@jbrowse/cli 5.0.0-beta.13 → 5.0.0-beta.14

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 (24) hide show
  1. package/README.md +19 -38
  2. package/dist/commands/add-track-utils/adapter-utils.js +0 -45
  3. package/dist/commands/add-track.js +5 -28
  4. package/dist/commands/make-density/density-generator.js +1 -1
  5. package/dist/commands/make-density/index.js +14 -26
  6. package/dist/commands/make-pif/index.js +1 -1
  7. package/dist/commands/text-index/file-list.js +1 -1
  8. package/dist/commands/validate/configManifest.generated.js +1027 -273
  9. package/dist/commands/validate/configSchema.generated.js +3227 -1445
  10. package/dist/commands/validate/index.js +4 -3
  11. package/dist/commands/validate/markRules/colorScale.js +124 -26
  12. package/dist/commands/validate/markRules/markProblems.js +49 -99
  13. package/dist/commands/validate/markRules/markRuleFacts.js +1 -1
  14. package/dist/commands/validate/markRules/markSpecs.js +4 -2
  15. package/dist/commands/validate/markRules/markVocabulary.js +21 -24
  16. package/dist/commands/validate/markRules/stepChannels.js +13 -47
  17. package/dist/commands/validate/markRules/stepOutputs.js +202 -0
  18. package/dist/commands/validate/schemaValidate.js +5 -2
  19. package/dist/commands/validate/validateConfig.js +47 -13
  20. package/dist/index.js +1 -1
  21. package/dist/version.js +1 -1
  22. package/package.json +4 -4
  23. package/dist/commands/shared/density.js +0 -12
  24. package/dist/commands/validate/markRules/aggregateFieldName.js +0 -9
package/dist/commands/validate/configManifest.generated.js CHANGED
@@ -11,6 +11,9 @@ export const configManifest = {
11
11
  "type": "((LocalPathLocation | UriLocation | BlobLocation | FileHandleLocation) | undefined)"
12
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  }
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  ],
14
+ "legacyKeys": [
15
+ "cytobandsLocation"
16
+ ],
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  "shorthandKeys": [
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  "uri",
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  "baseUri"
@@ -26,10 +29,6 @@ export const configManifest = {
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  "name": "fetchSizeLimit",
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  "type": "number"
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  },
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- {
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- "name": "densityAdapter",
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- "type": "(frozen | undefined)"
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- },
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  {
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  "name": "useSliceWorkerPool",
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  "type": "boolean"
@@ -43,6 +42,12 @@ export const configManifest = {
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  "type": "(LocalPathLocation | UriLocation | BlobLocation | FileHandleLocation)"
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  }
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  ],
45
+ "legacyKeys": [
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+ "sequenceAdapter"
47
+ ],
48
+ "droppedKeys": [
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+ "sequenceAdapter"
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+ ],
46
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  "shorthandKeys": [
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  "uri",
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  "baseUri"
@@ -75,12 +80,16 @@ export const configManifest = {
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  {
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  "name": "fetchSizeLimit",
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  "type": "number"
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- },
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- {
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- "name": "densityAdapter",
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- "type": "(frozen | undefined)"
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  }
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  ],
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+ "legacyKeys": [
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+ "sequenceAdapter",
87
+ "chunkSizeLimit"
88
+ ],
89
+ "droppedKeys": [
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+ "sequenceAdapter",
91
+ "chunkSizeLimit"
92
+ ],
84
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  "shorthandKeys": [
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  "uri",
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  "baseUri",
@@ -121,12 +130,14 @@ export const configManifest = {
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  {
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  "name": "htsgetTrackId",
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  "type": "string"
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- },
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- {
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- "name": "densityAdapter",
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- "type": "(frozen | undefined)"
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  }
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  ],
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+ "legacyKeys": [
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+ "sequenceAdapter"
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+ ],
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+ "droppedKeys": [
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+ "sequenceAdapter"
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+ ],
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  "shorthandKeys": []
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  },
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  "BigBedAdapter": {
@@ -150,10 +161,6 @@ export const configManifest = {
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  {
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  "name": "disableGeneHeuristic",
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  "type": "boolean"
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- },
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- {
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- "name": "densityAdapter",
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- "type": "(frozen | undefined)"
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  }
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  ],
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  "shorthandKeys": [
@@ -280,10 +287,6 @@ export const configManifest = {
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  {
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  "name": "disableGeneHeuristic",
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  "type": "boolean"
283
- },
284
- {
285
- "name": "densityAdapter",
286
- "type": "(frozen | undefined)"
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  }
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  ],
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  "shorthandKeys": [
@@ -362,6 +365,12 @@ export const configManifest = {
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  "type": "frozen"
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  }
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  ],
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+ "legacyKeys": [
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+ "featureClass"
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+ ],
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+ "droppedKeys": [
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+ "featureClass"
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+ ],
365
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  "shorthandKeys": []
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  },
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  "FromConfigRegionsAdapter": {
@@ -379,6 +388,12 @@ export const configManifest = {
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  "type": "frozen"
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  }
381
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  ],
391
+ "legacyKeys": [
392
+ "featureClass"
393
+ ],
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+ "droppedKeys": [
395
+ "featureClass"
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+ ],
382
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  "shorthandKeys": []
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  },
384
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  "FromConfigSequenceAdapter": {
@@ -396,6 +411,12 @@ export const configManifest = {
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  "type": "frozen"
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  }
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  ],
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+ "legacyKeys": [
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+ "featureClass"
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+ ],
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+ "droppedKeys": [
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+ "featureClass"
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+ ],
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  "shorthandKeys": []
400
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  },
401
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  "RefNameAliasAdapter": {
@@ -437,6 +458,9 @@ export const configManifest = {
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  "type": "boolean"
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  }
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  ],
461
+ "legacyKeys": [
462
+ "useUcscNameOverride"
463
+ ],
440
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  "shorthandKeys": [
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  "uri",
442
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  "baseUri"
@@ -493,10 +517,6 @@ export const configManifest = {
493
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  {
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  "name": "aggregateField",
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  "type": "string"
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- },
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- {
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- "name": "densityAdapter",
499
- "type": "(frozen | undefined)"
500
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  }
501
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  ],
502
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  "shorthandKeys": [
@@ -532,10 +552,6 @@ export const configManifest = {
532
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  {
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  "name": "dontRedispatch",
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  "type": "string[]"
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- },
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- {
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- "name": "densityAdapter",
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- "type": "(frozen | undefined)"
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  }
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  ],
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  "shorthandKeys": [
@@ -877,10 +893,6 @@ export const configManifest = {
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  {
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  "name": "fetchSizeLimit",
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  "type": "number"
880
- },
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- {
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- "name": "densityAdapter",
883
- "type": "(frozen | undefined)"
884
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  }
885
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  ],
886
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  "shorthandKeys": [
@@ -914,10 +926,6 @@ export const configManifest = {
914
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  {
915
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  "name": "fetchSizeLimit",
916
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  "type": "number"
917
- },
918
- {
919
- "name": "densityAdapter",
920
- "type": "(frozen | undefined)"
921
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  }
922
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  ],
923
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  "shorthandKeys": []
@@ -1229,6 +1237,12 @@ export const configManifest = {
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  "type": "(LocalPathLocation | UriLocation | BlobLocation | FileHandleLocation)"
1230
1238
  }
1231
1239
  ],
1240
+ "legacyKeys": [
1241
+ "resolutionMultiplier"
1242
+ ],
1243
+ "droppedKeys": [
1244
+ "resolutionMultiplier"
1245
+ ],
1232
1246
  "shorthandKeys": [
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1247
  "uri",
1234
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  "baseUri"
@@ -1492,6 +1506,12 @@ export const configManifest = {
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  "type": "string[]"
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  }
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  ],
1509
+ "legacyKeys": [
1510
+ "subadapters"
1511
+ ],
1512
+ "droppedKeys": [
1513
+ "subadapters"
1514
+ ],
1495
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  "shorthandKeys": [
1496
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  "uri",
1497
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  "baseUri",
@@ -1661,10 +1681,6 @@ export const configManifest = {
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  "name": "disableGeneHeuristic",
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  "type": "boolean"
1663
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  },
1664
- {
1665
- "name": "densityAdapter",
1666
- "type": "(frozen | undefined)"
1667
- },
1668
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  {
1669
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  "name": "scoreTransform",
1670
1686
  "type": "(JexlString | string)"
@@ -1779,6 +1795,16 @@ export const configManifest = {
1779
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  ]
1780
1796
  }
1781
1797
  ],
1798
+ "legacyKeys": [
1799
+ "rpcDriverName",
1800
+ "textSearchAdapter",
1801
+ "textSearchIndexingAttributes"
1802
+ ],
1803
+ "droppedKeys": [
1804
+ "rpcDriverName",
1805
+ "textSearchAdapter",
1806
+ "textSearchIndexingAttributes"
1807
+ ],
1782
1808
  "displayTypes": [
1783
1809
  "LinearBasicDisplay",
1784
1810
  "LinearMultiRowFeatureDisplay",
@@ -1884,6 +1910,16 @@ export const configManifest = {
1884
1910
  ]
1885
1911
  }
1886
1912
  ],
1913
+ "legacyKeys": [
1914
+ "rpcDriverName",
1915
+ "textSearchAdapter",
1916
+ "textSearchIndexingAttributes"
1917
+ ],
1918
+ "droppedKeys": [
1919
+ "rpcDriverName",
1920
+ "textSearchAdapter",
1921
+ "textSearchIndexingAttributes"
1922
+ ],
1887
1923
  "displayTypes": [
1888
1924
  "LinearAlignmentsDisplay",
1889
1925
  "LinearMarkDisplay"
@@ -1913,7 +1949,7 @@ export const configManifest = {
1913
1949
  },
1914
1950
  {
1915
1951
  "name": "sequenceType",
1916
- "type": "string"
1952
+ "type": "SequenceType"
1917
1953
  },
1918
1954
  {
1919
1955
  "name": "description",
@@ -1938,6 +1974,14 @@ export const configManifest = {
1938
1974
  ]
1939
1975
  }
1940
1976
  ],
1977
+ "legacyKeys": [
1978
+ "rpcDriverName",
1979
+ "rendering"
1980
+ ],
1981
+ "droppedKeys": [
1982
+ "rpcDriverName",
1983
+ "rendering"
1984
+ ],
1941
1985
  "displayTypes": [
1942
1986
  "LinearReferenceSequenceDisplay"
1943
1987
  ]
@@ -2039,6 +2083,16 @@ export const configManifest = {
2039
2083
  ]
2040
2084
  }
2041
2085
  ],
2086
+ "legacyKeys": [
2087
+ "rpcDriverName",
2088
+ "textSearchAdapter",
2089
+ "textSearchIndexingAttributes"
2090
+ ],
2091
+ "droppedKeys": [
2092
+ "rpcDriverName",
2093
+ "textSearchAdapter",
2094
+ "textSearchIndexingAttributes"
2095
+ ],
2042
2096
  "displayTypes": [
2043
2097
  "ChordVariantDisplay",
2044
2098
  "LinearVariantDisplay",
@@ -2143,6 +2197,16 @@ export const configManifest = {
2143
2197
  ]
2144
2198
  }
2145
2199
  ],
2200
+ "legacyKeys": [
2201
+ "rpcDriverName",
2202
+ "textSearchAdapter",
2203
+ "textSearchIndexingAttributes"
2204
+ ],
2205
+ "droppedKeys": [
2206
+ "rpcDriverName",
2207
+ "textSearchAdapter",
2208
+ "textSearchIndexingAttributes"
2209
+ ],
2146
2210
  "displayTypes": [
2147
2211
  "LDTrackDisplay"
2148
2212
  ]
@@ -2244,6 +2308,16 @@ export const configManifest = {
2244
2308
  ]
2245
2309
  }
2246
2310
  ],
2311
+ "legacyKeys": [
2312
+ "rpcDriverName",
2313
+ "textSearchAdapter",
2314
+ "textSearchIndexingAttributes"
2315
+ ],
2316
+ "droppedKeys": [
2317
+ "rpcDriverName",
2318
+ "textSearchAdapter",
2319
+ "textSearchIndexingAttributes"
2320
+ ],
2247
2321
  "displayTypes": [
2248
2322
  "LinearWiggleDisplay",
2249
2323
  "LinearMarkDisplay"
@@ -2346,6 +2420,16 @@ export const configManifest = {
2346
2420
  ]
2347
2421
  }
2348
2422
  ],
2423
+ "legacyKeys": [
2424
+ "rpcDriverName",
2425
+ "textSearchAdapter",
2426
+ "textSearchIndexingAttributes"
2427
+ ],
2428
+ "droppedKeys": [
2429
+ "rpcDriverName",
2430
+ "textSearchAdapter",
2431
+ "textSearchIndexingAttributes"
2432
+ ],
2349
2433
  "displayTypes": [
2350
2434
  "LinearWiggleDisplay",
2351
2435
  "LinearMarkDisplay"
@@ -2448,6 +2532,16 @@ export const configManifest = {
2448
2532
  ]
2449
2533
  }
2450
2534
  ],
2535
+ "legacyKeys": [
2536
+ "rpcDriverName",
2537
+ "textSearchAdapter",
2538
+ "textSearchIndexingAttributes"
2539
+ ],
2540
+ "droppedKeys": [
2541
+ "rpcDriverName",
2542
+ "textSearchAdapter",
2543
+ "textSearchIndexingAttributes"
2544
+ ],
2451
2545
  "displayTypes": [
2452
2546
  "LinearWiggleDisplay"
2453
2547
  ]
@@ -2549,6 +2643,16 @@ export const configManifest = {
2549
2643
  ]
2550
2644
  }
2551
2645
  ],
2646
+ "legacyKeys": [
2647
+ "rpcDriverName",
2648
+ "textSearchAdapter",
2649
+ "textSearchIndexingAttributes"
2650
+ ],
2651
+ "droppedKeys": [
2652
+ "rpcDriverName",
2653
+ "textSearchAdapter",
2654
+ "textSearchIndexingAttributes"
2655
+ ],
2552
2656
  "displayTypes": [
2553
2657
  "LinearMafDisplay",
2554
2658
  "LinearMarkDisplay"
@@ -2651,6 +2755,16 @@ export const configManifest = {
2651
2755
  ]
2652
2756
  }
2653
2757
  ],
2758
+ "legacyKeys": [
2759
+ "rpcDriverName",
2760
+ "textSearchAdapter",
2761
+ "textSearchIndexingAttributes"
2762
+ ],
2763
+ "droppedKeys": [
2764
+ "rpcDriverName",
2765
+ "textSearchAdapter",
2766
+ "textSearchIndexingAttributes"
2767
+ ],
2654
2768
  "displayTypes": [
2655
2769
  "LinearHicDisplay"
2656
2770
  ]
@@ -2752,6 +2866,18 @@ export const configManifest = {
2752
2866
  ]
2753
2867
  }
2754
2868
  ],
2869
+ "legacyKeys": [
2870
+ "rpcDriverName",
2871
+ "textSearchAdapter",
2872
+ "textSearchIndexingAttributes",
2873
+ "trackIds"
2874
+ ],
2875
+ "droppedKeys": [
2876
+ "rpcDriverName",
2877
+ "textSearchAdapter",
2878
+ "textSearchIndexingAttributes",
2879
+ "trackIds"
2880
+ ],
2755
2881
  "displayTypes": [
2756
2882
  "ChordSyntenyDisplay",
2757
2883
  "DotplotDisplay",
@@ -2858,6 +2984,16 @@ export const configManifest = {
2858
2984
  ]
2859
2985
  }
2860
2986
  ],
2987
+ "legacyKeys": [
2988
+ "rpcDriverName",
2989
+ "textSearchAdapter",
2990
+ "textSearchIndexingAttributes"
2991
+ ],
2992
+ "droppedKeys": [
2993
+ "rpcDriverName",
2994
+ "textSearchAdapter",
2995
+ "textSearchIndexingAttributes"
2996
+ ],
2861
2997
  "displayTypes": [
2862
2998
  "LinearManhattanDisplay"
2863
2999
  ]
@@ -2886,10 +3022,6 @@ export const configManifest = {
2886
3022
  "name": "height",
2887
3023
  "type": "number"
2888
3024
  },
2889
- {
2890
- "name": "mouseover",
2891
- "type": "(JexlString | string)"
2892
- },
2893
3025
  {
2894
3026
  "name": "heightMode",
2895
3027
  "type": "heightMode"
@@ -2898,18 +3030,14 @@ export const configManifest = {
2898
3030
  "name": "growMaxHeight",
2899
3031
  "type": "number"
2900
3032
  },
2901
- {
2902
- "name": "densityTier",
2903
- "type": "Density tier"
2904
- },
2905
- {
2906
- "name": "densityTierBpPerPx",
2907
- "type": "number"
2908
- },
2909
3033
  {
2910
3034
  "name": "filter",
2911
3035
  "type": "JexlExpression[]"
2912
3036
  },
3037
+ {
3038
+ "name": "mouseover",
3039
+ "type": "(JexlString | string)"
3040
+ },
2913
3041
  {
2914
3042
  "name": "maxFeatureScreenDensity",
2915
3043
  "type": "number"
@@ -3001,9 +3129,13 @@ export const configManifest = {
3001
3129
  }
3002
3130
  }
3003
3131
  },
3132
+ {
3133
+ "name": "showOutline",
3134
+ "type": "boolean"
3135
+ },
3004
3136
  {
3005
3137
  "name": "outlineColor",
3006
- "type": "CssColor"
3138
+ "type": "(CssColor | undefined)"
3007
3139
  },
3008
3140
  {
3009
3141
  "name": "featureHeight",
@@ -3015,7 +3147,7 @@ export const configManifest = {
3015
3147
  },
3016
3148
  {
3017
3149
  "name": "facet",
3018
- "type": "FacetConfigurationSchema",
3150
+ "type": "SectionFacetConfigurationSchema",
3019
3151
  "subSlots": [
3020
3152
  {
3021
3153
  "name": "field",
@@ -3025,6 +3157,11 @@ export const configManifest = {
3025
3157
  "name": "domain",
3026
3158
  "type": "string[]",
3027
3159
  "liftsNumbers": true
3160
+ },
3161
+ {
3162
+ "name": "hidden",
3163
+ "type": "string[]",
3164
+ "liftsNumbers": true
3028
3165
  }
3029
3166
  ],
3030
3167
  "shorthand": {
@@ -3037,11 +3174,11 @@ export const configManifest = {
3037
3174
  "subSlots": [
3038
3175
  {
3039
3176
  "name": "name",
3040
- "type": "(JexlString | string)"
3177
+ "type": "string"
3041
3178
  },
3042
3179
  {
3043
3180
  "name": "description",
3044
- "type": "(JexlString | string)"
3181
+ "type": "string"
3045
3182
  }
3046
3183
  ]
3047
3184
  },
@@ -3099,15 +3236,23 @@ export const configManifest = {
3099
3236
  }
3100
3237
  ],
3101
3238
  "legacyKeys": [
3239
+ "maxDisplayedBpPerPx",
3240
+ "jexlFilters",
3102
3241
  "color1",
3103
3242
  "color2",
3104
3243
  "color3",
3105
3244
  "outline",
3106
3245
  "maxHeight",
3107
- "jexlFilters",
3108
3246
  "renderer",
3109
3247
  "showDescriptions"
3110
3248
  ],
3249
+ "droppedKeys": [
3250
+ "maxFeatureScreenDensity",
3251
+ "maxDisplayedBpPerPx",
3252
+ "fetchSizeLimit",
3253
+ "mouseover",
3254
+ "maxHeight"
3255
+ ],
3111
3256
  "legacyValues": {
3112
3257
  "showLabels": [
3113
3258
  true,
@@ -3155,10 +3300,6 @@ export const configManifest = {
3155
3300
  "name": "height",
3156
3301
  "type": "number"
3157
3302
  },
3158
- {
3159
- "name": "mouseover",
3160
- "type": "(JexlString | string)"
3161
- },
3162
3303
  {
3163
3304
  "name": "rows",
3164
3305
  "type": "RowsConfigurationSchema",
@@ -3198,10 +3339,6 @@ export const configManifest = {
3198
3339
  "name": "clusterField",
3199
3340
  "type": "string"
3200
3341
  },
3201
- {
3202
- "name": "lengthField",
3203
- "type": "string"
3204
- },
3205
3342
  {
3206
3343
  "name": "color",
3207
3344
  "type": "FeatureColorConfigurationSchema",
@@ -3299,10 +3436,6 @@ export const configManifest = {
3299
3436
  "string": "field"
3300
3437
  }
3301
3438
  },
3302
- {
3303
- "name": "rowHeight",
3304
- "type": "number"
3305
- },
3306
3439
  {
3307
3440
  "name": "rowProportion",
3308
3441
  "type": "number"
@@ -3311,21 +3444,23 @@ export const configManifest = {
3311
3444
  "name": "showRowSeparators",
3312
3445
  "type": "boolean"
3313
3446
  },
3314
- {
3315
- "name": "densityTier",
3316
- "type": "Density tier"
3317
- },
3318
- {
3319
- "name": "densityTierBpPerPx",
3320
- "type": "number"
3321
- },
3322
3447
  {
3323
3448
  "name": "showLegend",
3324
3449
  "type": "boolean"
3325
3450
  },
3326
3451
  {
3327
3452
  "name": "rowGroups",
3328
- "type": "frozen"
3453
+ "type": "RowGroupConfigurationSchema[]",
3454
+ "subSlots": [
3455
+ {
3456
+ "name": "match",
3457
+ "type": "string"
3458
+ },
3459
+ {
3460
+ "name": "group",
3461
+ "type": "string"
3462
+ }
3463
+ ]
3329
3464
  },
3330
3465
  {
3331
3466
  "name": "facet",
@@ -3362,6 +3497,18 @@ export const configManifest = {
3362
3497
  "type": "number"
3363
3498
  }
3364
3499
  ],
3500
+ "legacyKeys": [
3501
+ "maxFeatureScreenDensity",
3502
+ "maxDisplayedBpPerPx",
3503
+ "mouseover",
3504
+ "jexlFilters"
3505
+ ],
3506
+ "droppedKeys": [
3507
+ "maxFeatureScreenDensity",
3508
+ "maxDisplayedBpPerPx",
3509
+ "fetchSizeLimit",
3510
+ "mouseover"
3511
+ ],
3365
3512
  "stateModelProps": [
3366
3513
  "id",
3367
3514
  "type",
@@ -3394,10 +3541,6 @@ export const configManifest = {
3394
3541
  "name": "height",
3395
3542
  "type": "number"
3396
3543
  },
3397
- {
3398
- "name": "mouseover",
3399
- "type": "(JexlString | string)"
3400
- },
3401
3544
  {
3402
3545
  "name": "featureHeight",
3403
3546
  "type": "number"
@@ -3410,14 +3553,6 @@ export const configManifest = {
3410
3553
  "name": "growMaxHeight",
3411
3554
  "type": "number"
3412
3555
  },
3413
- {
3414
- "name": "densityTier",
3415
- "type": "Density tier"
3416
- },
3417
- {
3418
- "name": "densityTierBpPerPx",
3419
- "type": "number"
3420
- },
3421
3556
  {
3422
3557
  "name": "readConnectionsLineWidth",
3423
3558
  "type": "number"
@@ -3427,7 +3562,7 @@ export const configManifest = {
3427
3562
  "type": "boolean"
3428
3563
  },
3429
3564
  {
3430
- "name": "hideNonCanonicalJunctions",
3565
+ "name": "showNonCanonicalJunctions",
3431
3566
  "type": "boolean"
3432
3567
  },
3433
3568
  {
@@ -3491,6 +3626,10 @@ export const configManifest = {
3491
3626
  {
3492
3627
  "name": "title",
3493
3628
  "type": "(string | undefined)"
3629
+ },
3630
+ {
3631
+ "name": "descending",
3632
+ "type": "(boolean | undefined)"
3494
3633
  }
3495
3634
  ],
3496
3635
  "shorthand": {
@@ -3505,10 +3644,21 @@ export const configManifest = {
3505
3644
  ]
3506
3645
  },
3507
3646
  "mapq": {
3508
- "scale": "categorical",
3647
+ "scale": "threshold",
3509
3648
  "domain": [
3510
- "255"
3511
- ]
3649
+ "1",
3650
+ "10",
3651
+ "30"
3652
+ ],
3653
+ "scheme": "cividis",
3654
+ "labels": [
3655
+ "MAPQ 0 (multi-mapping)",
3656
+ "MAPQ 1-9 (low)",
3657
+ "MAPQ 10-29",
3658
+ "MAPQ 30+ (high confidence)"
3659
+ ],
3660
+ "title": "Mapping quality",
3661
+ "descending": true
3512
3662
  },
3513
3663
  "insertSize": {
3514
3664
  "scale": "threshold"
@@ -3527,7 +3677,13 @@ export const configManifest = {
3527
3677
  "RL",
3528
3678
  "RR",
3529
3679
  "LL",
3530
- ""
3680
+ "",
3681
+ "unmappedMate",
3682
+ "interchrom",
3683
+ "splitInverted",
3684
+ "splitSameStrand",
3685
+ "segmentInverted",
3686
+ "segmentSameStrand"
3531
3687
  ]
3532
3688
  },
3533
3689
  "insertSizeAndOrientation": {
@@ -3547,7 +3703,7 @@ export const configManifest = {
3547
3703
  "subSlots": [
3548
3704
  {
3549
3705
  "name": "field",
3550
- "type": "(AlignmentsBaseColorField | undefined)"
3706
+ "type": "AlignmentsBaseColorField"
3551
3707
  },
3552
3708
  {
3553
3709
  "name": "scale",
@@ -3560,15 +3716,81 @@ export const configManifest = {
3560
3716
  },
3561
3717
  {
3562
3718
  "name": "modifications",
3563
- "type": "frozen"
3719
+ "type": "AlignmentsModificationsConfigurationSchema",
3720
+ "subSlots": [
3721
+ {
3722
+ "name": "threshold",
3723
+ "type": "number"
3724
+ },
3725
+ {
3726
+ "name": "unmodified",
3727
+ "type": "ModificationUnmodified"
3728
+ },
3729
+ {
3730
+ "name": "cytosineContext",
3731
+ "type": "CytosineContext"
3732
+ },
3733
+ {
3734
+ "name": "shownModifications",
3735
+ "type": "string[]"
3736
+ }
3737
+ ]
3564
3738
  },
3565
3739
  {
3566
- "name": "filterBy",
3567
- "type": "frozen"
3740
+ "name": "filter",
3741
+ "type": "ReadFilterConfigurationSchema",
3742
+ "subSlots": [
3743
+ {
3744
+ "name": "flagInclude",
3745
+ "type": "number"
3746
+ },
3747
+ {
3748
+ "name": "flagExclude",
3749
+ "type": "number"
3750
+ },
3751
+ {
3752
+ "name": "minMapq",
3753
+ "type": "(number | undefined)"
3754
+ },
3755
+ {
3756
+ "name": "readName",
3757
+ "type": "(string | undefined)"
3758
+ },
3759
+ {
3760
+ "name": "tagFilters",
3761
+ "type": "TagFilterConfigurationSchema[]",
3762
+ "subSlots": [
3763
+ {
3764
+ "name": "tag",
3765
+ "type": "string"
3766
+ },
3767
+ {
3768
+ "name": "value",
3769
+ "type": "(string | undefined)"
3770
+ }
3771
+ ]
3772
+ },
3773
+ {
3774
+ "name": "spliced",
3775
+ "type": "(CategoryFilter | undefined)"
3776
+ },
3777
+ {
3778
+ "name": "svSignal",
3779
+ "type": "(CategoryFilter | undefined)"
3780
+ },
3781
+ {
3782
+ "name": "singletons",
3783
+ "type": "(CategoryFilter | undefined)"
3784
+ },
3785
+ {
3786
+ "name": "split",
3787
+ "type": "(CategoryFilter | undefined)"
3788
+ }
3789
+ ]
3568
3790
  },
3569
3791
  {
3570
3792
  "name": "facet",
3571
- "type": "FacetConfigurationSchema",
3793
+ "type": "SectionFacetConfigurationSchema",
3572
3794
  "subSlots": [
3573
3795
  {
3574
3796
  "name": "field",
@@ -3578,6 +3800,11 @@ export const configManifest = {
3578
3800
  "name": "domain",
3579
3801
  "type": "string[]",
3580
3802
  "liftsNumbers": true
3803
+ },
3804
+ {
3805
+ "name": "hidden",
3806
+ "type": "string[]",
3807
+ "liftsNumbers": true
3581
3808
  }
3582
3809
  ],
3583
3810
  "shorthand": {
@@ -3662,11 +3889,11 @@ export const configManifest = {
3662
3889
  ]
3663
3890
  },
3664
3891
  {
3665
- "name": "mismatchAlpha",
3892
+ "name": "fadeLowQualityMismatches",
3666
3893
  "type": "boolean"
3667
3894
  },
3668
3895
  {
3669
- "name": "showLowFreqMismatches",
3896
+ "name": "fadeLowFrequencyMismatches",
3670
3897
  "type": "boolean"
3671
3898
  },
3672
3899
  {
@@ -3674,16 +3901,37 @@ export const configManifest = {
3674
3901
  "type": "boolean"
3675
3902
  },
3676
3903
  {
3677
- "name": "sortedBy",
3678
- "type": "(frozen | undefined)"
3679
- },
3680
- {
3681
- "name": "layoutOrder",
3682
- "type": "LayoutOrder"
3904
+ "name": "sort",
3905
+ "type": "AlignmentsSortConfigurationSchema",
3906
+ "subSlots": [
3907
+ {
3908
+ "name": "type",
3909
+ "type": "AlignmentsSortType"
3910
+ },
3911
+ {
3912
+ "name": "pos",
3913
+ "type": "(number | undefined)"
3914
+ },
3915
+ {
3916
+ "name": "refName",
3917
+ "type": "(string | undefined)"
3918
+ },
3919
+ {
3920
+ "name": "tag",
3921
+ "type": "(string | undefined)"
3922
+ },
3923
+ {
3924
+ "name": "within",
3925
+ "type": "(number | undefined)"
3926
+ }
3927
+ ],
3928
+ "shorthand": {
3929
+ "string": "type"
3930
+ }
3683
3931
  },
3684
3932
  {
3685
3933
  "name": "showOutline",
3686
- "type": "(frozen | undefined)"
3934
+ "type": "(boolean | undefined)"
3687
3935
  },
3688
3936
  {
3689
3937
  "name": "unit",
@@ -3718,27 +3966,19 @@ export const configManifest = {
3718
3966
  "type": "boolean"
3719
3967
  },
3720
3968
  {
3721
- "name": "flipStrandLongReadChains",
3722
- "type": "boolean"
3723
- },
3724
- {
3725
- "name": "colorSupplementaryChains",
3726
- "type": "boolean"
3727
- },
3728
- {
3729
- "name": "drawInter",
3969
+ "name": "showInterchrom",
3730
3970
  "type": "boolean"
3731
3971
  },
3732
3972
  {
3733
- "name": "drawProperPairArcs",
3734
- "type": "boolean"
3973
+ "name": "showOrdinaryPairs",
3974
+ "type": "(boolean | undefined)"
3735
3975
  },
3736
3976
  {
3737
3977
  "name": "minInterchromSupport",
3738
3978
  "type": "number"
3739
3979
  },
3740
3980
  {
3741
- "name": "drawLongRange",
3981
+ "name": "showLongRange",
3742
3982
  "type": "boolean"
3743
3983
  },
3744
3984
  {
@@ -3788,8 +4028,51 @@ export const configManifest = {
3788
4028
  }
3789
4029
  ],
3790
4030
  "legacyKeys": [
4031
+ "maxFeatureScreenDensity",
4032
+ "maxDisplayedBpPerPx",
4033
+ "mouseover",
4034
+ "jexlFilters",
3791
4035
  "colorBy",
3792
- "linkedReads"
4036
+ "drawInter",
4037
+ "drawLongRange",
4038
+ "filterBy",
4039
+ "pileupDisplay",
4040
+ "snpCoverageDisplay",
4041
+ "defaultRendering",
4042
+ "renderers",
4043
+ "colorScheme",
4044
+ "scaleType",
4045
+ "autoscale",
4046
+ "minScore",
4047
+ "maxScore",
4048
+ "numStdDev",
4049
+ "inverted",
4050
+ "multiTicks",
4051
+ "jitter",
4052
+ "lineWidth",
4053
+ "hideSmallIndels",
4054
+ "hideMismatches",
4055
+ "mismatchAlpha",
4056
+ "hideLargeIndels",
4057
+ "minSubfeatureWidth",
4058
+ "flipStrandLongReadChains"
4059
+ ],
4060
+ "droppedKeys": [
4061
+ "maxFeatureScreenDensity",
4062
+ "maxDisplayedBpPerPx",
4063
+ "fetchSizeLimit",
4064
+ "mouseover",
4065
+ "jexlFilters",
4066
+ "defaultRendering",
4067
+ "colorScheme",
4068
+ "numStdDev",
4069
+ "inverted",
4070
+ "multiTicks",
4071
+ "jitter",
4072
+ "hideSmallIndels",
4073
+ "hideLargeIndels",
4074
+ "minSubfeatureWidth",
4075
+ "flipStrandLongReadChains"
3793
4076
  ],
3794
4077
  "aliases": [
3795
4078
  "LinearPileupDisplay",
@@ -3930,8 +4213,14 @@ export const configManifest = {
3930
4213
  "type": "identifier"
3931
4214
  }
3932
4215
  ],
3933
- "stateModelProps": [
3934
- "id",
4216
+ "legacyKeys": [
4217
+ "renderer"
4218
+ ],
4219
+ "droppedKeys": [
4220
+ "renderer"
4221
+ ],
4222
+ "stateModelProps": [
4223
+ "id",
3935
4224
  "type",
3936
4225
  "configuration"
3937
4226
  ]
@@ -3947,6 +4236,14 @@ export const configManifest = {
3947
4236
  "type": "identifier"
3948
4237
  }
3949
4238
  ],
4239
+ "legacyKeys": [
4240
+ "renderer",
4241
+ "middle"
4242
+ ],
4243
+ "droppedKeys": [
4244
+ "renderer",
4245
+ "middle"
4246
+ ],
3950
4247
  "stateModelProps": [
3951
4248
  "id",
3952
4249
  "type",
@@ -3976,10 +4273,6 @@ export const configManifest = {
3976
4273
  "name": "height",
3977
4274
  "type": "number"
3978
4275
  },
3979
- {
3980
- "name": "mouseover",
3981
- "type": "(JexlString | string)"
3982
- },
3983
4276
  {
3984
4277
  "name": "featureHeight",
3985
4278
  "type": "number"
@@ -3992,14 +4285,6 @@ export const configManifest = {
3992
4285
  "name": "growMaxHeight",
3993
4286
  "type": "number"
3994
4287
  },
3995
- {
3996
- "name": "densityTier",
3997
- "type": "Density tier"
3998
- },
3999
- {
4000
- "name": "densityTierBpPerPx",
4001
- "type": "number"
4002
- },
4003
4288
  {
4004
4289
  "name": "readConnectionsLineWidth",
4005
4290
  "type": "number"
@@ -4009,7 +4294,7 @@ export const configManifest = {
4009
4294
  "type": "boolean"
4010
4295
  },
4011
4296
  {
4012
- "name": "hideNonCanonicalJunctions",
4297
+ "name": "showNonCanonicalJunctions",
4013
4298
  "type": "boolean"
4014
4299
  },
4015
4300
  {
@@ -4073,6 +4358,10 @@ export const configManifest = {
4073
4358
  {
4074
4359
  "name": "title",
4075
4360
  "type": "(string | undefined)"
4361
+ },
4362
+ {
4363
+ "name": "descending",
4364
+ "type": "(boolean | undefined)"
4076
4365
  }
4077
4366
  ],
4078
4367
  "shorthand": {
@@ -4087,10 +4376,21 @@ export const configManifest = {
4087
4376
  ]
4088
4377
  },
4089
4378
  "mapq": {
4090
- "scale": "categorical",
4379
+ "scale": "threshold",
4091
4380
  "domain": [
4092
- "255"
4093
- ]
4381
+ "1",
4382
+ "10",
4383
+ "30"
4384
+ ],
4385
+ "scheme": "cividis",
4386
+ "labels": [
4387
+ "MAPQ 0 (multi-mapping)",
4388
+ "MAPQ 1-9 (low)",
4389
+ "MAPQ 10-29",
4390
+ "MAPQ 30+ (high confidence)"
4391
+ ],
4392
+ "title": "Mapping quality",
4393
+ "descending": true
4094
4394
  },
4095
4395
  "insertSize": {
4096
4396
  "scale": "threshold"
@@ -4109,7 +4409,13 @@ export const configManifest = {
4109
4409
  "RL",
4110
4410
  "RR",
4111
4411
  "LL",
4112
- ""
4412
+ "",
4413
+ "unmappedMate",
4414
+ "interchrom",
4415
+ "splitInverted",
4416
+ "splitSameStrand",
4417
+ "segmentInverted",
4418
+ "segmentSameStrand"
4113
4419
  ]
4114
4420
  },
4115
4421
  "insertSizeAndOrientation": {
@@ -4130,7 +4436,7 @@ export const configManifest = {
4130
4436
  "subSlots": [
4131
4437
  {
4132
4438
  "name": "field",
4133
- "type": "(AlignmentsBaseColorField | undefined)"
4439
+ "type": "AlignmentsBaseColorField"
4134
4440
  },
4135
4441
  {
4136
4442
  "name": "scale",
@@ -4143,15 +4449,81 @@ export const configManifest = {
4143
4449
  },
4144
4450
  {
4145
4451
  "name": "modifications",
4146
- "type": "frozen"
4452
+ "type": "AlignmentsModificationsConfigurationSchema",
4453
+ "subSlots": [
4454
+ {
4455
+ "name": "threshold",
4456
+ "type": "number"
4457
+ },
4458
+ {
4459
+ "name": "unmodified",
4460
+ "type": "ModificationUnmodified"
4461
+ },
4462
+ {
4463
+ "name": "cytosineContext",
4464
+ "type": "CytosineContext"
4465
+ },
4466
+ {
4467
+ "name": "shownModifications",
4468
+ "type": "string[]"
4469
+ }
4470
+ ]
4147
4471
  },
4148
4472
  {
4149
- "name": "filterBy",
4150
- "type": "frozen"
4473
+ "name": "filter",
4474
+ "type": "ReadFilterConfigurationSchema",
4475
+ "subSlots": [
4476
+ {
4477
+ "name": "flagInclude",
4478
+ "type": "number"
4479
+ },
4480
+ {
4481
+ "name": "flagExclude",
4482
+ "type": "number"
4483
+ },
4484
+ {
4485
+ "name": "minMapq",
4486
+ "type": "(number | undefined)"
4487
+ },
4488
+ {
4489
+ "name": "readName",
4490
+ "type": "(string | undefined)"
4491
+ },
4492
+ {
4493
+ "name": "tagFilters",
4494
+ "type": "TagFilterConfigurationSchema[]",
4495
+ "subSlots": [
4496
+ {
4497
+ "name": "tag",
4498
+ "type": "string"
4499
+ },
4500
+ {
4501
+ "name": "value",
4502
+ "type": "(string | undefined)"
4503
+ }
4504
+ ]
4505
+ },
4506
+ {
4507
+ "name": "spliced",
4508
+ "type": "(CategoryFilter | undefined)"
4509
+ },
4510
+ {
4511
+ "name": "svSignal",
4512
+ "type": "(CategoryFilter | undefined)"
4513
+ },
4514
+ {
4515
+ "name": "singletons",
4516
+ "type": "(CategoryFilter | undefined)"
4517
+ },
4518
+ {
4519
+ "name": "split",
4520
+ "type": "(CategoryFilter | undefined)"
4521
+ }
4522
+ ]
4151
4523
  },
4152
4524
  {
4153
4525
  "name": "facet",
4154
- "type": "FacetConfigurationSchema",
4526
+ "type": "SectionFacetConfigurationSchema",
4155
4527
  "subSlots": [
4156
4528
  {
4157
4529
  "name": "field",
@@ -4161,6 +4533,11 @@ export const configManifest = {
4161
4533
  "name": "domain",
4162
4534
  "type": "string[]",
4163
4535
  "liftsNumbers": true
4536
+ },
4537
+ {
4538
+ "name": "hidden",
4539
+ "type": "string[]",
4540
+ "liftsNumbers": true
4164
4541
  }
4165
4542
  ],
4166
4543
  "shorthand": {
@@ -4245,11 +4622,11 @@ export const configManifest = {
4245
4622
  ]
4246
4623
  },
4247
4624
  {
4248
- "name": "mismatchAlpha",
4625
+ "name": "fadeLowQualityMismatches",
4249
4626
  "type": "boolean"
4250
4627
  },
4251
4628
  {
4252
- "name": "showLowFreqMismatches",
4629
+ "name": "fadeLowFrequencyMismatches",
4253
4630
  "type": "boolean"
4254
4631
  },
4255
4632
  {
@@ -4257,16 +4634,37 @@ export const configManifest = {
4257
4634
  "type": "boolean"
4258
4635
  },
4259
4636
  {
4260
- "name": "sortedBy",
4261
- "type": "(frozen | undefined)"
4262
- },
4263
- {
4264
- "name": "layoutOrder",
4265
- "type": "LayoutOrder"
4637
+ "name": "sort",
4638
+ "type": "LGVSyntenySortConfigurationSchema",
4639
+ "subSlots": [
4640
+ {
4641
+ "name": "type",
4642
+ "type": "LGVSyntenySortType"
4643
+ },
4644
+ {
4645
+ "name": "pos",
4646
+ "type": "(number | undefined)"
4647
+ },
4648
+ {
4649
+ "name": "refName",
4650
+ "type": "(string | undefined)"
4651
+ },
4652
+ {
4653
+ "name": "tag",
4654
+ "type": "(string | undefined)"
4655
+ },
4656
+ {
4657
+ "name": "within",
4658
+ "type": "(number | undefined)"
4659
+ }
4660
+ ],
4661
+ "shorthand": {
4662
+ "string": "type"
4663
+ }
4266
4664
  },
4267
4665
  {
4268
4666
  "name": "showOutline",
4269
- "type": "(frozen | undefined)"
4667
+ "type": "(boolean | undefined)"
4270
4668
  },
4271
4669
  {
4272
4670
  "name": "unit",
@@ -4301,27 +4699,19 @@ export const configManifest = {
4301
4699
  "type": "boolean"
4302
4700
  },
4303
4701
  {
4304
- "name": "flipStrandLongReadChains",
4702
+ "name": "showInterchrom",
4305
4703
  "type": "boolean"
4306
4704
  },
4307
4705
  {
4308
- "name": "colorSupplementaryChains",
4309
- "type": "boolean"
4310
- },
4311
- {
4312
- "name": "drawInter",
4313
- "type": "boolean"
4314
- },
4315
- {
4316
- "name": "drawProperPairArcs",
4317
- "type": "boolean"
4706
+ "name": "showOrdinaryPairs",
4707
+ "type": "(boolean | undefined)"
4318
4708
  },
4319
4709
  {
4320
4710
  "name": "minInterchromSupport",
4321
4711
  "type": "number"
4322
4712
  },
4323
4713
  {
4324
- "name": "drawLongRange",
4714
+ "name": "showLongRange",
4325
4715
  "type": "boolean"
4326
4716
  },
4327
4717
  {
@@ -4379,8 +4769,51 @@ export const configManifest = {
4379
4769
  }
4380
4770
  ],
4381
4771
  "legacyKeys": [
4772
+ "maxFeatureScreenDensity",
4773
+ "maxDisplayedBpPerPx",
4774
+ "mouseover",
4775
+ "jexlFilters",
4382
4776
  "colorBy",
4383
- "linkedReads"
4777
+ "drawInter",
4778
+ "drawLongRange",
4779
+ "filterBy",
4780
+ "pileupDisplay",
4781
+ "snpCoverageDisplay",
4782
+ "defaultRendering",
4783
+ "renderers",
4784
+ "colorScheme",
4785
+ "scaleType",
4786
+ "autoscale",
4787
+ "minScore",
4788
+ "maxScore",
4789
+ "numStdDev",
4790
+ "inverted",
4791
+ "multiTicks",
4792
+ "jitter",
4793
+ "lineWidth",
4794
+ "hideSmallIndels",
4795
+ "hideMismatches",
4796
+ "mismatchAlpha",
4797
+ "hideLargeIndels",
4798
+ "minSubfeatureWidth",
4799
+ "flipStrandLongReadChains"
4800
+ ],
4801
+ "droppedKeys": [
4802
+ "maxFeatureScreenDensity",
4803
+ "maxDisplayedBpPerPx",
4804
+ "fetchSizeLimit",
4805
+ "mouseover",
4806
+ "jexlFilters",
4807
+ "defaultRendering",
4808
+ "colorScheme",
4809
+ "numStdDev",
4810
+ "inverted",
4811
+ "multiTicks",
4812
+ "jitter",
4813
+ "hideSmallIndels",
4814
+ "hideLargeIndels",
4815
+ "minSubfeatureWidth",
4816
+ "flipStrandLongReadChains"
4384
4817
  ],
4385
4818
  "stateModelProps": [
4386
4819
  "id",
@@ -4410,10 +4843,6 @@ export const configManifest = {
4410
4843
  "name": "height",
4411
4844
  "type": "number"
4412
4845
  },
4413
- {
4414
- "name": "mouseover",
4415
- "type": "(JexlString | string)"
4416
- },
4417
4846
  {
4418
4847
  "name": "color",
4419
4848
  "type": "MultiWayGeneColorConfigurationSchema",
@@ -4467,8 +4896,39 @@ export const configManifest = {
4467
4896
  "type": "LodMode"
4468
4897
  },
4469
4898
  {
4470
- "name": "domain",
4471
- "type": "string[]"
4899
+ "name": "rows",
4900
+ "type": "LaneRowsConfigurationSchema",
4901
+ "subSlots": [
4902
+ {
4903
+ "name": "domain",
4904
+ "type": "string[]",
4905
+ "liftsNumbers": true
4906
+ },
4907
+ {
4908
+ "name": "labels",
4909
+ "type": "Map<string, string>"
4910
+ },
4911
+ {
4912
+ "name": "tree",
4913
+ "type": "(string | undefined)"
4914
+ },
4915
+ {
4916
+ "name": "treeProvenance",
4917
+ "type": "(frozen | undefined)"
4918
+ },
4919
+ {
4920
+ "name": "kept",
4921
+ "type": "string[]",
4922
+ "liftsNumbers": true
4923
+ },
4924
+ {
4925
+ "name": "field",
4926
+ "type": "LaneRowsField"
4927
+ }
4928
+ ],
4929
+ "shorthand": {
4930
+ "string": "field"
4931
+ }
4472
4932
  },
4473
4933
  {
4474
4934
  "name": "ribbonColor",
@@ -4520,6 +4980,10 @@ export const configManifest = {
4520
4980
  "type": "string[]",
4521
4981
  "liftsNumbers": true
4522
4982
  },
4983
+ {
4984
+ "name": "descending",
4985
+ "type": "(boolean | undefined)"
4986
+ },
4523
4987
  {
4524
4988
  "name": "title",
4525
4989
  "type": "(string | undefined)"
@@ -4529,8 +4993,55 @@ export const configManifest = {
4529
4993
  "string": "value"
4530
4994
  },
4531
4995
  "fieldPresets": {
4532
- "*": {
4533
- "scale": "categorical"
4996
+ "mapq": {
4997
+ "scale": "threshold",
4998
+ "domain": [
4999
+ "1",
5000
+ "10",
5001
+ "30"
5002
+ ],
5003
+ "scheme": "cividis",
5004
+ "labels": [
5005
+ "MAPQ 0 (multi-mapping)",
5006
+ "MAPQ 1-9 (low)",
5007
+ "MAPQ 10-29",
5008
+ "MAPQ 30+ (high confidence)"
5009
+ ],
5010
+ "title": "Mapping quality",
5011
+ "descending": true
5012
+ },
5013
+ "identity": {
5014
+ "scale": "linear",
5015
+ "domainMin": 0,
5016
+ "domainMax": 1,
5017
+ "scheme": "redgreyblue",
5018
+ "title": "Identity"
5019
+ },
5020
+ "dnds": {
5021
+ "scale": "linear",
5022
+ "domainMin": 0,
5023
+ "domainMax": 2,
5024
+ "domainMid": 1,
5025
+ "scheme": "blueyellowred",
5026
+ "title": "dN/dS"
5027
+ },
5028
+ "syntenicDepth": {
5029
+ "scale": "threshold",
5030
+ "domain": [
5031
+ "2",
5032
+ "3"
5033
+ ],
5034
+ "range": [
5035
+ "#bdbdbd",
5036
+ "#fdae6b",
5037
+ "#e6550d"
5038
+ ],
5039
+ "labels": [
5040
+ "One-to-one",
5041
+ "Shared by 2 genes",
5042
+ "Shared by 3 or more"
5043
+ ],
5044
+ "title": "Syntenic depth"
4534
5045
  }
4535
5046
  }
4536
5047
  },
@@ -4562,6 +5073,10 @@ export const configManifest = {
4562
5073
  "name": "text",
4563
5074
  "type": "string"
4564
5075
  },
5076
+ {
5077
+ "name": "inlineLaneNames",
5078
+ "type": "boolean"
5079
+ },
4565
5080
  {
4566
5081
  "name": "showGeneLabels",
4567
5082
  "type": "boolean"
@@ -4598,6 +5113,10 @@ export const configManifest = {
4598
5113
  "name": "interpolate",
4599
5114
  "type": "LineInterpolation"
4600
5115
  },
5116
+ {
5117
+ "name": "gapBp",
5118
+ "type": "(number | undefined)"
5119
+ },
4601
5120
  {
4602
5121
  "name": "linkShape",
4603
5122
  "type": "LinkShape"
@@ -4704,7 +5223,7 @@ export const configManifest = {
4704
5223
  },
4705
5224
  {
4706
5225
  "name": "descending",
4707
- "type": "boolean"
5226
+ "type": "(boolean | undefined)"
4708
5227
  },
4709
5228
  {
4710
5229
  "name": "missingLabel",
@@ -4814,11 +5333,7 @@ export const configManifest = {
4814
5333
  },
4815
5334
  {
4816
5335
  "name": "transform",
4817
- "type": "(filterConfigurationSchema | formulaConfigurationSchema | binConfigurationSchema | aggregateConfigurationSchema | coverageConfigurationSchema | flattenConfigurationSchema | cellsConfigurationSchema | pileupConfigurationSchema | mateConfigurationSchema)[]"
4818
- },
4819
- {
4820
- "name": "source",
4821
- "type": "MarkSource"
5336
+ "type": "(filterConfigurationSchema | formulaConfigurationSchema | binConfigurationSchema | aggregateConfigurationSchema | windowConfigurationSchema | coverageConfigurationSchema | flattenConfigurationSchema | cellsConfigurationSchema | pileupConfigurationSchema | mateConfigurationSchema)[]"
4822
5337
  },
4823
5338
  {
4824
5339
  "name": "minBpPerPx",
@@ -4845,12 +5360,26 @@ export const configManifest = {
4845
5360
  "type": "boolean"
4846
5361
  }
4847
5362
  ],
5363
+ "legacyKeys": [
5364
+ "maxFeatureScreenDensity",
5365
+ "maxDisplayedBpPerPx",
5366
+ "mouseover",
5367
+ "jexlFilters"
5368
+ ],
5369
+ "droppedKeys": [
5370
+ "maxFeatureScreenDensity",
5371
+ "maxDisplayedBpPerPx",
5372
+ "fetchSizeLimit",
5373
+ "mouseover"
5374
+ ],
4848
5375
  "stateModelProps": [
4849
5376
  "id",
4850
5377
  "type",
4851
5378
  "configuration",
4852
- "laneFilter",
4853
- "frozenLanes"
5379
+ "hiddenLaneNames",
5380
+ "frozenLanes",
5381
+ "lanePins",
5382
+ "laneFlipPins"
4854
5383
  ]
4855
5384
  },
4856
5385
  "LinearReferenceSequenceDisplay": {
@@ -4888,6 +5417,12 @@ export const configManifest = {
4888
5417
  "type": "boolean"
4889
5418
  }
4890
5419
  ],
5420
+ "legacyKeys": [
5421
+ "renderer"
5422
+ ],
5423
+ "droppedKeys": [
5424
+ "renderer"
5425
+ ],
4891
5426
  "stateModelProps": [
4892
5427
  "id",
4893
5428
  "type",
@@ -4916,10 +5451,6 @@ export const configManifest = {
4916
5451
  "name": "height",
4917
5452
  "type": "number"
4918
5453
  },
4919
- {
4920
- "name": "mouseover",
4921
- "type": "(JexlString | string)"
4922
- },
4923
5454
  {
4924
5455
  "name": "heightMode",
4925
5456
  "type": "heightMode"
@@ -4928,18 +5459,14 @@ export const configManifest = {
4928
5459
  "name": "growMaxHeight",
4929
5460
  "type": "number"
4930
5461
  },
4931
- {
4932
- "name": "densityTier",
4933
- "type": "Density tier"
4934
- },
4935
- {
4936
- "name": "densityTierBpPerPx",
4937
- "type": "number"
4938
- },
4939
5462
  {
4940
5463
  "name": "filter",
4941
5464
  "type": "JexlExpression[]"
4942
5465
  },
5466
+ {
5467
+ "name": "mouseover",
5468
+ "type": "(JexlString | string)"
5469
+ },
4943
5470
  {
4944
5471
  "name": "maxFeatureScreenDensity",
4945
5472
  "type": "number"
@@ -5031,9 +5558,13 @@ export const configManifest = {
5031
5558
  }
5032
5559
  }
5033
5560
  },
5561
+ {
5562
+ "name": "showOutline",
5563
+ "type": "boolean"
5564
+ },
5034
5565
  {
5035
5566
  "name": "outlineColor",
5036
- "type": "CssColor"
5567
+ "type": "(CssColor | undefined)"
5037
5568
  },
5038
5569
  {
5039
5570
  "name": "featureHeight",
@@ -5045,7 +5576,7 @@ export const configManifest = {
5045
5576
  },
5046
5577
  {
5047
5578
  "name": "facet",
5048
- "type": "FacetConfigurationSchema",
5579
+ "type": "SectionFacetConfigurationSchema",
5049
5580
  "subSlots": [
5050
5581
  {
5051
5582
  "name": "field",
@@ -5055,6 +5586,11 @@ export const configManifest = {
5055
5586
  "name": "domain",
5056
5587
  "type": "string[]",
5057
5588
  "liftsNumbers": true
5589
+ },
5590
+ {
5591
+ "name": "hidden",
5592
+ "type": "string[]",
5593
+ "liftsNumbers": true
5058
5594
  }
5059
5595
  ],
5060
5596
  "shorthand": {
@@ -5067,25 +5603,33 @@ export const configManifest = {
5067
5603
  "subSlots": [
5068
5604
  {
5069
5605
  "name": "name",
5070
- "type": "(JexlString | string)"
5606
+ "type": "string"
5071
5607
  },
5072
5608
  {
5073
5609
  "name": "description",
5074
- "type": "(JexlString | string)"
5610
+ "type": "string"
5075
5611
  }
5076
5612
  ]
5077
5613
  }
5078
5614
  ],
5079
5615
  "legacyKeys": [
5616
+ "maxDisplayedBpPerPx",
5617
+ "jexlFilters",
5080
5618
  "color1",
5081
5619
  "color2",
5082
5620
  "color3",
5083
5621
  "outline",
5084
5622
  "maxHeight",
5085
- "jexlFilters",
5086
5623
  "renderer",
5087
5624
  "showDescriptions"
5088
5625
  ],
5626
+ "droppedKeys": [
5627
+ "maxFeatureScreenDensity",
5628
+ "maxDisplayedBpPerPx",
5629
+ "fetchSizeLimit",
5630
+ "mouseover",
5631
+ "maxHeight"
5632
+ ],
5089
5633
  "legacyValues": {
5090
5634
  "showLabels": [
5091
5635
  true,
@@ -5130,10 +5674,6 @@ export const configManifest = {
5130
5674
  "name": "height",
5131
5675
  "type": "number"
5132
5676
  },
5133
- {
5134
- "name": "mouseover",
5135
- "type": "(JexlString | string)"
5136
- },
5137
5677
  {
5138
5678
  "name": "variantLayout",
5139
5679
  "type": "VariantLayout"
@@ -5168,7 +5708,7 @@ export const configManifest = {
5168
5708
  },
5169
5709
  {
5170
5710
  "name": "rows",
5171
- "type": "RowArrangementConfigurationSchema",
5711
+ "type": "SampleRowsConfigurationSchema",
5172
5712
  "subSlots": [
5173
5713
  {
5174
5714
  "name": "domain",
@@ -5191,8 +5731,15 @@ export const configManifest = {
5191
5731
  "name": "kept",
5192
5732
  "type": "string[]",
5193
5733
  "liftsNumbers": true
5734
+ },
5735
+ {
5736
+ "name": "field",
5737
+ "type": "SampleRowsField"
5194
5738
  }
5195
- ]
5739
+ ],
5740
+ "shorthand": {
5741
+ "string": "field"
5742
+ }
5196
5743
  },
5197
5744
  {
5198
5745
  "name": "showRowSeparators",
@@ -5332,8 +5879,35 @@ export const configManifest = {
5332
5879
  }
5333
5880
  ],
5334
5881
  "legacyKeys": [
5882
+ "maxFeatureScreenDensity",
5883
+ "maxDisplayedBpPerPx",
5884
+ "mouseover",
5335
5885
  "jexlFilters",
5336
- "renderingMode"
5886
+ "renderingMode",
5887
+ "showSidebarLabels",
5888
+ "showReferenceAlleles",
5889
+ "colorBy",
5890
+ "autoscale",
5891
+ "minScore",
5892
+ "maxScore",
5893
+ "scaleType",
5894
+ "inverted",
5895
+ "numStdDev",
5896
+ "minimalTicks"
5897
+ ],
5898
+ "droppedKeys": [
5899
+ "maxFeatureScreenDensity",
5900
+ "maxDisplayedBpPerPx",
5901
+ "fetchSizeLimit",
5902
+ "mouseover",
5903
+ "colorBy",
5904
+ "autoscale",
5905
+ "minScore",
5906
+ "maxScore",
5907
+ "scaleType",
5908
+ "inverted",
5909
+ "numStdDev",
5910
+ "minimalTicks"
5337
5911
  ],
5338
5912
  "aliases": [
5339
5913
  "MultiLinearVariantDisplay",
@@ -5403,6 +5977,9 @@ export const configManifest = {
5403
5977
  "type": "(LDColorScale | undefined)"
5404
5978
  }
5405
5979
  ],
5980
+ "shorthand": {
5981
+ "string": "field"
5982
+ },
5406
5983
  "fieldPresets": {
5407
5984
  "r2": {
5408
5985
  "scale": "linear",
@@ -5417,17 +5994,13 @@ export const configManifest = {
5417
5994
  },
5418
5995
  "fieldDefault": "r2"
5419
5996
  },
5420
- {
5421
- "name": "maxVariantSeparation",
5422
- "type": "number"
5423
- },
5424
5997
  {
5425
5998
  "name": "showVerticalGuides",
5426
5999
  "type": "boolean"
5427
6000
  },
5428
6001
  {
5429
6002
  "name": "showLabels",
5430
- "type": "boolean"
6003
+ "type": "LDShowLabels"
5431
6004
  },
5432
6005
  {
5433
6006
  "name": "tickHeight",
@@ -5439,8 +6012,47 @@ export const configManifest = {
5439
6012
  }
5440
6013
  ],
5441
6014
  "legacyKeys": [
5442
- "ldMetric"
6015
+ "maxFeatureScreenDensity",
6016
+ "maxDisplayedBpPerPx",
6017
+ "fetchSizeLimit",
6018
+ "mouseover",
6019
+ "jexlFilters",
6020
+ "ldMetric",
6021
+ "fitToHeight",
6022
+ "useGenomicPositions",
6023
+ "maxHeight",
6024
+ "colorScheme",
6025
+ "signedLD",
6026
+ "showLDTriangle",
6027
+ "showRecombination",
6028
+ "recombinationZoneHeight",
6029
+ "minorAlleleFrequencyFilter",
6030
+ "lengthCutoffFilter",
6031
+ "hweFilterThreshold",
6032
+ "callRateFilter"
5443
6033
  ],
6034
+ "droppedKeys": [
6035
+ "maxFeatureScreenDensity",
6036
+ "maxDisplayedBpPerPx",
6037
+ "fetchSizeLimit",
6038
+ "mouseover",
6039
+ "maxHeight",
6040
+ "colorScheme",
6041
+ "signedLD",
6042
+ "showLDTriangle",
6043
+ "showRecombination",
6044
+ "recombinationZoneHeight",
6045
+ "minorAlleleFrequencyFilter",
6046
+ "lengthCutoffFilter",
6047
+ "hweFilterThreshold",
6048
+ "callRateFilter"
6049
+ ],
6050
+ "legacyValues": {
6051
+ "showLabels": [
6052
+ true,
6053
+ false
6054
+ ]
6055
+ },
5444
6056
  "stateModelProps": [
5445
6057
  "id",
5446
6058
  "type",
@@ -5467,7 +6079,7 @@ export const configManifest = {
5467
6079
  },
5468
6080
  {
5469
6081
  "name": "rows",
5470
- "type": "RowsConfigurationSchema",
6082
+ "type": "QuantitativeRowsConfigurationSchema",
5471
6083
  "subSlots": [
5472
6084
  {
5473
6085
  "name": "domain",
@@ -5493,7 +6105,7 @@ export const configManifest = {
5493
6105
  },
5494
6106
  {
5495
6107
  "name": "field",
5496
- "type": "string"
6108
+ "type": "QuantitativeRowsField"
5497
6109
  }
5498
6110
  ],
5499
6111
  "shorthand": {
@@ -5584,10 +6196,11 @@ export const configManifest = {
5584
6196
  "*": {
5585
6197
  "scale": "threshold"
5586
6198
  }
5587
- }
6199
+ },
6200
+ "impliedField": "score"
5588
6201
  },
5589
6202
  {
5590
- "name": "scoreField",
6203
+ "name": "y",
5591
6204
  "type": "string"
5592
6205
  },
5593
6206
  {
@@ -5600,11 +6213,7 @@ export const configManifest = {
5600
6213
  },
5601
6214
  {
5602
6215
  "name": "size",
5603
- "type": "number"
5604
- },
5605
- {
5606
- "name": "lineWidth",
5607
- "type": "number"
6216
+ "type": "(number | undefined)"
5608
6217
  },
5609
6218
  {
5610
6219
  "name": "maxGapMultiple",
@@ -5688,8 +6297,12 @@ export const configManifest = {
5688
6297
  "type": "boolean"
5689
6298
  },
5690
6299
  {
5691
- "name": "summaryScoreMode",
5692
- "type": "Score type"
6300
+ "name": "aggregate",
6301
+ "type": "Aggregate"
6302
+ },
6303
+ {
6304
+ "name": "extent",
6305
+ "type": "Extent"
5693
6306
  },
5694
6307
  {
5695
6308
  "name": "showTree",
@@ -5713,9 +6326,31 @@ export const configManifest = {
5713
6326
  }
5714
6327
  ],
5715
6328
  "legacyKeys": [
6329
+ "maxFeatureScreenDensity",
6330
+ "maxDisplayedBpPerPx",
6331
+ "fetchSizeLimit",
6332
+ "mouseover",
6333
+ "jexlFilters",
5716
6334
  "displayCrossHatches",
5717
6335
  "minimalTicks",
5718
- "defaultRendering"
6336
+ "scaleType",
6337
+ "autoscale",
6338
+ "minScore",
6339
+ "maxScore",
6340
+ "numStdDev",
6341
+ "inverted",
6342
+ "renderers",
6343
+ "summaryScoreMode",
6344
+ "defaultRendering",
6345
+ "lineWidth"
6346
+ ],
6347
+ "droppedKeys": [
6348
+ "maxFeatureScreenDensity",
6349
+ "maxDisplayedBpPerPx",
6350
+ "fetchSizeLimit",
6351
+ "mouseover",
6352
+ "numStdDev",
6353
+ "inverted"
5719
6354
  ],
5720
6355
  "aliases": [
5721
6356
  "MultiLinearWiggleDisplay",
@@ -5751,11 +6386,7 @@ export const configManifest = {
5751
6386
  },
5752
6387
  {
5753
6388
  "name": "height",
5754
- "type": "(number | undefined)"
5755
- },
5756
- {
5757
- "name": "mouseover",
5758
- "type": "(JexlString | string)"
6389
+ "type": "number"
5759
6390
  },
5760
6391
  {
5761
6392
  "name": "rowHeight",
@@ -5920,7 +6551,7 @@ export const configManifest = {
5920
6551
  },
5921
6552
  {
5922
6553
  "name": "rows",
5923
- "type": "RowArrangementConfigurationSchema",
6554
+ "type": "SampleRowsConfigurationSchema",
5924
6555
  "subSlots": [
5925
6556
  {
5926
6557
  "name": "domain",
@@ -5943,8 +6574,15 @@ export const configManifest = {
5943
6574
  "name": "kept",
5944
6575
  "type": "string[]",
5945
6576
  "liftsNumbers": true
6577
+ },
6578
+ {
6579
+ "name": "field",
6580
+ "type": "SampleRowsField"
5946
6581
  }
5947
- ]
6582
+ ],
6583
+ "shorthand": {
6584
+ "string": "field"
6585
+ }
5948
6586
  },
5949
6587
  {
5950
6588
  "name": "rowColor",
@@ -5988,6 +6626,87 @@ export const configManifest = {
5988
6626
  "name": "coverageHeight",
5989
6627
  "type": "number"
5990
6628
  },
6629
+ {
6630
+ "name": "scales",
6631
+ "type": "ScalesConfigurationSchema",
6632
+ "subSlots": [
6633
+ {
6634
+ "name": "y",
6635
+ "type": "ValueScaleConfigurationSchema",
6636
+ "subSlots": [
6637
+ {
6638
+ "name": "type",
6639
+ "type": "ValueScaleType"
6640
+ },
6641
+ {
6642
+ "name": "domainMin",
6643
+ "type": "(number | undefined)"
6644
+ },
6645
+ {
6646
+ "name": "domainMax",
6647
+ "type": "(number | undefined)"
6648
+ },
6649
+ {
6650
+ "name": "zero",
6651
+ "type": "boolean"
6652
+ },
6653
+ {
6654
+ "name": "autoscaleGroup",
6655
+ "type": "(string | undefined)"
6656
+ },
6657
+ {
6658
+ "name": "symlogConstant",
6659
+ "type": "number"
6660
+ },
6661
+ {
6662
+ "name": "domainQuantile",
6663
+ "type": "number"
6664
+ },
6665
+ {
6666
+ "name": "grid",
6667
+ "type": "boolean"
6668
+ },
6669
+ {
6670
+ "name": "minimalTicks",
6671
+ "type": "boolean"
6672
+ },
6673
+ {
6674
+ "name": "title",
6675
+ "type": "(string | undefined)"
6676
+ },
6677
+ {
6678
+ "name": "rules",
6679
+ "type": "ValueScaleRuleConfigurationSchema[]",
6680
+ "subSlots": [
6681
+ {
6682
+ "name": "value",
6683
+ "type": "number"
6684
+ },
6685
+ {
6686
+ "name": "color",
6687
+ "type": "(CssColor | undefined)"
6688
+ },
6689
+ {
6690
+ "name": "label",
6691
+ "type": "string"
6692
+ }
6693
+ ],
6694
+ "shorthand": {
6695
+ "number": "value"
6696
+ }
6697
+ }
6698
+ ]
6699
+ }
6700
+ ]
6701
+ },
6702
+ {
6703
+ "name": "coverageSnpMinFrequency",
6704
+ "type": "number"
6705
+ },
6706
+ {
6707
+ "name": "showInterbaseIndicators",
6708
+ "type": "boolean"
6709
+ },
5991
6710
  {
5992
6711
  "name": "showConservation",
5993
6712
  "type": "boolean"
@@ -6017,6 +6736,18 @@ export const configManifest = {
6017
6736
  "type": "boolean"
6018
6737
  }
6019
6738
  ],
6739
+ "legacyKeys": [
6740
+ "maxFeatureScreenDensity",
6741
+ "maxDisplayedBpPerPx",
6742
+ "mouseover",
6743
+ "jexlFilters"
6744
+ ],
6745
+ "droppedKeys": [
6746
+ "maxFeatureScreenDensity",
6747
+ "maxDisplayedBpPerPx",
6748
+ "fetchSizeLimit",
6749
+ "mouseover"
6750
+ ],
6020
6751
  "stateModelProps": [
6021
6752
  "id",
6022
6753
  "type",
@@ -6081,6 +6812,9 @@ export const configManifest = {
6081
6812
  "type": "(number | undefined)"
6082
6813
  }
6083
6814
  ],
6815
+ "shorthand": {
6816
+ "string": "field"
6817
+ },
6084
6818
  "fieldPresets": {
6085
6819
  "count": {
6086
6820
  "scale": "linear"
@@ -6102,7 +6836,19 @@ export const configManifest = {
6102
6836
  }
6103
6837
  ],
6104
6838
  "legacyKeys": [
6105
- "useColorPercentile"
6839
+ "maxFeatureScreenDensity",
6840
+ "maxDisplayedBpPerPx",
6841
+ "fetchSizeLimit",
6842
+ "mouseover",
6843
+ "jexlFilters",
6844
+ "renderer"
6845
+ ],
6846
+ "droppedKeys": [
6847
+ "maxFeatureScreenDensity",
6848
+ "maxDisplayedBpPerPx",
6849
+ "fetchSizeLimit",
6850
+ "mouseover",
6851
+ "renderer"
6106
6852
  ],
6107
6853
  "stateModelProps": [
6108
6854
  "id",
@@ -6132,14 +6878,6 @@ export const configManifest = {
6132
6878
  "name": "forceLoad",
6133
6879
  "type": "boolean"
6134
6880
  },
6135
- {
6136
- "name": "densityTier",
6137
- "type": "Density tier"
6138
- },
6139
- {
6140
- "name": "densityTierBpPerPx",
6141
- "type": "number"
6142
- },
6143
6881
  {
6144
6882
  "name": "marks",
6145
6883
  "type": "MarkConfigurationSchema[]",
@@ -6152,6 +6890,10 @@ export const configManifest = {
6152
6890
  "name": "interpolate",
6153
6891
  "type": "LineInterpolation"
6154
6892
  },
6893
+ {
6894
+ "name": "gapBp",
6895
+ "type": "(number | undefined)"
6896
+ },
6155
6897
  {
6156
6898
  "name": "linkShape",
6157
6899
  "type": "LinkShape"
@@ -6258,7 +7000,7 @@ export const configManifest = {
6258
7000
  },
6259
7001
  {
6260
7002
  "name": "descending",
6261
- "type": "boolean"
7003
+ "type": "(boolean | undefined)"
6262
7004
  },
6263
7005
  {
6264
7006
  "name": "missingLabel",
@@ -6368,11 +7110,7 @@ export const configManifest = {
6368
7110
  },
6369
7111
  {
6370
7112
  "name": "transform",
6371
- "type": "(filterConfigurationSchema | formulaConfigurationSchema | binConfigurationSchema | aggregateConfigurationSchema | coverageConfigurationSchema | flattenConfigurationSchema | cellsConfigurationSchema | pileupConfigurationSchema | mateConfigurationSchema)[]"
6372
- },
6373
- {
6374
- "name": "source",
6375
- "type": "MarkSource"
7113
+ "type": "(filterConfigurationSchema | formulaConfigurationSchema | binConfigurationSchema | aggregateConfigurationSchema | windowConfigurationSchema | coverageConfigurationSchema | flattenConfigurationSchema | cellsConfigurationSchema | pileupConfigurationSchema | mateConfigurationSchema)[]"
6376
7114
  },
6377
7115
  {
6378
7116
  "name": "minBpPerPx",
@@ -6394,7 +7132,7 @@ export const configManifest = {
6394
7132
  },
6395
7133
  {
6396
7134
  "name": "transform",
6397
- "type": "(filterConfigurationSchema | formulaConfigurationSchema | binConfigurationSchema | aggregateConfigurationSchema | coverageConfigurationSchema | flattenConfigurationSchema | cellsConfigurationSchema | pileupConfigurationSchema | mateConfigurationSchema)[]"
7135
+ "type": "(filterConfigurationSchema | formulaConfigurationSchema | binConfigurationSchema | aggregateConfigurationSchema | windowConfigurationSchema | coverageConfigurationSchema | flattenConfigurationSchema | cellsConfigurationSchema | pileupConfigurationSchema | mateConfigurationSchema)[]"
6398
7136
  },
6399
7137
  {
6400
7138
  "name": "facet",
@@ -6409,9 +7147,14 @@ export const configManifest = {
6409
7147
  "type": "string[]",
6410
7148
  "liftsNumbers": true
6411
7149
  },
7150
+ {
7151
+ "name": "hidden",
7152
+ "type": "string[]",
7153
+ "liftsNumbers": true
7154
+ },
6412
7155
  {
6413
7156
  "name": "transform",
6414
- "type": "(filterConfigurationSchema | formulaConfigurationSchema | binConfigurationSchema | aggregateConfigurationSchema | coverageConfigurationSchema | flattenConfigurationSchema | cellsConfigurationSchema | pileupConfigurationSchema | mateConfigurationSchema)[]"
7157
+ "type": "(filterConfigurationSchema | formulaConfigurationSchema | binConfigurationSchema | aggregateConfigurationSchema | windowConfigurationSchema | coverageConfigurationSchema | flattenConfigurationSchema | cellsConfigurationSchema | pileupConfigurationSchema | mateConfigurationSchema)[]"
6415
7158
  }
6416
7159
  ],
6417
7160
  "shorthand": {
@@ -6590,10 +7333,17 @@ export const configManifest = {
6590
7333
  }
6591
7334
  ],
6592
7335
  "legacyKeys": [
6593
- "displayCrossHatches",
6594
- "minimalTicks",
7336
+ "maxFeatureScreenDensity",
7337
+ "maxDisplayedBpPerPx",
7338
+ "mouseover",
6595
7339
  "jexlFilters"
6596
7340
  ],
7341
+ "droppedKeys": [
7342
+ "maxFeatureScreenDensity",
7343
+ "maxDisplayedBpPerPx",
7344
+ "fetchSizeLimit",
7345
+ "mouseover"
7346
+ ],
6597
7347
  "stateModelProps": [
6598
7348
  "id",
6599
7349
  "type",
@@ -6601,8 +7351,7 @@ export const configManifest = {
6601
7351
  "clusterRegion",
6602
7352
  "sortRowsBy",
6603
7353
  "configuration",
6604
- "indexSnp",
6605
- "indexSnpPinned"
7354
+ "indexSnp"
6606
7355
  ]
6607
7356
  },
6608
7357
  "LinearMarkDisplay": {
@@ -6627,14 +7376,6 @@ export const configManifest = {
6627
7376
  "name": "forceLoad",
6628
7377
  "type": "boolean"
6629
7378
  },
6630
- {
6631
- "name": "densityTier",
6632
- "type": "Density tier"
6633
- },
6634
- {
6635
- "name": "densityTierBpPerPx",
6636
- "type": "number"
6637
- },
6638
7379
  {
6639
7380
  "name": "marks",
6640
7381
  "type": "MarkConfigurationSchema[]",
@@ -6647,6 +7388,10 @@ export const configManifest = {
6647
7388
  "name": "interpolate",
6648
7389
  "type": "LineInterpolation"
6649
7390
  },
7391
+ {
7392
+ "name": "gapBp",
7393
+ "type": "(number | undefined)"
7394
+ },
6650
7395
  {
6651
7396
  "name": "linkShape",
6652
7397
  "type": "LinkShape"
@@ -6753,7 +7498,7 @@ export const configManifest = {
6753
7498
  },
6754
7499
  {
6755
7500
  "name": "descending",
6756
- "type": "boolean"
7501
+ "type": "(boolean | undefined)"
6757
7502
  },
6758
7503
  {
6759
7504
  "name": "missingLabel",
@@ -6863,11 +7608,7 @@ export const configManifest = {
6863
7608
  },
6864
7609
  {
6865
7610
  "name": "transform",
6866
- "type": "(filterConfigurationSchema | formulaConfigurationSchema | binConfigurationSchema | aggregateConfigurationSchema | coverageConfigurationSchema | flattenConfigurationSchema | cellsConfigurationSchema | pileupConfigurationSchema | mateConfigurationSchema)[]"
6867
- },
6868
- {
6869
- "name": "source",
6870
- "type": "MarkSource"
7611
+ "type": "(filterConfigurationSchema | formulaConfigurationSchema | binConfigurationSchema | aggregateConfigurationSchema | windowConfigurationSchema | coverageConfigurationSchema | flattenConfigurationSchema | cellsConfigurationSchema | pileupConfigurationSchema | mateConfigurationSchema)[]"
6871
7612
  },
6872
7613
  {
6873
7614
  "name": "minBpPerPx",
@@ -6881,7 +7622,7 @@ export const configManifest = {
6881
7622
  },
6882
7623
  {
6883
7624
  "name": "transform",
6884
- "type": "(filterConfigurationSchema | formulaConfigurationSchema | binConfigurationSchema | aggregateConfigurationSchema | coverageConfigurationSchema | flattenConfigurationSchema | cellsConfigurationSchema | pileupConfigurationSchema | mateConfigurationSchema)[]"
7625
+ "type": "(filterConfigurationSchema | formulaConfigurationSchema | binConfigurationSchema | aggregateConfigurationSchema | windowConfigurationSchema | coverageConfigurationSchema | flattenConfigurationSchema | cellsConfigurationSchema | pileupConfigurationSchema | mateConfigurationSchema)[]"
6885
7626
  },
6886
7627
  {
6887
7628
  "name": "facet",
@@ -6896,9 +7637,14 @@ export const configManifest = {
6896
7637
  "type": "string[]",
6897
7638
  "liftsNumbers": true
6898
7639
  },
7640
+ {
7641
+ "name": "hidden",
7642
+ "type": "string[]",
7643
+ "liftsNumbers": true
7644
+ },
6899
7645
  {
6900
7646
  "name": "transform",
6901
- "type": "(filterConfigurationSchema | formulaConfigurationSchema | binConfigurationSchema | aggregateConfigurationSchema | coverageConfigurationSchema | flattenConfigurationSchema | cellsConfigurationSchema | pileupConfigurationSchema | mateConfigurationSchema)[]"
7647
+ "type": "(filterConfigurationSchema | formulaConfigurationSchema | binConfigurationSchema | aggregateConfigurationSchema | windowConfigurationSchema | coverageConfigurationSchema | flattenConfigurationSchema | cellsConfigurationSchema | pileupConfigurationSchema | mateConfigurationSchema)[]"
6902
7648
  }
6903
7649
  ],
6904
7650
  "shorthand": {
@@ -7077,10 +7823,17 @@ export const configManifest = {
7077
7823
  }
7078
7824
  ],
7079
7825
  "legacyKeys": [
7080
- "displayCrossHatches",
7081
- "minimalTicks",
7826
+ "maxFeatureScreenDensity",
7827
+ "maxDisplayedBpPerPx",
7828
+ "mouseover",
7082
7829
  "jexlFilters"
7083
7830
  ],
7831
+ "droppedKeys": [
7832
+ "maxFeatureScreenDensity",
7833
+ "maxDisplayedBpPerPx",
7834
+ "fetchSizeLimit",
7835
+ "mouseover"
7836
+ ],
7084
7837
  "aliases": [
7085
7838
  "LinearArcDisplay",
7086
7839
  "LinearPairedArcDisplay"
@@ -7731,6 +8484,7 @@ export const configManifest = {
7731
8484
  "filterBy",
7732
8485
  "filterBySetting",
7733
8486
  "hideMismatchesSetting",
8487
+ "sortedBy",
7734
8488
  "trackMaxHeight"
7735
8489
  ],
7736
8490
  "LinearVariantDisplay": [