@jbrowse/cli 5.0.0-beta.11 → 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 (12) hide show
  1. package/README.md +6 -6
  2. package/dist/commands/add-track.js +3 -3
  3. package/dist/commands/make-density/index.js +1 -1
  4. package/dist/commands/validate/configManifest.generated.js +221 -59
  5. package/dist/commands/validate/configSchema.generated.js +8508 -2932
  6. package/dist/commands/validate/index.js +1 -1
  7. package/dist/commands/validate/markRules/colorScale.js +33 -2
  8. package/dist/commands/validate/markRules/markVocabulary.js +1 -1
  9. package/dist/commands/validate/schemaValidate.js +2 -2
  10. package/dist/commands/validate/validateConfig.js +10 -23
  11. package/dist/version.js +1 -1
  12. package/package.json +4 -4
package/README.md CHANGED
@@ -340,14 +340,14 @@ any other appearance setting (labels, mouseover, filter).
340
340
  --multiwig bundles several BigWigs into one MultiQuantitativeTrack, in place of
341
341
  the positional track argument: pass a comma-separated list of BigWig files/URLs,
342
342
  or a .json file with an array of BigWig locations or subadapter objects (each
343
- carrying its own name/color/group). With --load, local list entries are copied
344
- like any other track file.
343
+ with its own name/color/group). With --load, local list entries are copied like
344
+ any other track file.
345
345
 
346
346
  --density attaches a features-per-bin bigWig (jbrowse make-density) as the
347
347
  adapter's densityAdapter, the band a display draws where the region is too large
348
348
  to fetch features. A local <file>.density.bw beside the track file is attached
349
349
  without the flag; a URL cannot be probed, so a remote sidecar needs it. The
350
- adapters carrying the slot are BamAdapter, CramAdapter, HtsgetBamAdapter,
350
+ adapters with the slot are BamAdapter, CramAdapter, HtsgetBamAdapter,
351
351
  Gff3TabixAdapter, GtfTabixAdapter, BedTabixAdapter, BigBedAdapter,
352
352
  VcfTabixAdapter and SplitVcfTabixAdapter.
353
353
 
@@ -382,7 +382,7 @@ $ jbrowse add-track genes.gff3.gz --load copy --color 'jexl:feature.strand==1?"b
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  # bundle several BigWigs into one MultiQuantitativeTrack (no positional track arg)
383
383
  $ jbrowse add-track --multiwig a.bw,b.bw,c.bw --load copy --name "Coverage"
384
384
 
385
- # ...or from a sources.json carrying per-row name/color for each BigWig
385
+ # ...or from a sources.json with per-row name/color for each BigWig
386
386
  $ jbrowse add-track --multiwig sources.json --name "CATlas ATAC"
387
387
 
388
388
  # attach a remote density sidecar (a local genes.gff3.density.bw needs no flag)
@@ -429,7 +429,7 @@ what it cannot draw in a corner notice rather than refusing the track. This
429
429
  command runs the display's own rule list over every "marks" list in the file: an
430
430
  error where a mark draws nothing, never draws or a step cannot run, and a
431
431
  warning where a slot waits unread or the marks draw in an arrangement the author
432
- may not have meant. With --json each finding carries the stable "rule" id of the
432
+ may not have meant. With --json each finding has the stable "rule" id of the
433
433
  rule that made it.
434
434
 
435
435
  Types registered by plugins are not known to this command, so they come through
@@ -756,7 +756,7 @@ SplitVcfTabixAdapter declare. add-track attaches it on its own when the default
756
756
  <file>.density.bw sits beside the track file, so building it before adding the
757
757
  track is all it takes; --density attaches one by path or URL.
758
758
 
759
- GFF3 counts only top-level features — a line whose attributes carry no Parent= —
759
+ GFF3 counts only top-level features — a line whose attributes have no Parent= —
760
760
  so a gene is one count rather than one per exon. GTF, BED and VCF have no parent
761
761
  link to follow, so every record counts.
762
762
 
package/dist/commands/add-track.js CHANGED
@@ -136,13 +136,13 @@ export async function run(args) {
136
136
  '--multiwig bundles several BigWigs into one MultiQuantitativeTrack, in ' +
137
137
  'place of the positional track argument: pass a comma-separated list of ' +
138
138
  'BigWig files/URLs, or a .json file with an array of BigWig locations or ' +
139
- 'subadapter objects (each carrying its own name/color/group). With --load, ' +
139
+ 'subadapter objects (each with its own name/color/group). With --load, ' +
140
140
  'local list entries are copied like any other track file.\n\n' +
141
141
  '--density attaches a features-per-bin bigWig (jbrowse make-density) as the ' +
142
142
  "adapter's densityAdapter, the band a display draws where the region is too " +
143
143
  'large to fetch features. A local <file>.density.bw beside the track file is ' +
144
144
  'attached without the flag; a URL cannot be probed, so a remote sidecar needs ' +
145
- 'it. The adapters carrying the slot are BamAdapter, CramAdapter, ' +
145
+ 'it. The adapters with the slot are BamAdapter, CramAdapter, ' +
146
146
  'HtsgetBamAdapter, Gff3TabixAdapter, GtfTabixAdapter, BedTabixAdapter, ' +
147
147
  'BigBedAdapter, VcfTabixAdapter and SplitVcfTabixAdapter.\n\n' +
148
148
  'For pairwise synteny adapters (PAF/Delta/Chain) --assemblyNames is ' +
@@ -174,7 +174,7 @@ export async function run(args) {
174
174
  '# bundle several BigWigs into one MultiQuantitativeTrack (no positional track arg)',
175
175
  '$ jbrowse add-track --multiwig a.bw,b.bw,c.bw --load copy --name "Coverage"',
176
176
  '',
177
- '# ...or from a sources.json carrying per-row name/color for each BigWig',
177
+ '# ...or from a sources.json with per-row name/color for each BigWig',
178
178
  '$ jbrowse add-track --multiwig sources.json --name "CATlas ATAC"',
179
179
  '',
180
180
  '# attach a remote density sidecar (a local genes.gff3.density.bw needs no flag)',
package/dist/commands/make-density/index.js CHANGED
@@ -46,7 +46,7 @@ export async function run(args) {
46
46
  'SplitVcfTabixAdapter declare. add-track attaches it on its own when the ' +
47
47
  'default <file>.density.bw sits beside the track file, so building it before ' +
48
48
  'adding the track is all it takes; --density attaches one by path or URL.\n\n' +
49
- 'GFF3 counts only top-level features — a line whose attributes carry no ' +
49
+ 'GFF3 counts only top-level features — a line whose attributes have no ' +
50
50
  'Parent= — so a gene is one count rather than one per exon. GTF, BED and VCF ' +
51
51
  'have no parent link to follow, so every record counts.\n\n' +
52
52
  'BAM and CRAM are out of scope: read depth is not feature density, and the ' +
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",
@@ -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",
@@ -5204,8 +5203,8 @@ export const configManifest = {
5204
5203
  "type": "boolean"
5205
5204
  },
5206
5205
  {
5207
- "name": "renderingMode",
5208
- "type": "RenderingMode"
5206
+ "name": "unit",
5207
+ "type": "VariantUnit"
5209
5208
  },
5210
5209
  {
5211
5210
  "name": "color",
@@ -5275,10 +5274,6 @@ export const configManifest = {
5275
5274
  "name": "field",
5276
5275
  "type": "string"
5277
5276
  },
5278
- {
5279
- "name": "scale",
5280
- "type": "(RowColorScale | undefined)"
5281
- },
5282
5277
  {
5283
5278
  "name": "domain",
5284
5279
  "type": "string[]",
@@ -5287,6 +5282,10 @@ export const configManifest = {
5287
5282
  {
5288
5283
  "name": "range",
5289
5284
  "type": "CssColorEntry[]"
5285
+ },
5286
+ {
5287
+ "name": "unknown",
5288
+ "type": "(CssColor | undefined)"
5290
5289
  }
5291
5290
  ],
5292
5291
  "shorthand": {
@@ -5333,7 +5332,8 @@ export const configManifest = {
5333
5332
  }
5334
5333
  ],
5335
5334
  "legacyKeys": [
5336
- "jexlFilters"
5335
+ "jexlFilters",
5336
+ "renderingMode"
5337
5337
  ],
5338
5338
  "aliases": [
5339
5339
  "MultiLinearVariantDisplay",
@@ -5375,8 +5375,47 @@ export const configManifest = {
5375
5375
  "type": "number"
5376
5376
  },
5377
5377
  {
5378
- "name": "ldMetric",
5379
- "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"
5380
5419
  },
5381
5420
  {
5382
5421
  "name": "maxVariantSeparation",
@@ -5399,6 +5438,9 @@ export const configManifest = {
5399
5438
  "type": "VariantLayout"
5400
5439
  }
5401
5440
  ],
5441
+ "legacyKeys": [
5442
+ "ldMetric"
5443
+ ],
5402
5444
  "stateModelProps": [
5403
5445
  "id",
5404
5446
  "type",
@@ -5466,10 +5508,6 @@ export const configManifest = {
5466
5508
  "name": "field",
5467
5509
  "type": "string"
5468
5510
  },
5469
- {
5470
- "name": "scale",
5471
- "type": "(RowColorScale | undefined)"
5472
- },
5473
5511
  {
5474
5512
  "name": "domain",
5475
5513
  "type": "string[]",
@@ -5478,6 +5516,10 @@ export const configManifest = {
5478
5516
  {
5479
5517
  "name": "range",
5480
5518
  "type": "CssColorEntry[]"
5519
+ },
5520
+ {
5521
+ "name": "unknown",
5522
+ "type": "(CssColor | undefined)"
5481
5523
  }
5482
5524
  ],
5483
5525
  "shorthand": {
@@ -5539,9 +5581,6 @@ export const configManifest = {
5539
5581
  "string": "value"
5540
5582
  },
5541
5583
  "fieldPresets": {
5542
- "source": {
5543
- "scale": "categorical"
5544
- },
5545
5584
  "*": {
5546
5585
  "scale": "threshold"
5547
5586
  }
@@ -5737,11 +5776,123 @@ export const configManifest = {
5737
5776
  {
5738
5777
  "name": "field",
5739
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)"
5740
5817
  }
5741
5818
  ],
5742
5819
  "shorthand": {
5743
5820
  "string": "field"
5744
- }
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"
5745
5896
  },
5746
5897
  {
5747
5898
  "name": "y",
@@ -5803,10 +5954,6 @@ export const configManifest = {
5803
5954
  "name": "field",
5804
5955
  "type": "string"
5805
5956
  },
5806
- {
5807
- "name": "scale",
5808
- "type": "(RowColorScale | undefined)"
5809
- },
5810
5957
  {
5811
5958
  "name": "domain",
5812
5959
  "type": "string[]",
@@ -5815,6 +5962,10 @@ export const configManifest = {
5815
5962
  {
5816
5963
  "name": "range",
5817
5964
  "type": "CssColorEntry[]"
5965
+ },
5966
+ {
5967
+ "name": "unknown",
5968
+ "type": "(CssColor | undefined)"
5818
5969
  }
5819
5970
  ],
5820
5971
  "shorthand": {
@@ -5902,8 +6053,8 @@ export const configManifest = {
5902
6053
  "type": "HicColorConfigurationSchema",
5903
6054
  "subSlots": [
5904
6055
  {
5905
- "name": "scale",
5906
- "type": "HicColorScale"
6056
+ "name": "field",
6057
+ "type": "HicColorField"
5907
6058
  },
5908
6059
  {
5909
6060
  "name": "scheme",
@@ -5917,15 +6068,25 @@ export const configManifest = {
5917
6068
  "name": "domainMin",
5918
6069
  "type": "(number | undefined)"
5919
6070
  },
5920
- {
5921
- "name": "domainMax",
5922
- "type": "(number | undefined)"
5923
- },
5924
6071
  {
5925
6072
  "name": "domainQuantile",
5926
6073
  "type": "number"
6074
+ },
6075
+ {
6076
+ "name": "scale",
6077
+ "type": "(HicColorScale | undefined)"
6078
+ },
6079
+ {
6080
+ "name": "domainMax",
6081
+ "type": "(number | undefined)"
5927
6082
  }
5928
- ]
6083
+ ],
6084
+ "fieldPresets": {
6085
+ "count": {
6086
+ "scale": "linear"
6087
+ }
6088
+ },
6089
+ "fieldDefault": "count"
5929
6090
  },
5930
6091
  {
5931
6092
  "name": "resolutionBias",
@@ -6300,10 +6461,6 @@ export const configManifest = {
6300
6461
  "name": "field",
6301
6462
  "type": "string"
6302
6463
  },
6303
- {
6304
- "name": "scale",
6305
- "type": "(RowColorScale | undefined)"
6306
- },
6307
6464
  {
6308
6465
  "name": "domain",
6309
6466
  "type": "string[]",
@@ -6312,6 +6469,10 @@ export const configManifest = {
6312
6469
  {
6313
6470
  "name": "range",
6314
6471
  "type": "CssColorEntry[]"
6472
+ },
6473
+ {
6474
+ "name": "unknown",
6475
+ "type": "(CssColor | undefined)"
6315
6476
  }
6316
6477
  ],
6317
6478
  "shorthand": {
@@ -6787,10 +6948,6 @@ export const configManifest = {
6787
6948
  "name": "field",
6788
6949
  "type": "string"
6789
6950
  },
6790
- {
6791
- "name": "scale",
6792
- "type": "(RowColorScale | undefined)"
6793
- },
6794
6951
  {
6795
6952
  "name": "domain",
6796
6953
  "type": "string[]",
@@ -6799,6 +6956,10 @@ export const configManifest = {
6799
6956
  {
6800
6957
  "name": "range",
6801
6958
  "type": "CssColorEntry[]"
6959
+ },
6960
+ {
6961
+ "name": "unknown",
6962
+ "type": "(CssColor | undefined)"
6802
6963
  }
6803
6964
  ],
6804
6965
  "shorthand": {
@@ -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",
@@ -7447,6 +7607,7 @@ export const configManifest = {
7447
7607
  "views"
7448
7608
  ],
7449
7609
  "passThrough": [
7610
+ "alpha",
7450
7611
  "colorBy"
7451
7612
  ]
7452
7613
  },
@@ -7458,10 +7619,9 @@ export const configManifest = {
7458
7619
  "color",
7459
7620
  "trackColors",
7460
7621
  "hideUnlabelled",
7461
- "alpha",
7622
+ "opacity",
7462
7623
  "minAlignmentLength",
7463
7624
  "lodMode",
7464
- "opacityByIdentity",
7465
7625
  "fadeThinAlignmentsMode",
7466
7626
  "type",
7467
7627
  "cigarMode",
@@ -7488,6 +7648,7 @@ export const configManifest = {
7488
7648
  "views"
7489
7649
  ],
7490
7650
  "passThrough": [
7651
+ "alpha",
7491
7652
  "colorBy"
7492
7653
  ]
7493
7654
  },
@@ -7579,6 +7740,7 @@ export const configManifest = {
7579
7740
  "clusterTree",
7580
7741
  "jexlFilters",
7581
7742
  "layout",
7743
+ "renderingModeSetting",
7582
7744
  "showSidebarLabelsSetting",
7583
7745
  "showTreeSetting",
7584
7746
  "subtreeFilter",