@jbrowse/cli 5.0.0-beta.10 → 5.0.0-beta.13

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 (15) hide show
  1. package/README.md +6 -6
  2. package/dist/commands/add-track-utils/adapter-utils.js +1 -9
  3. package/dist/commands/add-track.js +3 -3
  4. package/dist/commands/make-density/index.js +1 -1
  5. package/dist/commands/validate/configManifest.generated.js +236 -67
  6. package/dist/commands/validate/configSchema.generated.js +8632 -2974
  7. package/dist/commands/validate/index.js +1 -1
  8. package/dist/commands/validate/markRules/colorScale.js +33 -2
  9. package/dist/commands/validate/markRules/markProblems.js +62 -21
  10. package/dist/commands/validate/markRules/markSpecs.js +6 -18
  11. package/dist/commands/validate/markRules/markVocabulary.js +3 -1
  12. package/dist/commands/validate/schemaValidate.js +2 -2
  13. package/dist/commands/validate/validateConfig.js +25 -24
  14. package/dist/version.js +1 -1
  15. package/package.json +4 -4
package/dist/commands/validate/configManifest.generated.js CHANGED
@@ -981,7 +981,7 @@ export const configManifest = {
981
981
  },
982
982
  {
983
983
  "name": "bigWigs",
984
- "type": "frozen"
984
+ "type": "string[]"
985
985
  },
986
986
  {
987
987
  "name": "baseUri",
@@ -2757,7 +2757,8 @@ export const configManifest = {
2757
2757
  "DotplotDisplay",
2758
2758
  "LinearSyntenyDisplay",
2759
2759
  "LGVSyntenyDisplay",
2760
- "MultiWaySyntenyDisplay"
2760
+ "MultiWaySyntenyDisplay",
2761
+ "LinearMarkDisplay"
2761
2762
  ]
2762
2763
  },
2763
2764
  "GWASTrack": {
@@ -3124,7 +3125,6 @@ export const configManifest = {
3124
3125
  "id",
3125
3126
  "type",
3126
3127
  "configuration",
3127
- "filterSetting",
3128
3128
  "pinnedFeatureIds",
3129
3129
  "soloFeatureIds",
3130
3130
  "soloApplied",
@@ -3281,10 +3281,6 @@ export const configManifest = {
3281
3281
  "name": "field",
3282
3282
  "type": "string"
3283
3283
  },
3284
- {
3285
- "name": "scale",
3286
- "type": "(RowColorScale | undefined)"
3287
- },
3288
3284
  {
3289
3285
  "name": "domain",
3290
3286
  "type": "string[]",
@@ -3293,6 +3289,10 @@ export const configManifest = {
3293
3289
  {
3294
3290
  "name": "range",
3295
3291
  "type": "CssColorEntry[]"
3292
+ },
3293
+ {
3294
+ "name": "unknown",
3295
+ "type": "(CssColor | undefined)"
3296
3296
  }
3297
3297
  ],
3298
3298
  "shorthand": {
@@ -3319,10 +3319,6 @@ export const configManifest = {
3319
3319
  "name": "densityTierBpPerPx",
3320
3320
  "type": "number"
3321
3321
  },
3322
- {
3323
- "name": "colorRowLabels",
3324
- "type": "boolean"
3325
- },
3326
3322
  {
3327
3323
  "name": "showLegend",
3328
3324
  "type": "boolean"
@@ -3690,8 +3686,8 @@ export const configManifest = {
3690
3686
  "type": "(frozen | undefined)"
3691
3687
  },
3692
3688
  {
3693
- "name": "linkedReads",
3694
- "type": "LinkedReadsMode"
3689
+ "name": "unit",
3690
+ "type": "AlignmentsUnit"
3695
3691
  },
3696
3692
  {
3697
3693
  "name": "showBezierConnections",
@@ -3792,7 +3788,8 @@ export const configManifest = {
3792
3788
  }
3793
3789
  ],
3794
3790
  "legacyKeys": [
3795
- "colorBy"
3791
+ "colorBy",
3792
+ "linkedReads"
3796
3793
  ],
3797
3794
  "aliases": [
3798
3795
  "LinearPileupDisplay",
@@ -4124,7 +4121,8 @@ export const configManifest = {
4124
4121
  "*": {
4125
4122
  "scale": "categorical"
4126
4123
  }
4127
- }
4124
+ },
4125
+ "fieldDefault": "strand"
4128
4126
  },
4129
4127
  {
4130
4128
  "name": "baseColor",
@@ -4271,8 +4269,8 @@ export const configManifest = {
4271
4269
  "type": "(frozen | undefined)"
4272
4270
  },
4273
4271
  {
4274
- "name": "linkedReads",
4275
- "type": "LinkedReadsMode"
4272
+ "name": "unit",
4273
+ "type": "AlignmentsUnit"
4276
4274
  },
4277
4275
  {
4278
4276
  "name": "showBezierConnections",
@@ -4381,7 +4379,8 @@ export const configManifest = {
4381
4379
  }
4382
4380
  ],
4383
4381
  "legacyKeys": [
4384
- "colorBy"
4382
+ "colorBy",
4383
+ "linkedReads"
4385
4384
  ],
4386
4385
  "stateModelProps": [
4387
4386
  "id",
@@ -5101,7 +5100,6 @@ export const configManifest = {
5101
5100
  "id",
5102
5101
  "type",
5103
5102
  "configuration",
5104
- "filterSetting",
5105
5103
  "pinnedFeatureIds",
5106
5104
  "soloFeatureIds",
5107
5105
  "soloApplied",
@@ -5205,8 +5203,8 @@ export const configManifest = {
5205
5203
  "type": "boolean"
5206
5204
  },
5207
5205
  {
5208
- "name": "renderingMode",
5209
- "type": "RenderingMode"
5206
+ "name": "unit",
5207
+ "type": "VariantUnit"
5210
5208
  },
5211
5209
  {
5212
5210
  "name": "color",
@@ -5276,10 +5274,6 @@ export const configManifest = {
5276
5274
  "name": "field",
5277
5275
  "type": "string"
5278
5276
  },
5279
- {
5280
- "name": "scale",
5281
- "type": "(RowColorScale | undefined)"
5282
- },
5283
5277
  {
5284
5278
  "name": "domain",
5285
5279
  "type": "string[]",
@@ -5288,6 +5282,10 @@ export const configManifest = {
5288
5282
  {
5289
5283
  "name": "range",
5290
5284
  "type": "CssColorEntry[]"
5285
+ },
5286
+ {
5287
+ "name": "unknown",
5288
+ "type": "(CssColor | undefined)"
5291
5289
  }
5292
5290
  ],
5293
5291
  "shorthand": {
@@ -5334,7 +5332,8 @@ export const configManifest = {
5334
5332
  }
5335
5333
  ],
5336
5334
  "legacyKeys": [
5337
- "jexlFilters"
5335
+ "jexlFilters",
5336
+ "renderingMode"
5338
5337
  ],
5339
5338
  "aliases": [
5340
5339
  "MultiLinearVariantDisplay",
@@ -5346,8 +5345,7 @@ export const configManifest = {
5346
5345
  "runClustering",
5347
5346
  "clusterRegion",
5348
5347
  "sortRowsBy",
5349
- "configuration",
5350
- "filterSetting"
5348
+ "configuration"
5351
5349
  ]
5352
5350
  },
5353
5351
  "LDTrackDisplay": {
@@ -5377,8 +5375,47 @@ export const configManifest = {
5377
5375
  "type": "number"
5378
5376
  },
5379
5377
  {
5380
- "name": "ldMetric",
5381
- "type": "LDMetric"
5378
+ "name": "color",
5379
+ "type": "LDColorConfigurationSchema",
5380
+ "subSlots": [
5381
+ {
5382
+ "name": "field",
5383
+ "type": "LDColorField"
5384
+ },
5385
+ {
5386
+ "name": "scheme",
5387
+ "type": "(ColorScheme | undefined)"
5388
+ },
5389
+ {
5390
+ "name": "reverse",
5391
+ "type": "(boolean | undefined)"
5392
+ },
5393
+ {
5394
+ "name": "domainMin",
5395
+ "type": "(number | undefined)"
5396
+ },
5397
+ {
5398
+ "name": "domainMax",
5399
+ "type": "(number | undefined)"
5400
+ },
5401
+ {
5402
+ "name": "scale",
5403
+ "type": "(LDColorScale | undefined)"
5404
+ }
5405
+ ],
5406
+ "fieldPresets": {
5407
+ "r2": {
5408
+ "scale": "linear",
5409
+ "scheme": "reds",
5410
+ "title": "R²"
5411
+ },
5412
+ "dprime": {
5413
+ "scale": "linear",
5414
+ "scheme": "blues",
5415
+ "title": "D'"
5416
+ }
5417
+ },
5418
+ "fieldDefault": "r2"
5382
5419
  },
5383
5420
  {
5384
5421
  "name": "maxVariantSeparation",
@@ -5401,6 +5438,9 @@ export const configManifest = {
5401
5438
  "type": "VariantLayout"
5402
5439
  }
5403
5440
  ],
5441
+ "legacyKeys": [
5442
+ "ldMetric"
5443
+ ],
5404
5444
  "stateModelProps": [
5405
5445
  "id",
5406
5446
  "type",
@@ -5468,10 +5508,6 @@ export const configManifest = {
5468
5508
  "name": "field",
5469
5509
  "type": "string"
5470
5510
  },
5471
- {
5472
- "name": "scale",
5473
- "type": "(RowColorScale | undefined)"
5474
- },
5475
5511
  {
5476
5512
  "name": "domain",
5477
5513
  "type": "string[]",
@@ -5480,6 +5516,10 @@ export const configManifest = {
5480
5516
  {
5481
5517
  "name": "range",
5482
5518
  "type": "CssColorEntry[]"
5519
+ },
5520
+ {
5521
+ "name": "unknown",
5522
+ "type": "(CssColor | undefined)"
5483
5523
  }
5484
5524
  ],
5485
5525
  "shorthand": {
@@ -5541,9 +5581,6 @@ export const configManifest = {
5541
5581
  "string": "value"
5542
5582
  },
5543
5583
  "fieldPresets": {
5544
- "source": {
5545
- "scale": "categorical"
5546
- },
5547
5584
  "*": {
5548
5585
  "scale": "threshold"
5549
5586
  }
@@ -5739,11 +5776,123 @@ export const configManifest = {
5739
5776
  {
5740
5777
  "name": "field",
5741
5778
  "type": "MafColorField"
5779
+ },
5780
+ {
5781
+ "name": "domain",
5782
+ "type": "string[]",
5783
+ "liftsNumbers": true
5784
+ },
5785
+ {
5786
+ "name": "range",
5787
+ "type": "CssColorEntry[]"
5788
+ },
5789
+ {
5790
+ "name": "labels",
5791
+ "type": "string[]",
5792
+ "liftsNumbers": true
5793
+ },
5794
+ {
5795
+ "name": "title",
5796
+ "type": "(string | undefined)"
5797
+ },
5798
+ {
5799
+ "name": "scheme",
5800
+ "type": "(ColorScheme | undefined)"
5801
+ },
5802
+ {
5803
+ "name": "reverse",
5804
+ "type": "boolean"
5805
+ },
5806
+ {
5807
+ "name": "domainMin",
5808
+ "type": "(number | undefined)"
5809
+ },
5810
+ {
5811
+ "name": "domainMax",
5812
+ "type": "(number | undefined)"
5813
+ },
5814
+ {
5815
+ "name": "domainMid",
5816
+ "type": "(number | undefined)"
5742
5817
  }
5743
5818
  ],
5744
5819
  "shorthand": {
5745
5820
  "string": "field"
5746
- }
5821
+ },
5822
+ "fieldPresets": {
5823
+ "mismatch": {
5824
+ "scale": "categorical",
5825
+ "domain": [
5826
+ "A",
5827
+ "C",
5828
+ "G",
5829
+ "T",
5830
+ "N",
5831
+ "gap",
5832
+ "match"
5833
+ ],
5834
+ "title": "Mismatch to reference"
5835
+ },
5836
+ "base": {
5837
+ "scale": "categorical",
5838
+ "domain": [
5839
+ "A",
5840
+ "C",
5841
+ "G",
5842
+ "T",
5843
+ "N",
5844
+ "gap"
5845
+ ],
5846
+ "title": "Base"
5847
+ },
5848
+ "identity": {
5849
+ "scale": "linear",
5850
+ "domainMin": 0,
5851
+ "domainMax": 1,
5852
+ "scheme": "redgreyblue",
5853
+ "title": "Per-base identity to reference"
5854
+ },
5855
+ "chromosome": {
5856
+ "scale": "categorical",
5857
+ "domain": [
5858
+ "0",
5859
+ "1",
5860
+ "2",
5861
+ "3",
5862
+ "4"
5863
+ ],
5864
+ "range": [
5865
+ "hsl(210, 55%, 55%)",
5866
+ "hsl(28, 85%, 55%)",
5867
+ "hsl(350, 70%, 57%)",
5868
+ "hsl(275, 45%, 58%)",
5869
+ "hsl(150, 45%, 42%)"
5870
+ ],
5871
+ "labels": [
5872
+ "Main chromosome",
5873
+ "2nd source",
5874
+ "3rd source",
5875
+ "4th source",
5876
+ "Other source"
5877
+ ],
5878
+ "title": "Source chromosome"
5879
+ },
5880
+ "codon": {
5881
+ "scale": "categorical",
5882
+ "domain": [
5883
+ "nonsyn",
5884
+ "syn",
5885
+ "stop"
5886
+ ],
5887
+ "labels": [
5888
+ "Nonsynonymous",
5889
+ "Synonymous",
5890
+ "Stop gained"
5891
+ ],
5892
+ "title": "Codon change"
5893
+ }
5894
+ },
5895
+ "fieldDefault": "mismatch"
5747
5896
  },
5748
5897
  {
5749
5898
  "name": "y",
@@ -5805,10 +5954,6 @@ export const configManifest = {
5805
5954
  "name": "field",
5806
5955
  "type": "string"
5807
5956
  },
5808
- {
5809
- "name": "scale",
5810
- "type": "(RowColorScale | undefined)"
5811
- },
5812
5957
  {
5813
5958
  "name": "domain",
5814
5959
  "type": "string[]",
@@ -5817,6 +5962,10 @@ export const configManifest = {
5817
5962
  {
5818
5963
  "name": "range",
5819
5964
  "type": "CssColorEntry[]"
5965
+ },
5966
+ {
5967
+ "name": "unknown",
5968
+ "type": "(CssColor | undefined)"
5820
5969
  }
5821
5970
  ],
5822
5971
  "shorthand": {
@@ -5904,8 +6053,8 @@ export const configManifest = {
5904
6053
  "type": "HicColorConfigurationSchema",
5905
6054
  "subSlots": [
5906
6055
  {
5907
- "name": "scale",
5908
- "type": "HicColorScale"
6056
+ "name": "field",
6057
+ "type": "HicColorField"
5909
6058
  },
5910
6059
  {
5911
6060
  "name": "scheme",
@@ -5919,15 +6068,25 @@ export const configManifest = {
5919
6068
  "name": "domainMin",
5920
6069
  "type": "(number | undefined)"
5921
6070
  },
5922
- {
5923
- "name": "domainMax",
5924
- "type": "(number | undefined)"
5925
- },
5926
6071
  {
5927
6072
  "name": "domainQuantile",
5928
6073
  "type": "number"
6074
+ },
6075
+ {
6076
+ "name": "scale",
6077
+ "type": "(HicColorScale | undefined)"
6078
+ },
6079
+ {
6080
+ "name": "domainMax",
6081
+ "type": "(number | undefined)"
5929
6082
  }
5930
- ]
6083
+ ],
6084
+ "fieldPresets": {
6085
+ "count": {
6086
+ "scale": "linear"
6087
+ }
6088
+ },
6089
+ "fieldDefault": "count"
5931
6090
  },
5932
6091
  {
5933
6092
  "name": "resolutionBias",
@@ -6302,10 +6461,6 @@ export const configManifest = {
6302
6461
  "name": "field",
6303
6462
  "type": "string"
6304
6463
  },
6305
- {
6306
- "name": "scale",
6307
- "type": "(RowColorScale | undefined)"
6308
- },
6309
6464
  {
6310
6465
  "name": "domain",
6311
6466
  "type": "string[]",
@@ -6314,6 +6469,10 @@ export const configManifest = {
6314
6469
  {
6315
6470
  "name": "range",
6316
6471
  "type": "CssColorEntry[]"
6472
+ },
6473
+ {
6474
+ "name": "unknown",
6475
+ "type": "(CssColor | undefined)"
6317
6476
  }
6318
6477
  ],
6319
6478
  "shorthand": {
@@ -6442,7 +6601,6 @@ export const configManifest = {
6442
6601
  "clusterRegion",
6443
6602
  "sortRowsBy",
6444
6603
  "configuration",
6445
- "filterSetting",
6446
6604
  "indexSnp",
6447
6605
  "indexSnpPinned"
6448
6606
  ]
@@ -6790,10 +6948,6 @@ export const configManifest = {
6790
6948
  "name": "field",
6791
6949
  "type": "string"
6792
6950
  },
6793
- {
6794
- "name": "scale",
6795
- "type": "(RowColorScale | undefined)"
6796
- },
6797
6951
  {
6798
6952
  "name": "domain",
6799
6953
  "type": "string[]",
@@ -6802,6 +6956,10 @@ export const configManifest = {
6802
6956
  {
6803
6957
  "name": "range",
6804
6958
  "type": "CssColorEntry[]"
6959
+ },
6960
+ {
6961
+ "name": "unknown",
6962
+ "type": "(CssColor | undefined)"
6805
6963
  }
6806
6964
  ],
6807
6965
  "shorthand": {
@@ -6923,14 +7081,17 @@ export const configManifest = {
6923
7081
  "minimalTicks",
6924
7082
  "jexlFilters"
6925
7083
  ],
7084
+ "aliases": [
7085
+ "LinearArcDisplay",
7086
+ "LinearPairedArcDisplay"
7087
+ ],
6926
7088
  "stateModelProps": [
6927
7089
  "id",
6928
7090
  "type",
6929
7091
  "runClustering",
6930
7092
  "clusterRegion",
6931
7093
  "sortRowsBy",
6932
- "configuration",
6933
- "filterSetting"
7094
+ "configuration"
6934
7095
  ]
6935
7096
  }
6936
7097
  },
@@ -6947,11 +7108,11 @@ export const configManifest = {
6947
7108
  },
6948
7109
  {
6949
7110
  "name": "ixFilePath",
6950
- "type": "(LocalPathLocation | UriLocation | BlobLocation | FileHandleLocation)"
7111
+ "type": "((LocalPathLocation | UriLocation | BlobLocation | FileHandleLocation) | undefined)"
6951
7112
  },
6952
7113
  {
6953
7114
  "name": "ixxFilePath",
6954
- "type": "(LocalPathLocation | UriLocation | BlobLocation | FileHandleLocation)"
7115
+ "type": "((LocalPathLocation | UriLocation | BlobLocation | FileHandleLocation) | undefined)"
6955
7116
  },
6956
7117
  {
6957
7118
  "name": "assemblyNames",
@@ -7385,9 +7546,8 @@ export const configManifest = {
7385
7546
  "color",
7386
7547
  "trackColors",
7387
7548
  "hideUnlabelled",
7388
- "alpha",
7549
+ "opacity",
7389
7550
  "minAlignmentLength",
7390
- "opacityByIdentity",
7391
7551
  "fadeThinAlignmentsMode",
7392
7552
  "type",
7393
7553
  "offsetRadians",
@@ -7422,7 +7582,7 @@ export const configManifest = {
7422
7582
  "color",
7423
7583
  "trackColors",
7424
7584
  "hideUnlabelled",
7425
- "alpha",
7585
+ "opacity",
7426
7586
  "minAlignmentLength",
7427
7587
  "lodMode",
7428
7588
  "type",
@@ -7431,6 +7591,7 @@ export const configManifest = {
7431
7591
  "assemblyNames",
7432
7592
  "drawCigar",
7433
7593
  "showGridlines",
7594
+ "showTickLabels",
7434
7595
  "lockAspectRatio",
7435
7596
  "lineWidth",
7436
7597
  "minIdentity",
@@ -7446,6 +7607,7 @@ export const configManifest = {
7446
7607
  "views"
7447
7608
  ],
7448
7609
  "passThrough": [
7610
+ "alpha",
7449
7611
  "colorBy"
7450
7612
  ]
7451
7613
  },
@@ -7457,10 +7619,9 @@ export const configManifest = {
7457
7619
  "color",
7458
7620
  "trackColors",
7459
7621
  "hideUnlabelled",
7460
- "alpha",
7622
+ "opacity",
7461
7623
  "minAlignmentLength",
7462
7624
  "lodMode",
7463
- "opacityByIdentity",
7464
7625
  "fadeThinAlignmentsMode",
7465
7626
  "type",
7466
7627
  "cigarMode",
@@ -7487,6 +7648,7 @@ export const configManifest = {
7487
7648
  "views"
7488
7649
  ],
7489
7650
  "passThrough": [
7651
+ "alpha",
7490
7652
  "colorBy"
7491
7653
  ]
7492
7654
  },
@@ -7558,6 +7720,9 @@ export const configManifest = {
7558
7720
  "*": [
7559
7721
  "heightPreConfig"
7560
7722
  ],
7723
+ "LinearBasicDisplay": [
7724
+ "jexlFiltersSetting"
7725
+ ],
7561
7726
  "LinearAlignmentsDisplay": [
7562
7727
  "PileupDisplay",
7563
7728
  "SNPCoverageDisplay",
@@ -7568,10 +7733,14 @@ export const configManifest = {
7568
7733
  "hideMismatchesSetting",
7569
7734
  "trackMaxHeight"
7570
7735
  ],
7736
+ "LinearVariantDisplay": [
7737
+ "jexlFiltersSetting"
7738
+ ],
7571
7739
  "LinearMultiSampleVariantDisplay": [
7572
7740
  "clusterTree",
7573
7741
  "jexlFilters",
7574
7742
  "layout",
7743
+ "renderingModeSetting",
7575
7744
  "showSidebarLabelsSetting",
7576
7745
  "showTreeSetting",
7577
7746
  "subtreeFilter",