
2578
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  {
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  "name": "formatDetails",
@@ -2674,7 +2679,7 @@ export const configManifest = {
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  },
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  {
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  "name": "displays",
2677
- "type": "(LinearBasicDisplayConfigurationSchema | LinearMultiRowFeatureDisplayConfigurationSchema | LinearAlignmentsDisplayConfigurationSchema | ChordVariantDisplayConfigurationSchema | DotplotDisplayConfigurationSchema | LinearSyntenyDisplayConfigurationSchema | LGVSyntenyDisplayConfigurationSchema | MultiWaySyntenyDisplayConfigurationSchema | LinearReferenceSequenceDisplayConfigurationSchema | LinearVariantDisplayConfigurationSchema | LinearMultiSampleVariantDisplayConfigurationSchema | LinearMultiSampleVariantMatrixDisplayConfigurationSchema | LDTrackDisplayConfigurationSchema | LinearWiggleDisplayConfigurationSchema | MultiLinearWiggleDisplayConfigurationSchema | LinearGCContentDisplayConfigurationSchema | LinearGCContentTrackDisplayConfigurationSchema | LinearMafDisplayConfigurationSchema | LinearHicDisplayConfigurationSchema | LinearArcDisplayConfigurationSchema | LinearPairedArcDisplayConfigurationSchema | LinearManhattanDisplayConfigurationSchema)[]"
2682
+ "type": "(LinearBasicDisplayConfigurationSchema | LinearMultiRowFeatureDisplayConfigurationSchema | LinearAlignmentsDisplayConfigurationSchema | ChordVariantDisplayConfigurationSchema | ChordSyntenyDisplayConfigurationSchema | DotplotDisplayConfigurationSchema | LinearSyntenyDisplayConfigurationSchema | LGVSyntenyDisplayConfigurationSchema | MultiWaySyntenyDisplayConfigurationSchema | LinearReferenceSequenceDisplayConfigurationSchema | LinearVariantDisplayConfigurationSchema | LinearMultiSampleVariantDisplayConfigurationSchema | LinearMultiSampleVariantMatrixDisplayConfigurationSchema | LDTrackDisplayConfigurationSchema | LinearWiggleDisplayConfigurationSchema | MultiLinearWiggleDisplayConfigurationSchema | LinearGCContentDisplayConfigurationSchema | LinearGCContentTrackDisplayConfigurationSchema | LinearMafDisplayConfigurationSchema | LinearHicDisplayConfigurationSchema | LinearArcDisplayConfigurationSchema | LinearPairedArcDisplayConfigurationSchema | LinearManhattanDisplayConfigurationSchema | LinearMarkDisplayConfigurationSchema)[]"
2678
2683
  },
2679
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  {
2680
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  "name": "formatDetails",
@@ -2775,7 +2780,7 @@ export const configManifest = {
2775
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  },
2776
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  {
2777
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  "name": "displays",
2778
- "type": "(LinearBasicDisplayConfigurationSchema | LinearMultiRowFeatureDisplayConfigurationSchema | LinearAlignmentsDisplayConfigurationSchema | ChordVariantDisplayConfigurationSchema | DotplotDisplayConfigurationSchema | LinearSyntenyDisplayConfigurationSchema | LGVSyntenyDisplayConfigurationSchema | MultiWaySyntenyDisplayConfigurationSchema | LinearReferenceSequenceDisplayConfigurationSchema | LinearVariantDisplayConfigurationSchema | LinearMultiSampleVariantDisplayConfigurationSchema | LinearMultiSampleVariantMatrixDisplayConfigurationSchema | LDTrackDisplayConfigurationSchema | LinearWiggleDisplayConfigurationSchema | MultiLinearWiggleDisplayConfigurationSchema | LinearGCContentDisplayConfigurationSchema | LinearGCContentTrackDisplayConfigurationSchema | LinearMafDisplayConfigurationSchema | LinearHicDisplayConfigurationSchema | LinearArcDisplayConfigurationSchema | LinearPairedArcDisplayConfigurationSchema | LinearManhattanDisplayConfigurationSchema)[]"
2783
+ "type": "(LinearBasicDisplayConfigurationSchema | LinearMultiRowFeatureDisplayConfigurationSchema | LinearAlignmentsDisplayConfigurationSchema | ChordVariantDisplayConfigurationSchema | ChordSyntenyDisplayConfigurationSchema | DotplotDisplayConfigurationSchema | LinearSyntenyDisplayConfigurationSchema | LGVSyntenyDisplayConfigurationSchema | MultiWaySyntenyDisplayConfigurationSchema | LinearReferenceSequenceDisplayConfigurationSchema | LinearVariantDisplayConfigurationSchema | LinearMultiSampleVariantDisplayConfigurationSchema | LinearMultiSampleVariantMatrixDisplayConfigurationSchema | LDTrackDisplayConfigurationSchema | LinearWiggleDisplayConfigurationSchema | MultiLinearWiggleDisplayConfigurationSchema | LinearGCContentDisplayConfigurationSchema | LinearGCContentTrackDisplayConfigurationSchema | LinearMafDisplayConfigurationSchema | LinearHicDisplayConfigurationSchema | LinearArcDisplayConfigurationSchema | LinearPairedArcDisplayConfigurationSchema | LinearManhattanDisplayConfigurationSchema | LinearMarkDisplayConfigurationSchema)[]"
2779
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  },
2780
2785
  {
2781
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  "name": "formatDetails",
@@ -2852,7 +2857,7 @@ export const configManifest = {
2852
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  },
2853
2858
  {
2854
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  "name": "heightMode",
2855
- "type": "(JexlString | (heightMode | undefined))"
2860
+ "type": "(JexlString | heightMode)"
2856
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  },
2857
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  {
2858
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  "name": "growMaxHeight",
@@ -2872,11 +2877,11 @@ export const configManifest = {
2872
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  },
2873
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  {
2874
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  "name": "showLegend",
2875
- "type": "(JexlString | (boolean | undefined))"
2880
+ "type": "(JexlString | boolean)"
2876
2881
  },
2877
2882
  {
2878
2883
  "name": "showLabels",
2879
- "type": "(JexlString | (showLabels | undefined))"
2884
+ "type": "(JexlString | showLabels)"
2880
2885
  },
2881
2886
  {
2882
2887
  "name": "maxLabelFeatureDensity",
@@ -2908,7 +2913,7 @@ export const configManifest = {
2908
2913
  },
2909
2914
  {
2910
2915
  "name": "displayMode",
2911
- "type": "(JexlString | (displayMode | undefined))"
2916
+ "type": "(JexlString | displayMode)"
2912
2917
  },
2913
2918
  {
2914
2919
  "name": "geneGlyphMode",
@@ -2916,11 +2921,11 @@ export const configManifest = {
2916
2921
  },
2917
2922
  {
2918
2923
  "name": "subfeatureLabels",
2919
- "type": "(JexlString | (subfeatureLabels | undefined))"
2924
+ "type": "(JexlString | subfeatureLabels)"
2920
2925
  },
2921
2926
  {
2922
2927
  "name": "displayDirectionalChevrons",
2923
- "type": "(JexlString | (boolean | undefined))"
2928
+ "type": "(JexlString | boolean)"
2924
2929
  },
2925
2930
  {
2926
2931
  "name": "transcriptTypes",
@@ -2982,6 +2987,18 @@ export const configManifest = {
2982
2987
  "color3",
2983
2988
  "outline"
2984
2989
  ],
2990
+ "legacyValues": {
2991
+ "showLabels": [
2992
+ true,
2993
+ false,
2994
+ "on",
2995
+ "off"
2996
+ ],
2997
+ "displayMode": [
2998
+ "reducedRepresentation",
2999
+ "collapse"
3000
+ ]
3001
+ },
2985
3002
  "aliases": [
2986
3003
  "LinearFeatureDisplay"
2987
3004
  ],
@@ -3074,7 +3091,7 @@ export const configManifest = {
3074
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  },
3075
3092
  {
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  "name": "showLegend",
3077
- "type": "(JexlString | (boolean | undefined))"
3094
+ "type": "(JexlString | boolean)"
3078
3095
  },
3079
3096
  {
3080
3097
  "name": "legend",
@@ -3144,11 +3161,11 @@ export const configManifest = {
3144
3161
  },
3145
3162
  {
3146
3163
  "name": "featureHeight",
3147
- "type": "(JexlString | (number | undefined))"
3164
+ "type": "(JexlString | number)"
3148
3165
  },
3149
3166
  {
3150
3167
  "name": "heightMode",
3151
- "type": "(JexlString | (heightMode | undefined))"
3168
+ "type": "(JexlString | heightMode)"
3152
3169
  },
3153
3170
  {
3154
3171
  "name": "growMaxHeight",
@@ -3168,11 +3185,11 @@ export const configManifest = {
3168
3185
  },
3169
3186
  {
3170
3187
  "name": "showSashimiLabels",
3171
- "type": "(JexlString | (boolean | undefined))"
3188
+ "type": "(JexlString | boolean)"
3172
3189
  },
3173
3190
  {
3174
3191
  "name": "hideNonCanonicalJunctions",
3175
- "type": "(JexlString | (boolean | undefined))"
3192
+ "type": "(JexlString | boolean)"
3176
3193
  },
3177
3194
  {
3178
3195
  "name": "maxHeight",
@@ -3180,7 +3197,7 @@ export const configManifest = {
3180
3197
  },
3181
3198
  {
3182
3199
  "name": "colorBy",
3183
- "type": "(JexlString | (frozen | undefined))"
3200
+ "type": "(JexlString | frozen)"
3184
3201
  },
3185
3202
  {
3186
3203
  "name": "filterBy",
@@ -3220,7 +3237,7 @@ export const configManifest = {
3220
3237
  },
3221
3238
  {
3222
3239
  "name": "mismatchAlpha",
3223
- "type": "(JexlString | (boolean | undefined))"
3240
+ "type": "(JexlString | boolean)"
3224
3241
  },
3225
3242
  {
3226
3243
  "name": "showLowFreqMismatches",
@@ -3228,7 +3245,7 @@ export const configManifest = {
3228
3245
  },
3229
3246
  {
3230
3247
  "name": "showLegend",
3231
- "type": "(JexlString | (boolean | undefined))"
3248
+ "type": "(JexlString | boolean)"
3232
3249
  },
3233
3250
  {
3234
3251
  "name": "sortedBy",
@@ -3248,7 +3265,7 @@ export const configManifest = {
3248
3265
  },
3249
3266
  {
3250
3267
  "name": "linkedReads",
3251
- "type": "(JexlString | (LinkedReadsMode | undefined))"
3268
+ "type": "(JexlString | LinkedReadsMode)"
3252
3269
  },
3253
3270
  {
3254
3271
  "name": "showBezierConnections",
@@ -3308,19 +3325,19 @@ export const configManifest = {
3308
3325
  },
3309
3326
  {
3310
3327
  "name": "readConnections",
3311
- "type": "(JexlString | (ReadConnectionsMode | undefined))"
3328
+ "type": "(JexlString | ReadConnectionsMode)"
3312
3329
  },
3313
3330
  {
3314
3331
  "name": "readConnectionsDown",
3315
- "type": "(JexlString | (boolean | undefined))"
3332
+ "type": "(JexlString | boolean)"
3316
3333
  },
3317
3334
  {
3318
3335
  "name": "showSashimiArcs",
3319
- "type": "(JexlString | (boolean | undefined))"
3336
+ "type": "(JexlString | boolean)"
3320
3337
  },
3321
3338
  {
3322
3339
  "name": "sashimiArcsMode",
3323
- "type": "(JexlString | (SashimiArcsMode | undefined))"
3340
+ "type": "(JexlString | SashimiArcsMode)"
3324
3341
  },
3325
3342
  {
3326
3343
  "name": "minSashimiScore",
@@ -3336,7 +3353,7 @@ export const configManifest = {
3336
3353
  },
3337
3354
  {
3338
3355
  "name": "showSoftClipping",
3339
- "type": "(JexlString | (boolean | undefined))"
3356
+ "type": "(JexlString | boolean)"
3340
3357
  }
3341
3358
  ],
3342
3359
  "aliases": [
@@ -3388,6 +3405,36 @@ export const configManifest = {
3388
3405
  "configuration"
3389
3406
  ]
3390
3407
  },
3408
+ "ChordSyntenyDisplay": {
3409
+ "slots": [
3410
+ {
3411
+ "name": "type",
3412
+ "type": "\"ChordSyntenyDisplay\""
3413
+ },
3414
+ {
3415
+ "name": "displayId",
3416
+ "type": "identifier"
3417
+ },
3418
+ {
3419
+ "name": "color",
3420
+ "type": "(JexlString | string)"
3421
+ },
3422
+ {
3423
+ "name": "colorSelected",
3424
+ "type": "(JexlString | string)"
3425
+ },
3426
+ {
3427
+ "name": "colorHover",
3428
+ "type": "(JexlString | string)"
3429
+ }
3430
+ ],
3431
+ "stateModelProps": [
3432
+ "id",
3433
+ "type",
3434
+ "bezierRadiusRatio",
3435
+ "configuration"
3436
+ ]
3437
+ },
3391
3438
  "DotplotDisplay": {
3392
3439
  "slots": [
3393
3440
  {
@@ -3417,11 +3464,11 @@ export const configManifest = {
3417
3464
  },
3418
3465
  {
3419
3466
  "name": "drawCurves",
3420
- "type": "(JexlString | (boolean | undefined))"
3467
+ "type": "(JexlString | boolean)"
3421
3468
  },
3422
3469
  {
3423
3470
  "name": "drawLocationMarkers",
3424
- "type": "(JexlString | (boolean | undefined))"
3471
+ "type": "(JexlString | boolean)"
3425
3472
  }
3426
3473
  ],
3427
3474
  "stateModelProps": [
@@ -3462,11 +3509,11 @@ export const configManifest = {
3462
3509
  },
3463
3510
  {
3464
3511
  "name": "featureHeight",
3465
- "type": "(JexlString | (number | undefined))"
3512
+ "type": "(JexlString | number)"
3466
3513
  },
3467
3514
  {
3468
3515
  "name": "heightMode",
3469
- "type": "(JexlString | (heightMode | undefined))"
3516
+ "type": "(JexlString | heightMode)"
3470
3517
  },
3471
3518
  {
3472
3519
  "name": "growMaxHeight",
@@ -3486,11 +3533,11 @@ export const configManifest = {
3486
3533
  },
3487
3534
  {
3488
3535
  "name": "showSashimiLabels",
3489
- "type": "(JexlString | (boolean | undefined))"
3536
+ "type": "(JexlString | boolean)"
3490
3537
  },
3491
3538
  {
3492
3539
  "name": "hideNonCanonicalJunctions",
3493
- "type": "(JexlString | (boolean | undefined))"
3540
+ "type": "(JexlString | boolean)"
3494
3541
  },
3495
3542
  {
3496
3543
  "name": "maxHeight",
@@ -3498,7 +3545,7 @@ export const configManifest = {
3498
3545
  },
3499
3546
  {
3500
3547
  "name": "colorBy",
3501
- "type": "(JexlString | (frozen | undefined))"
3548
+ "type": "(JexlString | frozen)"
3502
3549
  },
3503
3550
  {
3504
3551
  "name": "filterBy",
@@ -3538,7 +3585,7 @@ export const configManifest = {
3538
3585
  },
3539
3586
  {
3540
3587
  "name": "mismatchAlpha",
3541
- "type": "(JexlString | (boolean | undefined))"
3588
+ "type": "(JexlString | boolean)"
3542
3589
  },
3543
3590
  {
3544
3591
  "name": "showLowFreqMismatches",
@@ -3546,7 +3593,7 @@ export const configManifest = {
3546
3593
  },
3547
3594
  {
3548
3595
  "name": "showLegend",
3549
- "type": "(JexlString | (boolean | undefined))"
3596
+ "type": "(JexlString | boolean)"
3550
3597
  },
3551
3598
  {
3552
3599
  "name": "sortedBy",
@@ -3566,7 +3613,7 @@ export const configManifest = {
3566
3613
  },
3567
3614
  {
3568
3615
  "name": "linkedReads",
3569
- "type": "(JexlString | (LinkedReadsMode | undefined))"
3616
+ "type": "(JexlString | LinkedReadsMode)"
3570
3617
  },
3571
3618
  {
3572
3619
  "name": "showBezierConnections",
@@ -3626,19 +3673,19 @@ export const configManifest = {
3626
3673
  },
3627
3674
  {
3628
3675
  "name": "readConnections",
3629
- "type": "(JexlString | (ReadConnectionsMode | undefined))"
3676
+ "type": "(JexlString | ReadConnectionsMode)"
3630
3677
  },
3631
3678
  {
3632
3679
  "name": "readConnectionsDown",
3633
- "type": "(JexlString | (boolean | undefined))"
3680
+ "type": "(JexlString | boolean)"
3634
3681
  },
3635
3682
  {
3636
3683
  "name": "showSashimiArcs",
3637
- "type": "(JexlString | (boolean | undefined))"
3684
+ "type": "(JexlString | boolean)"
3638
3685
  },
3639
3686
  {
3640
3687
  "name": "sashimiArcsMode",
3641
- "type": "(JexlString | (SashimiArcsMode | undefined))"
3688
+ "type": "(JexlString | SashimiArcsMode)"
3642
3689
  },
3643
3690
  {
3644
3691
  "name": "minSashimiScore",
@@ -3654,7 +3701,7 @@ export const configManifest = {
3654
3701
  },
3655
3702
  {
3656
3703
  "name": "showSoftClipping",
3657
- "type": "(JexlString | (boolean | undefined))"
3704
+ "type": "(JexlString | boolean)"
3658
3705
  },
3659
3706
  {
3660
3707
  "name": "hideSelfAlignments",
@@ -3724,7 +3771,7 @@ export const configManifest = {
3724
3771
  },
3725
3772
  {
3726
3773
  "name": "showLegend",
3727
- "type": "(JexlString | (boolean | undefined))"
3774
+ "type": "(JexlString | boolean)"
3728
3775
  },
3729
3776
  {
3730
3777
  "name": "showLaneTicks",
@@ -3818,7 +3865,7 @@ export const configManifest = {
3818
3865
  },
3819
3866
  {
3820
3867
  "name": "heightMode",
3821
- "type": "(JexlString | (heightMode | undefined))"
3868
+ "type": "(JexlString | heightMode)"
3822
3869
  },
3823
3870
  {
3824
3871
  "name": "growMaxHeight",
@@ -3838,11 +3885,11 @@ export const configManifest = {
3838
3885
  },
3839
3886
  {
3840
3887
  "name": "showLegend",
3841
- "type": "(JexlString | (boolean | undefined))"
3888
+ "type": "(JexlString | boolean)"
3842
3889
  },
3843
3890
  {
3844
3891
  "name": "showLabels",
3845
- "type": "(JexlString | (showLabels | undefined))"
3892
+ "type": "(JexlString | showLabels)"
3846
3893
  },
3847
3894
  {
3848
3895
  "name": "maxLabelFeatureDensity",
@@ -3874,7 +3921,7 @@ export const configManifest = {
3874
3921
  },
3875
3922
  {
3876
3923
  "name": "displayMode",
3877
- "type": "(JexlString | (displayMode | undefined))"
3924
+ "type": "(JexlString | displayMode)"
3878
3925
  },
3879
3926
  {
3880
3927
  "name": "geneGlyphMode",
@@ -3882,11 +3929,11 @@ export const configManifest = {
3882
3929
  },
3883
3930
  {
3884
3931
  "name": "subfeatureLabels",
3885
- "type": "(JexlString | (subfeatureLabels | undefined))"
3932
+ "type": "(JexlString | subfeatureLabels)"
3886
3933
  },
3887
3934
  {
3888
3935
  "name": "displayDirectionalChevrons",
3889
- "type": "(JexlString | (boolean | undefined))"
3936
+ "type": "(JexlString | boolean)"
3890
3937
  },
3891
3938
  {
3892
3939
  "name": "transcriptTypes",
@@ -3940,6 +3987,18 @@ export const configManifest = {
3940
3987
  "color3",
3941
3988
  "outline"
3942
3989
  ],
3990
+ "legacyValues": {
3991
+ "showLabels": [
3992
+ true,
3993
+ false,
3994
+ "on",
3995
+ "off"
3996
+ ],
3997
+ "displayMode": [
3998
+ "reducedRepresentation",
3999
+ "collapse"
4000
+ ]
4001
+ },
3943
4002
  "stateModelProps": [
3944
4003
  "id",
3945
4004
  "type",
@@ -4029,7 +4088,7 @@ export const configManifest = {
4029
4088
  },
4030
4089
  {
4031
4090
  "name": "showLegend",
4032
- "type": "(JexlString | (boolean | undefined))"
4091
+ "type": "(JexlString | boolean)"
4033
4092
  },
4034
4093
  {
4035
4094
  "name": "colorBy",
@@ -4154,7 +4213,7 @@ export const configManifest = {
4154
4213
  },
4155
4214
  {
4156
4215
  "name": "showLegend",
4157
- "type": "(JexlString | (boolean | undefined))"
4216
+ "type": "(JexlString | boolean)"
4158
4217
  },
4159
4218
  {
4160
4219
  "name": "colorBy",
@@ -4227,7 +4286,7 @@ export const configManifest = {
4227
4286
  },
4228
4287
  {
4229
4288
  "name": "showLegend",
4230
- "type": "(JexlString | (boolean | undefined))"
4289
+ "type": "(JexlString | boolean)"
4231
4290
  },
4232
4291
  {
4233
4292
  "name": "showLDTriangle",
@@ -4314,6 +4373,10 @@ export const configManifest = {
4314
4373
  "name": "displayCrossHatches",
4315
4374
  "type": "(JexlString | boolean)"
4316
4375
  },
4376
+ {
4377
+ "name": "scoreField",
4378
+ "type": "(JexlString | string)"
4379
+ },
4317
4380
  {
4318
4381
  "name": "symlogConstant",
4319
4382
  "type": "(JexlString | number)"
@@ -4340,16 +4403,20 @@ export const configManifest = {
4340
4403
  },
4341
4404
  {
4342
4405
  "name": "scatterPointSize",
4343
- "type": "(JexlString | (number | undefined))"
4406
+ "type": "(JexlString | number)"
4344
4407
  },
4345
4408
  {
4346
4409
  "name": "lineWidth",
4347
- "type": "(JexlString | (number | undefined))"
4410
+ "type": "(JexlString | number)"
4348
4411
  },
4349
4412
  {
4350
4413
  "name": "maxGapMultiple",
4351
4414
  "type": "(JexlString | number)"
4352
4415
  },
4416
+ {
4417
+ "name": "showLegend",
4418
+ "type": "(JexlString | boolean)"
4419
+ },
4353
4420
  {
4354
4421
  "name": "scoreRules",
4355
4422
  "type": "(JexlString | frozen)"
@@ -4404,6 +4471,10 @@ export const configManifest = {
4404
4471
  "name": "displayCrossHatches",
4405
4472
  "type": "(JexlString | boolean)"
4406
4473
  },
4474
+ {
4475
+ "name": "scoreField",
4476
+ "type": "(JexlString | string)"
4477
+ },
4407
4478
  {
4408
4479
  "name": "symlogConstant",
4409
4480
  "type": "(JexlString | number)"
@@ -4430,11 +4501,11 @@ export const configManifest = {
4430
4501
  },
4431
4502
  {
4432
4503
  "name": "scatterPointSize",
4433
- "type": "(JexlString | (number | undefined))"
4504
+ "type": "(JexlString | number)"
4434
4505
  },
4435
4506
  {
4436
4507
  "name": "lineWidth",
4437
- "type": "(JexlString | (number | undefined))"
4508
+ "type": "(JexlString | number)"
4438
4509
  },
4439
4510
  {
4440
4511
  "name": "maxGapMultiple",
@@ -4474,7 +4545,7 @@ export const configManifest = {
4474
4545
  },
4475
4546
  {
4476
4547
  "name": "showLegend",
4477
- "type": "(JexlString | (boolean | undefined))"
4548
+ "type": "(JexlString | boolean)"
4478
4549
  }
4479
4550
  ],
4480
4551
  "stateModelProps": [
@@ -4542,6 +4613,10 @@ export const configManifest = {
4542
4613
  "name": "displayCrossHatches",
4543
4614
  "type": "(JexlString | boolean)"
4544
4615
  },
4616
+ {
4617
+ "name": "scoreField",
4618
+ "type": "(JexlString | string)"
4619
+ },
4545
4620
  {
4546
4621
  "name": "symlogConstant",
4547
4622
  "type": "(JexlString | number)"
@@ -4568,16 +4643,20 @@ export const configManifest = {
4568
4643
  },
4569
4644
  {
4570
4645
  "name": "scatterPointSize",
4571
- "type": "(JexlString | (number | undefined))"
4646
+ "type": "(JexlString | number)"
4572
4647
  },
4573
4648
  {
4574
4649
  "name": "lineWidth",
4575
- "type": "(JexlString | (number | undefined))"
4650
+ "type": "(JexlString | number)"
4576
4651
  },
4577
4652
  {
4578
4653
  "name": "maxGapMultiple",
4579
4654
  "type": "(JexlString | number)"
4580
4655
  },
4656
+ {
4657
+ "name": "showLegend",
4658
+ "type": "(JexlString | boolean)"
4659
+ },
4581
4660
  {
4582
4661
  "name": "scoreRules",
4583
4662
  "type": "(JexlString | frozen)"
@@ -4660,6 +4739,10 @@ export const configManifest = {
4660
4739
  "name": "displayCrossHatches",
4661
4740
  "type": "(JexlString | boolean)"
4662
4741
  },
4742
+ {
4743
+ "name": "scoreField",
4744
+ "type": "(JexlString | string)"
4745
+ },
4663
4746
  {
4664
4747
  "name": "symlogConstant",
4665
4748
  "type": "(JexlString | number)"
@@ -4686,16 +4769,20 @@ export const configManifest = {
4686
4769
  },
4687
4770
  {
4688
4771
  "name": "scatterPointSize",
4689
- "type": "(JexlString | (number | undefined))"
4772
+ "type": "(JexlString | number)"
4690
4773
  },
4691
4774
  {
4692
4775
  "name": "lineWidth",
4693
- "type": "(JexlString | (number | undefined))"
4776
+ "type": "(JexlString | number)"
4694
4777
  },
4695
4778
  {
4696
4779
  "name": "maxGapMultiple",
4697
4780
  "type": "(JexlString | number)"
4698
4781
  },
4782
+ {
4783
+ "name": "showLegend",
4784
+ "type": "(JexlString | boolean)"
4785
+ },
4699
4786
  {
4700
4787
  "name": "scoreRules",
4701
4788
  "type": "(JexlString | frozen)"
@@ -4792,7 +4879,7 @@ export const configManifest = {
4792
4879
  },
4793
4880
  {
4794
4881
  "name": "showLegend",
4795
- "type": "(JexlString | (boolean | undefined))"
4882
+ "type": "(JexlString | boolean)"
4796
4883
  },
4797
4884
  {
4798
4885
  "name": "showCoverage",
@@ -4881,7 +4968,7 @@ export const configManifest = {
4881
4968
  },
4882
4969
  {
4883
4970
  "name": "showLegend",
4884
- "type": "(JexlString | (boolean | undefined))"
4971
+ "type": "(JexlString | boolean)"
4885
4972
  },
4886
4973
  {
4887
4974
  "name": "resolutionBias",
@@ -4994,7 +5081,7 @@ export const configManifest = {
4994
5081
  },
4995
5082
  {
4996
5083
  "name": "lineWidth",
4997
- "type": "(JexlString | (number | undefined))"
5084
+ "type": "(JexlString | number)"
4998
5085
  },
4999
5086
  {
5000
5087
  "name": "minScore",
@@ -5037,6 +5124,14 @@ export const configManifest = {
5037
5124
  "name": "colorBy",
5038
5125
  "type": "(JexlString | GwasColorBy)"
5039
5126
  },
5127
+ {
5128
+ "name": "colorField",
5129
+ "type": "(JexlString | string)"
5130
+ },
5131
+ {
5132
+ "name": "scoreField",
5133
+ "type": "(JexlString | string)"
5134
+ },
5040
5135
  {
5041
5136
  "name": "minScore",
5042
5137
  "type": "(JexlString | number)"
@@ -5071,11 +5166,11 @@ export const configManifest = {
5071
5166
  },
5072
5167
  {
5073
5168
  "name": "scatterPointSize",
5074
- "type": "(JexlString | (number | undefined))"
5169
+ "type": "(JexlString | number)"
5075
5170
  },
5076
5171
  {
5077
- "name": "showLdLegend",
5078
- "type": "(JexlString | (boolean | undefined))"
5172
+ "name": "showLegend",
5173
+ "type": "(JexlString | boolean)"
5079
5174
  }
5080
5175
  ],
5081
5176
  "stateModelProps": [
@@ -5085,6 +5180,266 @@ export const configManifest = {
5085
5180
  "indexSnp",
5086
5181
  "indexSnpPinned"
5087
5182
  ]
5183
+ },
5184
+ "LinearMarkDisplay": {
5185
+ "slots": [
5186
+ {
5187
+ "name": "type",
5188
+ "type": "\"LinearMarkDisplay\""
5189
+ },
5190
+ {
5191
+ "name": "displayId",
5192
+ "type": "identifier"
5193
+ },
5194
+ {
5195
+ "name": "height",
5196
+ "type": "(JexlString | number)"
5197
+ },
5198
+ {
5199
+ "name": "fetchSizeLimit",
5200
+ "type": "(JexlString | number)"
5201
+ },
5202
+ {
5203
+ "name": "forceLoad",
5204
+ "type": "(JexlString | boolean)"
5205
+ },
5206
+ {
5207
+ "name": "densityTier",
5208
+ "type": "(JexlString | Density tier)"
5209
+ },
5210
+ {
5211
+ "name": "densityTierBpPerPx",
5212
+ "type": "(JexlString | number)"
5213
+ },
5214
+ {
5215
+ "name": "marks",
5216
+ "type": "MarkConfigurationSchema[]",
5217
+ "subSlots": [
5218
+ {
5219
+ "name": "shape",
5220
+ "type": "(JexlString | MarkShape)"
5221
+ },
5222
+ {
5223
+ "name": "encoding",
5224
+ "type": "MarkEncodingConfigurationSchema",
5225
+ "subSlots": [
5226
+ {
5227
+ "name": "x",
5228
+ "type": "(JexlString | string)"
5229
+ },
5230
+ {
5231
+ "name": "x2",
5232
+ "type": "(JexlString | string)"
5233
+ },
5234
+ {
5235
+ "name": "y",
5236
+ "type": "MarkValueConfigurationSchema",
5237
+ "subSlots": [
5238
+ {
5239
+ "name": "field",
5240
+ "type": "(JexlString | string)"
5241
+ },
5242
+ {
5243
+ "name": "scale",
5244
+ "type": "(JexlString | MarkValueScale)"
5245
+ },
5246
+ {
5247
+ "name": "domain",
5248
+ "type": "(JexlString | string[])"
5249
+ },
5250
+ {
5251
+ "name": "resolve",
5252
+ "type": "(JexlString | MarkValueResolve)"
5253
+ }
5254
+ ]
5255
+ },
5256
+ {
5257
+ "name": "row",
5258
+ "type": "(JexlString | string)"
5259
+ },
5260
+ {
5261
+ "name": "color",
5262
+ "type": "MarkColorConfigurationSchema",
5263
+ "subSlots": [
5264
+ {
5265
+ "name": "value",
5266
+ "type": "(JexlString | string)"
5267
+ },
5268
+ {
5269
+ "name": "field",
5270
+ "type": "(JexlString | string)"
5271
+ },
5272
+ {
5273
+ "name": "scale",
5274
+ "type": "(JexlString | MarkColorScale)"
5275
+ },
5276
+ {
5277
+ "name": "palette",
5278
+ "type": "(JexlString | string[])"
5279
+ },
5280
+ {
5281
+ "name": "domain",
5282
+ "type": "(JexlString | string[])"
5283
+ },
5284
+ {
5285
+ "name": "ramp",
5286
+ "type": "(JexlString | string[])"
5287
+ }
5288
+ ]
5289
+ },
5290
+ {
5291
+ "name": "glyph",
5292
+ "type": "MarkGlyphConfigurationSchema",
5293
+ "subSlots": [
5294
+ {
5295
+ "name": "value",
5296
+ "type": "(JexlString | string)"
5297
+ },
5298
+ {
5299
+ "name": "field",
5300
+ "type": "(JexlString | string)"
5301
+ },
5302
+ {
5303
+ "name": "scale",
5304
+ "type": "(JexlString | MarkGlyphScale)"
5305
+ },
5306
+ {
5307
+ "name": "range",
5308
+ "type": "(JexlString | string[])"
5309
+ },
5310
+ {
5311
+ "name": "domain",
5312
+ "type": "(JexlString | string[])"
5313
+ }
5314
+ ]
5315
+ }
5316
+ ]
5317
+ },
5318
+ {
5319
+ "name": "transform",
5320
+ "type": "MarkTransformStepConfigurationSchema[]",
5321
+ "subSlots": [
5322
+ {
5323
+ "name": "type",
5324
+ "type": "(JexlString | MarkTransformType)"
5325
+ },
5326
+ {
5327
+ "name": "expr",
5328
+ "type": "(JexlString | string)"
5329
+ },
5330
+ {
5331
+ "name": "field",
5332
+ "type": "(JexlString | string)"
5333
+ },
5334
+ {
5335
+ "name": "step",
5336
+ "type": "(JexlString | (number | \"auto\"))"
5337
+ },
5338
+ {
5339
+ "name": "as",
5340
+ "type": "(JexlString | string[])"
5341
+ },
5342
+ {
5343
+ "name": "fields",
5344
+ "type": "(JexlString | string[])"
5345
+ },
5346
+ {
5347
+ "name": "padding",
5348
+ "type": "(JexlString | number)"
5349
+ },
5350
+ {
5351
+ "name": "groupby",
5352
+ "type": "(JexlString | string[])"
5353
+ },
5354
+ {
5355
+ "name": "ops",
5356
+ "type": "MarkAggregateOpConfigurationSchema[]",
5357
+ "subSlots": [
5358
+ {
5359
+ "name": "op",
5360
+ "type": "(JexlString | MarkAggregateOpName)"
5361
+ },
5362
+ {
5363
+ "name": "field",
5364
+ "type": "(JexlString | string)"
5365
+ },
5366
+ {
5367
+ "name": "as",
5368
+ "type": "(JexlString | string)"
5369
+ }
5370
+ ]
5371
+ }
5372
+ ]
5373
+ },
5374
+ {
5375
+ "name": "source",
5376
+ "type": "(JexlString | MarkSource)"
5377
+ },
5378
+ {
5379
+ "name": "minBpPerPx",
5380
+ "type": "(JexlString | number)"
5381
+ },
5382
+ {
5383
+ "name": "maxBpPerPx",
5384
+ "type": "(JexlString | number)"
5385
+ }
5386
+ ]
5387
+ },
5388
+ {
5389
+ "name": "minScore",
5390
+ "type": "(JexlString | number)"
5391
+ },
5392
+ {
5393
+ "name": "maxScore",
5394
+ "type": "(JexlString | number)"
5395
+ },
5396
+ {
5397
+ "name": "scaleType",
5398
+ "type": "(JexlString | Scale type)"
5399
+ },
5400
+ {
5401
+ "name": "autoscale",
5402
+ "type": "(JexlString | Autoscale type)"
5403
+ },
5404
+ {
5405
+ "name": "numStdDev",
5406
+ "type": "(JexlString | number)"
5407
+ },
5408
+ {
5409
+ "name": "displayCrossHatches",
5410
+ "type": "(JexlString | boolean)"
5411
+ },
5412
+ {
5413
+ "name": "origin",
5414
+ "type": "(JexlString | number)"
5415
+ },
5416
+ {
5417
+ "name": "minWidthPx",
5418
+ "type": "(JexlString | number)"
5419
+ },
5420
+ {
5421
+ "name": "scatterPointSize",
5422
+ "type": "(JexlString | number)"
5423
+ },
5424
+ {
5425
+ "name": "minimalTicks",
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+ "type": "(JexlString | boolean)"
5427
+ },
5428
+ {
5429
+ "name": "showLegend",
5430
+ "type": "(JexlString | boolean)"
5431
+ },
5432
+ {
5433
+ "name": "jexlFilters",
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+ "type": "(JexlString | string[])"
5435
+ }
5436
+ ],
5437
+ "stateModelProps": [
5438
+ "id",
5439
+ "type",
5440
+ "configuration",
5441
+ "jexlFiltersSetting"
5442
+ ]
5088
5443
  }
5089
5444
  },
5090
5445
  "textSearchAdapters": {
@@ -5216,6 +5571,260 @@ export const configManifest = {
5216
5571
  ]
5217
5572
  }
5218
5573
  },
5574
+ "internetAccounts": {
5575
+ "OAuthInternetAccount": {
5576
+ "slots": [
5577
+ {
5578
+ "name": "type",
5579
+ "type": "\"OAuthInternetAccount\""
5580
+ },
5581
+ {
5582
+ "name": "internetAccountId",
5583
+ "type": "identifier"
5584
+ },
5585
+ {
5586
+ "name": "name",
5587
+ "type": "(JexlString | string)"
5588
+ },
5589
+ {
5590
+ "name": "description",
5591
+ "type": "(JexlString | string)"
5592
+ },
5593
+ {
5594
+ "name": "authHeader",
5595
+ "type": "(JexlString | string)"
5596
+ },
5597
+ {
5598
+ "name": "tokenType",
5599
+ "type": "(JexlString | string)"
5600
+ },
5601
+ {
5602
+ "name": "domains",
5603
+ "type": "(JexlString | string[])"
5604
+ },
5605
+ {
5606
+ "name": "authEndpoint",
5607
+ "type": "(JexlString | string)"
5608
+ },
5609
+ {
5610
+ "name": "tokenEndpoint",
5611
+ "type": "(JexlString | string)"
5612
+ },
5613
+ {
5614
+ "name": "needsPKCE",
5615
+ "type": "(JexlString | boolean)"
5616
+ },
5617
+ {
5618
+ "name": "clientId",
5619
+ "type": "(JexlString | string)"
5620
+ },
5621
+ {
5622
+ "name": "scopes",
5623
+ "type": "(JexlString | string)"
5624
+ },
5625
+ {
5626
+ "name": "state",
5627
+ "type": "(JexlString | string)"
5628
+ },
5629
+ {
5630
+ "name": "responseType",
5631
+ "type": "(JexlString | string)"
5632
+ }
5633
+ ]
5634
+ },
5635
+ "ExternalTokenInternetAccount": {
5636
+ "slots": [
5637
+ {
5638
+ "name": "type",
5639
+ "type": "\"ExternalTokenInternetAccount\""
5640
+ },
5641
+ {
5642
+ "name": "internetAccountId",
5643
+ "type": "identifier"
5644
+ },
5645
+ {
5646
+ "name": "name",
5647
+ "type": "(JexlString | string)"
5648
+ },
5649
+ {
5650
+ "name": "description",
5651
+ "type": "(JexlString | string)"
5652
+ },
5653
+ {
5654
+ "name": "authHeader",
5655
+ "type": "(JexlString | string)"
5656
+ },
5657
+ {
5658
+ "name": "tokenType",
5659
+ "type": "(JexlString | string)"
5660
+ },
5661
+ {
5662
+ "name": "domains",
5663
+ "type": "(JexlString | string[])"
5664
+ },
5665
+ {
5666
+ "name": "validateWithHEAD",
5667
+ "type": "(JexlString | boolean)"
5668
+ }
5669
+ ]
5670
+ },
5671
+ "HTTPBasicInternetAccount": {
5672
+ "slots": [
5673
+ {
5674
+ "name": "type",
5675
+ "type": "\"HTTPBasicInternetAccount\""
5676
+ },
5677
+ {
5678
+ "name": "internetAccountId",
5679
+ "type": "identifier"
5680
+ },
5681
+ {
5682
+ "name": "name",
5683
+ "type": "(JexlString | string)"
5684
+ },
5685
+ {
5686
+ "name": "description",
5687
+ "type": "(JexlString | string)"
5688
+ },
5689
+ {
5690
+ "name": "authHeader",
5691
+ "type": "(JexlString | string)"
5692
+ },
5693
+ {
5694
+ "name": "tokenType",
5695
+ "type": "(JexlString | string)"
5696
+ },
5697
+ {
5698
+ "name": "domains",
5699
+ "type": "(JexlString | string[])"
5700
+ },
5701
+ {
5702
+ "name": "validateWithHEAD",
5703
+ "type": "(JexlString | boolean)"
5704
+ }
5705
+ ]
5706
+ },
5707
+ "DropboxOAuthInternetAccount": {
5708
+ "slots": [
5709
+ {
5710
+ "name": "type",
5711
+ "type": "\"DropboxOAuthInternetAccount\""
5712
+ },
5713
+ {
5714
+ "name": "internetAccountId",
5715
+ "type": "identifier"
5716
+ },
5717
+ {
5718
+ "name": "name",
5719
+ "type": "(JexlString | string)"
5720
+ },
5721
+ {
5722
+ "name": "description",
5723
+ "type": "(JexlString | string)"
5724
+ },
5725
+ {
5726
+ "name": "authHeader",
5727
+ "type": "(JexlString | string)"
5728
+ },
5729
+ {
5730
+ "name": "tokenType",
5731
+ "type": "(JexlString | string)"
5732
+ },
5733
+ {
5734
+ "name": "domains",
5735
+ "type": "(JexlString | string[])"
5736
+ },
5737
+ {
5738
+ "name": "authEndpoint",
5739
+ "type": "(JexlString | string)"
5740
+ },
5741
+ {
5742
+ "name": "tokenEndpoint",
5743
+ "type": "(JexlString | string)"
5744
+ },
5745
+ {
5746
+ "name": "needsPKCE",
5747
+ "type": "(JexlString | boolean)"
5748
+ },
5749
+ {
5750
+ "name": "clientId",
5751
+ "type": "(JexlString | string)"
5752
+ },
5753
+ {
5754
+ "name": "scopes",
5755
+ "type": "(JexlString | string)"
5756
+ },
5757
+ {
5758
+ "name": "state",
5759
+ "type": "(JexlString | string)"
5760
+ },
5761
+ {
5762
+ "name": "responseType",
5763
+ "type": "(JexlString | string)"
5764
+ }
5765
+ ]
5766
+ },
5767
+ "GoogleDriveOAuthInternetAccount": {
5768
+ "slots": [
5769
+ {
5770
+ "name": "type",
5771
+ "type": "\"GoogleDriveOAuthInternetAccount\""
5772
+ },
5773
+ {
5774
+ "name": "internetAccountId",
5775
+ "type": "identifier"
5776
+ },
5777
+ {
5778
+ "name": "name",
5779
+ "type": "(JexlString | string)"
5780
+ },
5781
+ {
5782
+ "name": "description",
5783
+ "type": "(JexlString | string)"
5784
+ },
5785
+ {
5786
+ "name": "authHeader",
5787
+ "type": "(JexlString | string)"
5788
+ },
5789
+ {
5790
+ "name": "tokenType",
5791
+ "type": "(JexlString | string)"
5792
+ },
5793
+ {
5794
+ "name": "domains",
5795
+ "type": "(JexlString | string[])"
5796
+ },
5797
+ {
5798
+ "name": "authEndpoint",
5799
+ "type": "(JexlString | string)"
5800
+ },
5801
+ {
5802
+ "name": "tokenEndpoint",
5803
+ "type": "(JexlString | string)"
5804
+ },
5805
+ {
5806
+ "name": "needsPKCE",
5807
+ "type": "(JexlString | boolean)"
5808
+ },
5809
+ {
5810
+ "name": "clientId",
5811
+ "type": "(JexlString | string)"
5812
+ },
5813
+ {
5814
+ "name": "scopes",
5815
+ "type": "(JexlString | string)"
5816
+ },
5817
+ {
5818
+ "name": "state",
5819
+ "type": "(JexlString | string)"
5820
+ },
5821
+ {
5822
+ "name": "responseType",
5823
+ "type": "(JexlString | string)"
5824
+ }
5825
+ ]
5826
+ }
5827
+ },
5219
5828
  "views": {
5220
5829
  "LinearGenomeView": {
5221
5830
  "stateModelProps": [
@@ -5284,6 +5893,7 @@ export const configManifest = {
5284
5893
  ],
5285
5894
  "launchKeys": [
5286
5895
  "assembly",
5896
+ "autoDiagonalize",
5287
5897
  "displayedRegionNames",
5288
5898
  "tracks"
5289
5899
  ]