@jbrowse/cli 5.0.0-beta.11 → 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.
- package/README.md +23 -42
- package/dist/commands/add-track-utils/adapter-utils.js +0 -45
- package/dist/commands/add-track.js +7 -30
- package/dist/commands/make-density/density-generator.js +1 -1
- package/dist/commands/make-density/index.js +14 -26
- package/dist/commands/make-pif/index.js +1 -1
- package/dist/commands/text-index/file-list.js +1 -1
- package/dist/commands/validate/configManifest.generated.js +1242 -326
- package/dist/commands/validate/configSchema.generated.js +11066 -3708
- package/dist/commands/validate/index.js +5 -4
- package/dist/commands/validate/markRules/colorScale.js +157 -28
- package/dist/commands/validate/markRules/markProblems.js +49 -99
- package/dist/commands/validate/markRules/markRuleFacts.js +1 -1
- package/dist/commands/validate/markRules/markSpecs.js +4 -2
- package/dist/commands/validate/markRules/markVocabulary.js +21 -24
- package/dist/commands/validate/markRules/stepChannels.js +13 -47
- package/dist/commands/validate/markRules/stepOutputs.js +202 -0
- package/dist/commands/validate/schemaValidate.js +7 -4
- package/dist/commands/validate/validateConfig.js +54 -33
- package/dist/index.js +1 -1
- package/dist/version.js +1 -1
- package/package.json +4 -4
- package/dist/commands/shared/density.js +0 -12
- package/dist/commands/validate/markRules/aggregateFieldName.js +0 -9
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@@ -11,6 +11,9 @@ export const configManifest = {
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"type": "((LocalPathLocation | UriLocation | BlobLocation | FileHandleLocation) | undefined)"
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}
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"legacyKeys": [
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"cytobandsLocation"
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"shorthandKeys": [
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"uri",
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"baseUri"
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"name": "fetchSizeLimit",
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"type": "number"
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{
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"name": "densityAdapter",
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"type": "(frozen | undefined)"
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"name": "useSliceWorkerPool",
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"type": "boolean"
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"type": "(LocalPathLocation | UriLocation | BlobLocation | FileHandleLocation)"
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"legacyKeys": [
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"droppedKeys": [
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"shorthandKeys": [
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"uri",
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"baseUri"
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"name": "fetchSizeLimit",
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"type": "number"
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{
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"name": "densityAdapter",
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"type": "(frozen | undefined)"
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"legacyKeys": [
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"chunkSizeLimit"
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"droppedKeys": [
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"sequenceAdapter",
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"chunkSizeLimit"
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{
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"name": "htsgetTrackId",
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"type": "string"
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"name": "densityAdapter",
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"legacyKeys": [
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"BigBedAdapter": {
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"name": "disableGeneHeuristic",
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"type": "boolean"
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"name": "disableGeneHeuristic",
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"FromConfigRegionsAdapter": {
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"FromConfigSequenceAdapter": {
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"RefNameAliasAdapter": {
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"name": "aggregateField",
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"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": "
|
|
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": "
|
|
3177
|
+
"type": "string"
|
|
3041
3178
|
},
|
|
3042
3179
|
{
|
|
3043
3180
|
"name": "description",
|
|
3044
|
-
"type": "
|
|
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",
|
|
@@ -3281,10 +3418,6 @@ export const configManifest = {
|
|
|
3281
3418
|
"name": "field",
|
|
3282
3419
|
"type": "string"
|
|
3283
3420
|
},
|
|
3284
|
-
{
|
|
3285
|
-
"name": "scale",
|
|
3286
|
-
"type": "(RowColorScale | undefined)"
|
|
3287
|
-
},
|
|
3288
3421
|
{
|
|
3289
3422
|
"name": "domain",
|
|
3290
3423
|
"type": "string[]",
|
|
@@ -3293,16 +3426,16 @@ export const configManifest = {
|
|
|
3293
3426
|
{
|
|
3294
3427
|
"name": "range",
|
|
3295
3428
|
"type": "CssColorEntry[]"
|
|
3429
|
+
},
|
|
3430
|
+
{
|
|
3431
|
+
"name": "unknown",
|
|
3432
|
+
"type": "(CssColor | undefined)"
|
|
3296
3433
|
}
|
|
3297
3434
|
],
|
|
3298
3435
|
"shorthand": {
|
|
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"
|
|
@@ -3311,25 +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
|
-
{
|
|
3323
|
-
"name": "colorRowLabels",
|
|
3324
|
-
"type": "boolean"
|
|
3325
|
-
},
|
|
3326
3447
|
{
|
|
3327
3448
|
"name": "showLegend",
|
|
3328
3449
|
"type": "boolean"
|
|
3329
3450
|
},
|
|
3330
3451
|
{
|
|
3331
3452
|
"name": "rowGroups",
|
|
3332
|
-
"type": "
|
|
3453
|
+
"type": "RowGroupConfigurationSchema[]",
|
|
3454
|
+
"subSlots": [
|
|
3455
|
+
{
|
|
3456
|
+
"name": "match",
|
|
3457
|
+
"type": "string"
|
|
3458
|
+
},
|
|
3459
|
+
{
|
|
3460
|
+
"name": "group",
|
|
3461
|
+
"type": "string"
|
|
3462
|
+
}
|
|
3463
|
+
]
|
|
3333
3464
|
},
|
|
3334
3465
|
{
|
|
3335
3466
|
"name": "facet",
|
|
@@ -3366,6 +3497,18 @@ export const configManifest = {
|
|
|
3366
3497
|
"type": "number"
|
|
3367
3498
|
}
|
|
3368
3499
|
],
|
|
3500
|
+
"legacyKeys": [
|
|
3501
|
+
"maxFeatureScreenDensity",
|
|
3502
|
+
"maxDisplayedBpPerPx",
|
|
3503
|
+
"mouseover",
|
|
3504
|
+
"jexlFilters"
|
|
3505
|
+
],
|
|
3506
|
+
"droppedKeys": [
|
|
3507
|
+
"maxFeatureScreenDensity",
|
|
3508
|
+
"maxDisplayedBpPerPx",
|
|
3509
|
+
"fetchSizeLimit",
|
|
3510
|
+
"mouseover"
|
|
3511
|
+
],
|
|
3369
3512
|
"stateModelProps": [
|
|
3370
3513
|
"id",
|
|
3371
3514
|
"type",
|
|
@@ -3398,10 +3541,6 @@ export const configManifest = {
|
|
|
3398
3541
|
"name": "height",
|
|
3399
3542
|
"type": "number"
|
|
3400
3543
|
},
|
|
3401
|
-
{
|
|
3402
|
-
"name": "mouseover",
|
|
3403
|
-
"type": "(JexlString | string)"
|
|
3404
|
-
},
|
|
3405
3544
|
{
|
|
3406
3545
|
"name": "featureHeight",
|
|
3407
3546
|
"type": "number"
|
|
@@ -3414,14 +3553,6 @@ export const configManifest = {
|
|
|
3414
3553
|
"name": "growMaxHeight",
|
|
3415
3554
|
"type": "number"
|
|
3416
3555
|
},
|
|
3417
|
-
{
|
|
3418
|
-
"name": "densityTier",
|
|
3419
|
-
"type": "Density tier"
|
|
3420
|
-
},
|
|
3421
|
-
{
|
|
3422
|
-
"name": "densityTierBpPerPx",
|
|
3423
|
-
"type": "number"
|
|
3424
|
-
},
|
|
3425
3556
|
{
|
|
3426
3557
|
"name": "readConnectionsLineWidth",
|
|
3427
3558
|
"type": "number"
|
|
@@ -3431,7 +3562,7 @@ export const configManifest = {
|
|
|
3431
3562
|
"type": "boolean"
|
|
3432
3563
|
},
|
|
3433
3564
|
{
|
|
3434
|
-
"name": "
|
|
3565
|
+
"name": "showNonCanonicalJunctions",
|
|
3435
3566
|
"type": "boolean"
|
|
3436
3567
|
},
|
|
3437
3568
|
{
|
|
@@ -3495,6 +3626,10 @@ export const configManifest = {
|
|
|
3495
3626
|
{
|
|
3496
3627
|
"name": "title",
|
|
3497
3628
|
"type": "(string | undefined)"
|
|
3629
|
+
},
|
|
3630
|
+
{
|
|
3631
|
+
"name": "descending",
|
|
3632
|
+
"type": "(boolean | undefined)"
|
|
3498
3633
|
}
|
|
3499
3634
|
],
|
|
3500
3635
|
"shorthand": {
|
|
@@ -3509,10 +3644,21 @@ export const configManifest = {
|
|
|
3509
3644
|
]
|
|
3510
3645
|
},
|
|
3511
3646
|
"mapq": {
|
|
3512
|
-
"scale": "
|
|
3647
|
+
"scale": "threshold",
|
|
3513
3648
|
"domain": [
|
|
3514
|
-
"
|
|
3515
|
-
|
|
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
|
|
3516
3662
|
},
|
|
3517
3663
|
"insertSize": {
|
|
3518
3664
|
"scale": "threshold"
|
|
@@ -3531,7 +3677,13 @@ export const configManifest = {
|
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|
3531
3677
|
"RL",
|
|
3532
3678
|
"RR",
|
|
3533
3679
|
"LL",
|
|
3534
|
-
""
|
|
3680
|
+
"",
|
|
3681
|
+
"unmappedMate",
|
|
3682
|
+
"interchrom",
|
|
3683
|
+
"splitInverted",
|
|
3684
|
+
"splitSameStrand",
|
|
3685
|
+
"segmentInverted",
|
|
3686
|
+
"segmentSameStrand"
|
|
3535
3687
|
]
|
|
3536
3688
|
},
|
|
3537
3689
|
"insertSizeAndOrientation": {
|
|
@@ -3551,7 +3703,7 @@ export const configManifest = {
|
|
|
3551
3703
|
"subSlots": [
|
|
3552
3704
|
{
|
|
3553
3705
|
"name": "field",
|
|
3554
|
-
"type": "
|
|
3706
|
+
"type": "AlignmentsBaseColorField"
|
|
3555
3707
|
},
|
|
3556
3708
|
{
|
|
3557
3709
|
"name": "scale",
|
|
@@ -3564,15 +3716,81 @@ export const configManifest = {
|
|
|
3564
3716
|
},
|
|
3565
3717
|
{
|
|
3566
3718
|
"name": "modifications",
|
|
3567
|
-
"type": "
|
|
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
|
+
]
|
|
3568
3738
|
},
|
|
3569
3739
|
{
|
|
3570
|
-
"name": "
|
|
3571
|
-
"type": "
|
|
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
|
+
]
|
|
3572
3790
|
},
|
|
3573
3791
|
{
|
|
3574
3792
|
"name": "facet",
|
|
3575
|
-
"type": "
|
|
3793
|
+
"type": "SectionFacetConfigurationSchema",
|
|
3576
3794
|
"subSlots": [
|
|
3577
3795
|
{
|
|
3578
3796
|
"name": "field",
|
|
@@ -3582,6 +3800,11 @@ export const configManifest = {
|
|
|
3582
3800
|
"name": "domain",
|
|
3583
3801
|
"type": "string[]",
|
|
3584
3802
|
"liftsNumbers": true
|
|
3803
|
+
},
|
|
3804
|
+
{
|
|
3805
|
+
"name": "hidden",
|
|
3806
|
+
"type": "string[]",
|
|
3807
|
+
"liftsNumbers": true
|
|
3585
3808
|
}
|
|
3586
3809
|
],
|
|
3587
3810
|
"shorthand": {
|
|
@@ -3666,11 +3889,11 @@ export const configManifest = {
|
|
|
3666
3889
|
]
|
|
3667
3890
|
},
|
|
3668
3891
|
{
|
|
3669
|
-
"name": "
|
|
3892
|
+
"name": "fadeLowQualityMismatches",
|
|
3670
3893
|
"type": "boolean"
|
|
3671
3894
|
},
|
|
3672
3895
|
{
|
|
3673
|
-
"name": "
|
|
3896
|
+
"name": "fadeLowFrequencyMismatches",
|
|
3674
3897
|
"type": "boolean"
|
|
3675
3898
|
},
|
|
3676
3899
|
{
|
|
@@ -3678,20 +3901,41 @@ export const configManifest = {
|
|
|
3678
3901
|
"type": "boolean"
|
|
3679
3902
|
},
|
|
3680
3903
|
{
|
|
3681
|
-
"name": "
|
|
3682
|
-
"type": "
|
|
3683
|
-
|
|
3684
|
-
|
|
3685
|
-
|
|
3686
|
-
|
|
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
|
+
}
|
|
3687
3931
|
},
|
|
3688
3932
|
{
|
|
3689
3933
|
"name": "showOutline",
|
|
3690
|
-
"type": "(
|
|
3934
|
+
"type": "(boolean | undefined)"
|
|
3691
3935
|
},
|
|
3692
3936
|
{
|
|
3693
|
-
"name": "
|
|
3694
|
-
"type": "
|
|
3937
|
+
"name": "unit",
|
|
3938
|
+
"type": "AlignmentsUnit"
|
|
3695
3939
|
},
|
|
3696
3940
|
{
|
|
3697
3941
|
"name": "showBezierConnections",
|
|
@@ -3722,27 +3966,19 @@ export const configManifest = {
|
|
|
3722
3966
|
"type": "boolean"
|
|
3723
3967
|
},
|
|
3724
3968
|
{
|
|
3725
|
-
"name": "
|
|
3969
|
+
"name": "showInterchrom",
|
|
3726
3970
|
"type": "boolean"
|
|
3727
3971
|
},
|
|
3728
3972
|
{
|
|
3729
|
-
"name": "
|
|
3730
|
-
"type": "boolean"
|
|
3731
|
-
},
|
|
3732
|
-
{
|
|
3733
|
-
"name": "drawInter",
|
|
3734
|
-
"type": "boolean"
|
|
3735
|
-
},
|
|
3736
|
-
{
|
|
3737
|
-
"name": "drawProperPairArcs",
|
|
3738
|
-
"type": "boolean"
|
|
3973
|
+
"name": "showOrdinaryPairs",
|
|
3974
|
+
"type": "(boolean | undefined)"
|
|
3739
3975
|
},
|
|
3740
3976
|
{
|
|
3741
3977
|
"name": "minInterchromSupport",
|
|
3742
3978
|
"type": "number"
|
|
3743
3979
|
},
|
|
3744
3980
|
{
|
|
3745
|
-
"name": "
|
|
3981
|
+
"name": "showLongRange",
|
|
3746
3982
|
"type": "boolean"
|
|
3747
3983
|
},
|
|
3748
3984
|
{
|
|
@@ -3792,7 +4028,51 @@ export const configManifest = {
|
|
|
3792
4028
|
}
|
|
3793
4029
|
],
|
|
3794
4030
|
"legacyKeys": [
|
|
3795
|
-
"
|
|
4031
|
+
"maxFeatureScreenDensity",
|
|
4032
|
+
"maxDisplayedBpPerPx",
|
|
4033
|
+
"mouseover",
|
|
4034
|
+
"jexlFilters",
|
|
4035
|
+
"colorBy",
|
|
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"
|
|
3796
4076
|
],
|
|
3797
4077
|
"aliases": [
|
|
3798
4078
|
"LinearPileupDisplay",
|
|
@@ -3933,6 +4213,12 @@ export const configManifest = {
|
|
|
3933
4213
|
"type": "identifier"
|
|
3934
4214
|
}
|
|
3935
4215
|
],
|
|
4216
|
+
"legacyKeys": [
|
|
4217
|
+
"renderer"
|
|
4218
|
+
],
|
|
4219
|
+
"droppedKeys": [
|
|
4220
|
+
"renderer"
|
|
4221
|
+
],
|
|
3936
4222
|
"stateModelProps": [
|
|
3937
4223
|
"id",
|
|
3938
4224
|
"type",
|
|
@@ -3950,6 +4236,14 @@ export const configManifest = {
|
|
|
3950
4236
|
"type": "identifier"
|
|
3951
4237
|
}
|
|
3952
4238
|
],
|
|
4239
|
+
"legacyKeys": [
|
|
4240
|
+
"renderer",
|
|
4241
|
+
"middle"
|
|
4242
|
+
],
|
|
4243
|
+
"droppedKeys": [
|
|
4244
|
+
"renderer",
|
|
4245
|
+
"middle"
|
|
4246
|
+
],
|
|
3953
4247
|
"stateModelProps": [
|
|
3954
4248
|
"id",
|
|
3955
4249
|
"type",
|
|
@@ -3979,10 +4273,6 @@ export const configManifest = {
|
|
|
3979
4273
|
"name": "height",
|
|
3980
4274
|
"type": "number"
|
|
3981
4275
|
},
|
|
3982
|
-
{
|
|
3983
|
-
"name": "mouseover",
|
|
3984
|
-
"type": "(JexlString | string)"
|
|
3985
|
-
},
|
|
3986
4276
|
{
|
|
3987
4277
|
"name": "featureHeight",
|
|
3988
4278
|
"type": "number"
|
|
@@ -3995,14 +4285,6 @@ export const configManifest = {
|
|
|
3995
4285
|
"name": "growMaxHeight",
|
|
3996
4286
|
"type": "number"
|
|
3997
4287
|
},
|
|
3998
|
-
{
|
|
3999
|
-
"name": "densityTier",
|
|
4000
|
-
"type": "Density tier"
|
|
4001
|
-
},
|
|
4002
|
-
{
|
|
4003
|
-
"name": "densityTierBpPerPx",
|
|
4004
|
-
"type": "number"
|
|
4005
|
-
},
|
|
4006
4288
|
{
|
|
4007
4289
|
"name": "readConnectionsLineWidth",
|
|
4008
4290
|
"type": "number"
|
|
@@ -4012,7 +4294,7 @@ export const configManifest = {
|
|
|
4012
4294
|
"type": "boolean"
|
|
4013
4295
|
},
|
|
4014
4296
|
{
|
|
4015
|
-
"name": "
|
|
4297
|
+
"name": "showNonCanonicalJunctions",
|
|
4016
4298
|
"type": "boolean"
|
|
4017
4299
|
},
|
|
4018
4300
|
{
|
|
@@ -4076,6 +4358,10 @@ export const configManifest = {
|
|
|
4076
4358
|
{
|
|
4077
4359
|
"name": "title",
|
|
4078
4360
|
"type": "(string | undefined)"
|
|
4361
|
+
},
|
|
4362
|
+
{
|
|
4363
|
+
"name": "descending",
|
|
4364
|
+
"type": "(boolean | undefined)"
|
|
4079
4365
|
}
|
|
4080
4366
|
],
|
|
4081
4367
|
"shorthand": {
|
|
@@ -4090,10 +4376,21 @@ export const configManifest = {
|
|
|
4090
4376
|
]
|
|
4091
4377
|
},
|
|
4092
4378
|
"mapq": {
|
|
4093
|
-
"scale": "
|
|
4379
|
+
"scale": "threshold",
|
|
4094
4380
|
"domain": [
|
|
4095
|
-
"
|
|
4096
|
-
|
|
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
|
|
4097
4394
|
},
|
|
4098
4395
|
"insertSize": {
|
|
4099
4396
|
"scale": "threshold"
|
|
@@ -4112,7 +4409,13 @@ export const configManifest = {
|
|
|
4112
4409
|
"RL",
|
|
4113
4410
|
"RR",
|
|
4114
4411
|
"LL",
|
|
4115
|
-
""
|
|
4412
|
+
"",
|
|
4413
|
+
"unmappedMate",
|
|
4414
|
+
"interchrom",
|
|
4415
|
+
"splitInverted",
|
|
4416
|
+
"splitSameStrand",
|
|
4417
|
+
"segmentInverted",
|
|
4418
|
+
"segmentSameStrand"
|
|
4116
4419
|
]
|
|
4117
4420
|
},
|
|
4118
4421
|
"insertSizeAndOrientation": {
|
|
@@ -4124,7 +4427,8 @@ export const configManifest = {
|
|
|
4124
4427
|
"*": {
|
|
4125
4428
|
"scale": "categorical"
|
|
4126
4429
|
}
|
|
4127
|
-
}
|
|
4430
|
+
},
|
|
4431
|
+
"fieldDefault": "strand"
|
|
4128
4432
|
},
|
|
4129
4433
|
{
|
|
4130
4434
|
"name": "baseColor",
|
|
@@ -4132,7 +4436,7 @@ export const configManifest = {
|
|
|
4132
4436
|
"subSlots": [
|
|
4133
4437
|
{
|
|
4134
4438
|
"name": "field",
|
|
4135
|
-
"type": "
|
|
4439
|
+
"type": "AlignmentsBaseColorField"
|
|
4136
4440
|
},
|
|
4137
4441
|
{
|
|
4138
4442
|
"name": "scale",
|
|
@@ -4145,15 +4449,81 @@ export const configManifest = {
|
|
|
4145
4449
|
},
|
|
4146
4450
|
{
|
|
4147
4451
|
"name": "modifications",
|
|
4148
|
-
"type": "
|
|
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
|
+
]
|
|
4149
4471
|
},
|
|
4150
4472
|
{
|
|
4151
|
-
"name": "
|
|
4152
|
-
"type": "
|
|
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
|
+
]
|
|
4153
4523
|
},
|
|
4154
4524
|
{
|
|
4155
4525
|
"name": "facet",
|
|
4156
|
-
"type": "
|
|
4526
|
+
"type": "SectionFacetConfigurationSchema",
|
|
4157
4527
|
"subSlots": [
|
|
4158
4528
|
{
|
|
4159
4529
|
"name": "field",
|
|
@@ -4163,6 +4533,11 @@ export const configManifest = {
|
|
|
4163
4533
|
"name": "domain",
|
|
4164
4534
|
"type": "string[]",
|
|
4165
4535
|
"liftsNumbers": true
|
|
4536
|
+
},
|
|
4537
|
+
{
|
|
4538
|
+
"name": "hidden",
|
|
4539
|
+
"type": "string[]",
|
|
4540
|
+
"liftsNumbers": true
|
|
4166
4541
|
}
|
|
4167
4542
|
],
|
|
4168
4543
|
"shorthand": {
|
|
@@ -4247,11 +4622,11 @@ export const configManifest = {
|
|
|
4247
4622
|
]
|
|
4248
4623
|
},
|
|
4249
4624
|
{
|
|
4250
|
-
"name": "
|
|
4625
|
+
"name": "fadeLowQualityMismatches",
|
|
4251
4626
|
"type": "boolean"
|
|
4252
4627
|
},
|
|
4253
4628
|
{
|
|
4254
|
-
"name": "
|
|
4629
|
+
"name": "fadeLowFrequencyMismatches",
|
|
4255
4630
|
"type": "boolean"
|
|
4256
4631
|
},
|
|
4257
4632
|
{
|
|
@@ -4259,20 +4634,41 @@ export const configManifest = {
|
|
|
4259
4634
|
"type": "boolean"
|
|
4260
4635
|
},
|
|
4261
4636
|
{
|
|
4262
|
-
"name": "
|
|
4263
|
-
"type": "
|
|
4264
|
-
|
|
4265
|
-
|
|
4266
|
-
|
|
4267
|
-
|
|
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
|
+
}
|
|
4268
4664
|
},
|
|
4269
4665
|
{
|
|
4270
4666
|
"name": "showOutline",
|
|
4271
|
-
"type": "(
|
|
4667
|
+
"type": "(boolean | undefined)"
|
|
4272
4668
|
},
|
|
4273
4669
|
{
|
|
4274
|
-
"name": "
|
|
4275
|
-
"type": "
|
|
4670
|
+
"name": "unit",
|
|
4671
|
+
"type": "AlignmentsUnit"
|
|
4276
4672
|
},
|
|
4277
4673
|
{
|
|
4278
4674
|
"name": "showBezierConnections",
|
|
@@ -4303,27 +4699,19 @@ export const configManifest = {
|
|
|
4303
4699
|
"type": "boolean"
|
|
4304
4700
|
},
|
|
4305
4701
|
{
|
|
4306
|
-
"name": "
|
|
4307
|
-
"type": "boolean"
|
|
4308
|
-
},
|
|
4309
|
-
{
|
|
4310
|
-
"name": "colorSupplementaryChains",
|
|
4702
|
+
"name": "showInterchrom",
|
|
4311
4703
|
"type": "boolean"
|
|
4312
4704
|
},
|
|
4313
4705
|
{
|
|
4314
|
-
"name": "
|
|
4315
|
-
"type": "boolean"
|
|
4316
|
-
},
|
|
4317
|
-
{
|
|
4318
|
-
"name": "drawProperPairArcs",
|
|
4319
|
-
"type": "boolean"
|
|
4706
|
+
"name": "showOrdinaryPairs",
|
|
4707
|
+
"type": "(boolean | undefined)"
|
|
4320
4708
|
},
|
|
4321
4709
|
{
|
|
4322
4710
|
"name": "minInterchromSupport",
|
|
4323
4711
|
"type": "number"
|
|
4324
4712
|
},
|
|
4325
4713
|
{
|
|
4326
|
-
"name": "
|
|
4714
|
+
"name": "showLongRange",
|
|
4327
4715
|
"type": "boolean"
|
|
4328
4716
|
},
|
|
4329
4717
|
{
|
|
@@ -4381,7 +4769,51 @@ export const configManifest = {
|
|
|
4381
4769
|
}
|
|
4382
4770
|
],
|
|
4383
4771
|
"legacyKeys": [
|
|
4384
|
-
"
|
|
4772
|
+
"maxFeatureScreenDensity",
|
|
4773
|
+
"maxDisplayedBpPerPx",
|
|
4774
|
+
"mouseover",
|
|
4775
|
+
"jexlFilters",
|
|
4776
|
+
"colorBy",
|
|
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"
|
|
4385
4817
|
],
|
|
4386
4818
|
"stateModelProps": [
|
|
4387
4819
|
"id",
|
|
@@ -4411,10 +4843,6 @@ export const configManifest = {
|
|
|
4411
4843
|
"name": "height",
|
|
4412
4844
|
"type": "number"
|
|
4413
4845
|
},
|
|
4414
|
-
{
|
|
4415
|
-
"name": "mouseover",
|
|
4416
|
-
"type": "(JexlString | string)"
|
|
4417
|
-
},
|
|
4418
4846
|
{
|
|
4419
4847
|
"name": "color",
|
|
4420
4848
|
"type": "MultiWayGeneColorConfigurationSchema",
|
|
@@ -4468,8 +4896,39 @@ export const configManifest = {
|
|
|
4468
4896
|
"type": "LodMode"
|
|
4469
4897
|
},
|
|
4470
4898
|
{
|
|
4471
|
-
"name": "
|
|
4472
|
-
"type": "
|
|
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
|
+
}
|
|
4473
4932
|
},
|
|
4474
4933
|
{
|
|
4475
4934
|
"name": "ribbonColor",
|
|
@@ -4521,6 +4980,10 @@ export const configManifest = {
|
|
|
4521
4980
|
"type": "string[]",
|
|
4522
4981
|
"liftsNumbers": true
|
|
4523
4982
|
},
|
|
4983
|
+
{
|
|
4984
|
+
"name": "descending",
|
|
4985
|
+
"type": "(boolean | undefined)"
|
|
4986
|
+
},
|
|
4524
4987
|
{
|
|
4525
4988
|
"name": "title",
|
|
4526
4989
|
"type": "(string | undefined)"
|
|
@@ -4530,8 +4993,55 @@ export const configManifest = {
|
|
|
4530
4993
|
"string": "value"
|
|
4531
4994
|
},
|
|
4532
4995
|
"fieldPresets": {
|
|
4533
|
-
"
|
|
4534
|
-
"scale": "
|
|
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"
|
|
4535
5045
|
}
|
|
4536
5046
|
}
|
|
4537
5047
|
},
|
|
@@ -4563,6 +5073,10 @@ export const configManifest = {
|
|
|
4563
5073
|
"name": "text",
|
|
4564
5074
|
"type": "string"
|
|
4565
5075
|
},
|
|
5076
|
+
{
|
|
5077
|
+
"name": "inlineLaneNames",
|
|
5078
|
+
"type": "boolean"
|
|
5079
|
+
},
|
|
4566
5080
|
{
|
|
4567
5081
|
"name": "showGeneLabels",
|
|
4568
5082
|
"type": "boolean"
|
|
@@ -4599,6 +5113,10 @@ export const configManifest = {
|
|
|
4599
5113
|
"name": "interpolate",
|
|
4600
5114
|
"type": "LineInterpolation"
|
|
4601
5115
|
},
|
|
5116
|
+
{
|
|
5117
|
+
"name": "gapBp",
|
|
5118
|
+
"type": "(number | undefined)"
|
|
5119
|
+
},
|
|
4602
5120
|
{
|
|
4603
5121
|
"name": "linkShape",
|
|
4604
5122
|
"type": "LinkShape"
|
|
@@ -4705,7 +5223,7 @@ export const configManifest = {
|
|
|
4705
5223
|
},
|
|
4706
5224
|
{
|
|
4707
5225
|
"name": "descending",
|
|
4708
|
-
"type": "boolean"
|
|
5226
|
+
"type": "(boolean | undefined)"
|
|
4709
5227
|
},
|
|
4710
5228
|
{
|
|
4711
5229
|
"name": "missingLabel",
|
|
@@ -4815,11 +5333,7 @@ export const configManifest = {
|
|
|
4815
5333
|
},
|
|
4816
5334
|
{
|
|
4817
5335
|
"name": "transform",
|
|
4818
|
-
"type": "(filterConfigurationSchema | formulaConfigurationSchema | binConfigurationSchema | aggregateConfigurationSchema | coverageConfigurationSchema | flattenConfigurationSchema | cellsConfigurationSchema | pileupConfigurationSchema | mateConfigurationSchema)[]"
|
|
4819
|
-
},
|
|
4820
|
-
{
|
|
4821
|
-
"name": "source",
|
|
4822
|
-
"type": "MarkSource"
|
|
5336
|
+
"type": "(filterConfigurationSchema | formulaConfigurationSchema | binConfigurationSchema | aggregateConfigurationSchema | windowConfigurationSchema | coverageConfigurationSchema | flattenConfigurationSchema | cellsConfigurationSchema | pileupConfigurationSchema | mateConfigurationSchema)[]"
|
|
4823
5337
|
},
|
|
4824
5338
|
{
|
|
4825
5339
|
"name": "minBpPerPx",
|
|
@@ -4846,12 +5360,26 @@ export const configManifest = {
|
|
|
4846
5360
|
"type": "boolean"
|
|
4847
5361
|
}
|
|
4848
5362
|
],
|
|
5363
|
+
"legacyKeys": [
|
|
5364
|
+
"maxFeatureScreenDensity",
|
|
5365
|
+
"maxDisplayedBpPerPx",
|
|
5366
|
+
"mouseover",
|
|
5367
|
+
"jexlFilters"
|
|
5368
|
+
],
|
|
5369
|
+
"droppedKeys": [
|
|
5370
|
+
"maxFeatureScreenDensity",
|
|
5371
|
+
"maxDisplayedBpPerPx",
|
|
5372
|
+
"fetchSizeLimit",
|
|
5373
|
+
"mouseover"
|
|
5374
|
+
],
|
|
4849
5375
|
"stateModelProps": [
|
|
4850
5376
|
"id",
|
|
4851
5377
|
"type",
|
|
4852
5378
|
"configuration",
|
|
4853
|
-
"
|
|
4854
|
-
"frozenLanes"
|
|
5379
|
+
"hiddenLaneNames",
|
|
5380
|
+
"frozenLanes",
|
|
5381
|
+
"lanePins",
|
|
5382
|
+
"laneFlipPins"
|
|
4855
5383
|
]
|
|
4856
5384
|
},
|
|
4857
5385
|
"LinearReferenceSequenceDisplay": {
|
|
@@ -4889,6 +5417,12 @@ export const configManifest = {
|
|
|
4889
5417
|
"type": "boolean"
|
|
4890
5418
|
}
|
|
4891
5419
|
],
|
|
5420
|
+
"legacyKeys": [
|
|
5421
|
+
"renderer"
|
|
5422
|
+
],
|
|
5423
|
+
"droppedKeys": [
|
|
5424
|
+
"renderer"
|
|
5425
|
+
],
|
|
4892
5426
|
"stateModelProps": [
|
|
4893
5427
|
"id",
|
|
4894
5428
|
"type",
|
|
@@ -4917,10 +5451,6 @@ export const configManifest = {
|
|
|
4917
5451
|
"name": "height",
|
|
4918
5452
|
"type": "number"
|
|
4919
5453
|
},
|
|
4920
|
-
{
|
|
4921
|
-
"name": "mouseover",
|
|
4922
|
-
"type": "(JexlString | string)"
|
|
4923
|
-
},
|
|
4924
5454
|
{
|
|
4925
5455
|
"name": "heightMode",
|
|
4926
5456
|
"type": "heightMode"
|
|
@@ -4929,18 +5459,14 @@ export const configManifest = {
|
|
|
4929
5459
|
"name": "growMaxHeight",
|
|
4930
5460
|
"type": "number"
|
|
4931
5461
|
},
|
|
4932
|
-
{
|
|
4933
|
-
"name": "densityTier",
|
|
4934
|
-
"type": "Density tier"
|
|
4935
|
-
},
|
|
4936
|
-
{
|
|
4937
|
-
"name": "densityTierBpPerPx",
|
|
4938
|
-
"type": "number"
|
|
4939
|
-
},
|
|
4940
5462
|
{
|
|
4941
5463
|
"name": "filter",
|
|
4942
5464
|
"type": "JexlExpression[]"
|
|
4943
5465
|
},
|
|
5466
|
+
{
|
|
5467
|
+
"name": "mouseover",
|
|
5468
|
+
"type": "(JexlString | string)"
|
|
5469
|
+
},
|
|
4944
5470
|
{
|
|
4945
5471
|
"name": "maxFeatureScreenDensity",
|
|
4946
5472
|
"type": "number"
|
|
@@ -5032,9 +5558,13 @@ export const configManifest = {
|
|
|
5032
5558
|
}
|
|
5033
5559
|
}
|
|
5034
5560
|
},
|
|
5561
|
+
{
|
|
5562
|
+
"name": "showOutline",
|
|
5563
|
+
"type": "boolean"
|
|
5564
|
+
},
|
|
5035
5565
|
{
|
|
5036
5566
|
"name": "outlineColor",
|
|
5037
|
-
"type": "CssColor"
|
|
5567
|
+
"type": "(CssColor | undefined)"
|
|
5038
5568
|
},
|
|
5039
5569
|
{
|
|
5040
5570
|
"name": "featureHeight",
|
|
@@ -5046,7 +5576,7 @@ export const configManifest = {
|
|
|
5046
5576
|
},
|
|
5047
5577
|
{
|
|
5048
5578
|
"name": "facet",
|
|
5049
|
-
"type": "
|
|
5579
|
+
"type": "SectionFacetConfigurationSchema",
|
|
5050
5580
|
"subSlots": [
|
|
5051
5581
|
{
|
|
5052
5582
|
"name": "field",
|
|
@@ -5056,6 +5586,11 @@ export const configManifest = {
|
|
|
5056
5586
|
"name": "domain",
|
|
5057
5587
|
"type": "string[]",
|
|
5058
5588
|
"liftsNumbers": true
|
|
5589
|
+
},
|
|
5590
|
+
{
|
|
5591
|
+
"name": "hidden",
|
|
5592
|
+
"type": "string[]",
|
|
5593
|
+
"liftsNumbers": true
|
|
5059
5594
|
}
|
|
5060
5595
|
],
|
|
5061
5596
|
"shorthand": {
|
|
@@ -5068,25 +5603,33 @@ export const configManifest = {
|
|
|
5068
5603
|
"subSlots": [
|
|
5069
5604
|
{
|
|
5070
5605
|
"name": "name",
|
|
5071
|
-
"type": "
|
|
5606
|
+
"type": "string"
|
|
5072
5607
|
},
|
|
5073
5608
|
{
|
|
5074
5609
|
"name": "description",
|
|
5075
|
-
"type": "
|
|
5610
|
+
"type": "string"
|
|
5076
5611
|
}
|
|
5077
5612
|
]
|
|
5078
5613
|
}
|
|
5079
5614
|
],
|
|
5080
5615
|
"legacyKeys": [
|
|
5616
|
+
"maxDisplayedBpPerPx",
|
|
5617
|
+
"jexlFilters",
|
|
5081
5618
|
"color1",
|
|
5082
5619
|
"color2",
|
|
5083
5620
|
"color3",
|
|
5084
5621
|
"outline",
|
|
5085
5622
|
"maxHeight",
|
|
5086
|
-
"jexlFilters",
|
|
5087
5623
|
"renderer",
|
|
5088
5624
|
"showDescriptions"
|
|
5089
5625
|
],
|
|
5626
|
+
"droppedKeys": [
|
|
5627
|
+
"maxFeatureScreenDensity",
|
|
5628
|
+
"maxDisplayedBpPerPx",
|
|
5629
|
+
"fetchSizeLimit",
|
|
5630
|
+
"mouseover",
|
|
5631
|
+
"maxHeight"
|
|
5632
|
+
],
|
|
5090
5633
|
"legacyValues": {
|
|
5091
5634
|
"showLabels": [
|
|
5092
5635
|
true,
|
|
@@ -5131,10 +5674,6 @@ export const configManifest = {
|
|
|
5131
5674
|
"name": "height",
|
|
5132
5675
|
"type": "number"
|
|
5133
5676
|
},
|
|
5134
|
-
{
|
|
5135
|
-
"name": "mouseover",
|
|
5136
|
-
"type": "(JexlString | string)"
|
|
5137
|
-
},
|
|
5138
5677
|
{
|
|
5139
5678
|
"name": "variantLayout",
|
|
5140
5679
|
"type": "VariantLayout"
|
|
@@ -5169,7 +5708,7 @@ export const configManifest = {
|
|
|
5169
5708
|
},
|
|
5170
5709
|
{
|
|
5171
5710
|
"name": "rows",
|
|
5172
|
-
"type": "
|
|
5711
|
+
"type": "SampleRowsConfigurationSchema",
|
|
5173
5712
|
"subSlots": [
|
|
5174
5713
|
{
|
|
5175
5714
|
"name": "domain",
|
|
@@ -5192,8 +5731,15 @@ export const configManifest = {
|
|
|
5192
5731
|
"name": "kept",
|
|
5193
5732
|
"type": "string[]",
|
|
5194
5733
|
"liftsNumbers": true
|
|
5734
|
+
},
|
|
5735
|
+
{
|
|
5736
|
+
"name": "field",
|
|
5737
|
+
"type": "SampleRowsField"
|
|
5195
5738
|
}
|
|
5196
|
-
]
|
|
5739
|
+
],
|
|
5740
|
+
"shorthand": {
|
|
5741
|
+
"string": "field"
|
|
5742
|
+
}
|
|
5197
5743
|
},
|
|
5198
5744
|
{
|
|
5199
5745
|
"name": "showRowSeparators",
|
|
@@ -5204,8 +5750,8 @@ export const configManifest = {
|
|
|
5204
5750
|
"type": "boolean"
|
|
5205
5751
|
},
|
|
5206
5752
|
{
|
|
5207
|
-
"name": "
|
|
5208
|
-
"type": "
|
|
5753
|
+
"name": "unit",
|
|
5754
|
+
"type": "VariantUnit"
|
|
5209
5755
|
},
|
|
5210
5756
|
{
|
|
5211
5757
|
"name": "color",
|
|
@@ -5275,10 +5821,6 @@ export const configManifest = {
|
|
|
5275
5821
|
"name": "field",
|
|
5276
5822
|
"type": "string"
|
|
5277
5823
|
},
|
|
5278
|
-
{
|
|
5279
|
-
"name": "scale",
|
|
5280
|
-
"type": "(RowColorScale | undefined)"
|
|
5281
|
-
},
|
|
5282
5824
|
{
|
|
5283
5825
|
"name": "domain",
|
|
5284
5826
|
"type": "string[]",
|
|
@@ -5287,6 +5829,10 @@ export const configManifest = {
|
|
|
5287
5829
|
{
|
|
5288
5830
|
"name": "range",
|
|
5289
5831
|
"type": "CssColorEntry[]"
|
|
5832
|
+
},
|
|
5833
|
+
{
|
|
5834
|
+
"name": "unknown",
|
|
5835
|
+
"type": "(CssColor | undefined)"
|
|
5290
5836
|
}
|
|
5291
5837
|
],
|
|
5292
5838
|
"shorthand": {
|
|
@@ -5333,7 +5879,35 @@ export const configManifest = {
|
|
|
5333
5879
|
}
|
|
5334
5880
|
],
|
|
5335
5881
|
"legacyKeys": [
|
|
5336
|
-
"
|
|
5882
|
+
"maxFeatureScreenDensity",
|
|
5883
|
+
"maxDisplayedBpPerPx",
|
|
5884
|
+
"mouseover",
|
|
5885
|
+
"jexlFilters",
|
|
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",
|
|
@@ -5375,12 +5949,50 @@ export const configManifest = {
|
|
|
5375
5949
|
"type": "number"
|
|
5376
5950
|
},
|
|
5377
5951
|
{
|
|
5378
|
-
"name": "
|
|
5379
|
-
"type": "
|
|
5380
|
-
|
|
5381
|
-
|
|
5382
|
-
|
|
5383
|
-
|
|
5952
|
+
"name": "color",
|
|
5953
|
+
"type": "LDColorConfigurationSchema",
|
|
5954
|
+
"subSlots": [
|
|
5955
|
+
{
|
|
5956
|
+
"name": "field",
|
|
5957
|
+
"type": "LDColorField"
|
|
5958
|
+
},
|
|
5959
|
+
{
|
|
5960
|
+
"name": "scheme",
|
|
5961
|
+
"type": "(ColorScheme | undefined)"
|
|
5962
|
+
},
|
|
5963
|
+
{
|
|
5964
|
+
"name": "reverse",
|
|
5965
|
+
"type": "(boolean | undefined)"
|
|
5966
|
+
},
|
|
5967
|
+
{
|
|
5968
|
+
"name": "domainMin",
|
|
5969
|
+
"type": "(number | undefined)"
|
|
5970
|
+
},
|
|
5971
|
+
{
|
|
5972
|
+
"name": "domainMax",
|
|
5973
|
+
"type": "(number | undefined)"
|
|
5974
|
+
},
|
|
5975
|
+
{
|
|
5976
|
+
"name": "scale",
|
|
5977
|
+
"type": "(LDColorScale | undefined)"
|
|
5978
|
+
}
|
|
5979
|
+
],
|
|
5980
|
+
"shorthand": {
|
|
5981
|
+
"string": "field"
|
|
5982
|
+
},
|
|
5983
|
+
"fieldPresets": {
|
|
5984
|
+
"r2": {
|
|
5985
|
+
"scale": "linear",
|
|
5986
|
+
"scheme": "reds",
|
|
5987
|
+
"title": "R²"
|
|
5988
|
+
},
|
|
5989
|
+
"dprime": {
|
|
5990
|
+
"scale": "linear",
|
|
5991
|
+
"scheme": "blues",
|
|
5992
|
+
"title": "D'"
|
|
5993
|
+
}
|
|
5994
|
+
},
|
|
5995
|
+
"fieldDefault": "r2"
|
|
5384
5996
|
},
|
|
5385
5997
|
{
|
|
5386
5998
|
"name": "showVerticalGuides",
|
|
@@ -5388,7 +6000,7 @@ export const configManifest = {
|
|
|
5388
6000
|
},
|
|
5389
6001
|
{
|
|
5390
6002
|
"name": "showLabels",
|
|
5391
|
-
"type": "
|
|
6003
|
+
"type": "LDShowLabels"
|
|
5392
6004
|
},
|
|
5393
6005
|
{
|
|
5394
6006
|
"name": "tickHeight",
|
|
@@ -5399,6 +6011,48 @@ export const configManifest = {
|
|
|
5399
6011
|
"type": "VariantLayout"
|
|
5400
6012
|
}
|
|
5401
6013
|
],
|
|
6014
|
+
"legacyKeys": [
|
|
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"
|
|
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
|
+
},
|
|
5402
6056
|
"stateModelProps": [
|
|
5403
6057
|
"id",
|
|
5404
6058
|
"type",
|
|
@@ -5425,7 +6079,7 @@ export const configManifest = {
|
|
|
5425
6079
|
},
|
|
5426
6080
|
{
|
|
5427
6081
|
"name": "rows",
|
|
5428
|
-
"type": "
|
|
6082
|
+
"type": "QuantitativeRowsConfigurationSchema",
|
|
5429
6083
|
"subSlots": [
|
|
5430
6084
|
{
|
|
5431
6085
|
"name": "domain",
|
|
@@ -5451,7 +6105,7 @@ export const configManifest = {
|
|
|
5451
6105
|
},
|
|
5452
6106
|
{
|
|
5453
6107
|
"name": "field",
|
|
5454
|
-
"type": "
|
|
6108
|
+
"type": "QuantitativeRowsField"
|
|
5455
6109
|
}
|
|
5456
6110
|
],
|
|
5457
6111
|
"shorthand": {
|
|
@@ -5466,10 +6120,6 @@ export const configManifest = {
|
|
|
5466
6120
|
"name": "field",
|
|
5467
6121
|
"type": "string"
|
|
5468
6122
|
},
|
|
5469
|
-
{
|
|
5470
|
-
"name": "scale",
|
|
5471
|
-
"type": "(RowColorScale | undefined)"
|
|
5472
|
-
},
|
|
5473
6123
|
{
|
|
5474
6124
|
"name": "domain",
|
|
5475
6125
|
"type": "string[]",
|
|
@@ -5478,6 +6128,10 @@ export const configManifest = {
|
|
|
5478
6128
|
{
|
|
5479
6129
|
"name": "range",
|
|
5480
6130
|
"type": "CssColorEntry[]"
|
|
6131
|
+
},
|
|
6132
|
+
{
|
|
6133
|
+
"name": "unknown",
|
|
6134
|
+
"type": "(CssColor | undefined)"
|
|
5481
6135
|
}
|
|
5482
6136
|
],
|
|
5483
6137
|
"shorthand": {
|
|
@@ -5539,16 +6193,14 @@ export const configManifest = {
|
|
|
5539
6193
|
"string": "value"
|
|
5540
6194
|
},
|
|
5541
6195
|
"fieldPresets": {
|
|
5542
|
-
"source": {
|
|
5543
|
-
"scale": "categorical"
|
|
5544
|
-
},
|
|
5545
6196
|
"*": {
|
|
5546
6197
|
"scale": "threshold"
|
|
5547
6198
|
}
|
|
5548
|
-
}
|
|
6199
|
+
},
|
|
6200
|
+
"impliedField": "score"
|
|
5549
6201
|
},
|
|
5550
6202
|
{
|
|
5551
|
-
"name": "
|
|
6203
|
+
"name": "y",
|
|
5552
6204
|
"type": "string"
|
|
5553
6205
|
},
|
|
5554
6206
|
{
|
|
@@ -5561,11 +6213,7 @@ export const configManifest = {
|
|
|
5561
6213
|
},
|
|
5562
6214
|
{
|
|
5563
6215
|
"name": "size",
|
|
5564
|
-
"type": "number"
|
|
5565
|
-
},
|
|
5566
|
-
{
|
|
5567
|
-
"name": "lineWidth",
|
|
5568
|
-
"type": "number"
|
|
6216
|
+
"type": "(number | undefined)"
|
|
5569
6217
|
},
|
|
5570
6218
|
{
|
|
5571
6219
|
"name": "maxGapMultiple",
|
|
@@ -5649,8 +6297,12 @@ export const configManifest = {
|
|
|
5649
6297
|
"type": "boolean"
|
|
5650
6298
|
},
|
|
5651
6299
|
{
|
|
5652
|
-
"name": "
|
|
5653
|
-
"type": "
|
|
6300
|
+
"name": "aggregate",
|
|
6301
|
+
"type": "Aggregate"
|
|
6302
|
+
},
|
|
6303
|
+
{
|
|
6304
|
+
"name": "extent",
|
|
6305
|
+
"type": "Extent"
|
|
5654
6306
|
},
|
|
5655
6307
|
{
|
|
5656
6308
|
"name": "showTree",
|
|
@@ -5674,9 +6326,31 @@ export const configManifest = {
|
|
|
5674
6326
|
}
|
|
5675
6327
|
],
|
|
5676
6328
|
"legacyKeys": [
|
|
6329
|
+
"maxFeatureScreenDensity",
|
|
6330
|
+
"maxDisplayedBpPerPx",
|
|
6331
|
+
"fetchSizeLimit",
|
|
6332
|
+
"mouseover",
|
|
6333
|
+
"jexlFilters",
|
|
5677
6334
|
"displayCrossHatches",
|
|
5678
6335
|
"minimalTicks",
|
|
5679
|
-
"
|
|
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"
|
|
5680
6354
|
],
|
|
5681
6355
|
"aliases": [
|
|
5682
6356
|
"MultiLinearWiggleDisplay",
|
|
@@ -5712,11 +6386,7 @@ export const configManifest = {
|
|
|
5712
6386
|
},
|
|
5713
6387
|
{
|
|
5714
6388
|
"name": "height",
|
|
5715
|
-
"type": "
|
|
5716
|
-
},
|
|
5717
|
-
{
|
|
5718
|
-
"name": "mouseover",
|
|
5719
|
-
"type": "(JexlString | string)"
|
|
6389
|
+
"type": "number"
|
|
5720
6390
|
},
|
|
5721
6391
|
{
|
|
5722
6392
|
"name": "rowHeight",
|
|
@@ -5737,11 +6407,123 @@ export const configManifest = {
|
|
|
5737
6407
|
{
|
|
5738
6408
|
"name": "field",
|
|
5739
6409
|
"type": "MafColorField"
|
|
6410
|
+
},
|
|
6411
|
+
{
|
|
6412
|
+
"name": "domain",
|
|
6413
|
+
"type": "string[]",
|
|
6414
|
+
"liftsNumbers": true
|
|
6415
|
+
},
|
|
6416
|
+
{
|
|
6417
|
+
"name": "range",
|
|
6418
|
+
"type": "CssColorEntry[]"
|
|
6419
|
+
},
|
|
6420
|
+
{
|
|
6421
|
+
"name": "labels",
|
|
6422
|
+
"type": "string[]",
|
|
6423
|
+
"liftsNumbers": true
|
|
6424
|
+
},
|
|
6425
|
+
{
|
|
6426
|
+
"name": "title",
|
|
6427
|
+
"type": "(string | undefined)"
|
|
6428
|
+
},
|
|
6429
|
+
{
|
|
6430
|
+
"name": "scheme",
|
|
6431
|
+
"type": "(ColorScheme | undefined)"
|
|
6432
|
+
},
|
|
6433
|
+
{
|
|
6434
|
+
"name": "reverse",
|
|
6435
|
+
"type": "boolean"
|
|
6436
|
+
},
|
|
6437
|
+
{
|
|
6438
|
+
"name": "domainMin",
|
|
6439
|
+
"type": "(number | undefined)"
|
|
6440
|
+
},
|
|
6441
|
+
{
|
|
6442
|
+
"name": "domainMax",
|
|
6443
|
+
"type": "(number | undefined)"
|
|
6444
|
+
},
|
|
6445
|
+
{
|
|
6446
|
+
"name": "domainMid",
|
|
6447
|
+
"type": "(number | undefined)"
|
|
5740
6448
|
}
|
|
5741
6449
|
],
|
|
5742
6450
|
"shorthand": {
|
|
5743
6451
|
"string": "field"
|
|
5744
|
-
}
|
|
6452
|
+
},
|
|
6453
|
+
"fieldPresets": {
|
|
6454
|
+
"mismatch": {
|
|
6455
|
+
"scale": "categorical",
|
|
6456
|
+
"domain": [
|
|
6457
|
+
"A",
|
|
6458
|
+
"C",
|
|
6459
|
+
"G",
|
|
6460
|
+
"T",
|
|
6461
|
+
"N",
|
|
6462
|
+
"gap",
|
|
6463
|
+
"match"
|
|
6464
|
+
],
|
|
6465
|
+
"title": "Mismatch to reference"
|
|
6466
|
+
},
|
|
6467
|
+
"base": {
|
|
6468
|
+
"scale": "categorical",
|
|
6469
|
+
"domain": [
|
|
6470
|
+
"A",
|
|
6471
|
+
"C",
|
|
6472
|
+
"G",
|
|
6473
|
+
"T",
|
|
6474
|
+
"N",
|
|
6475
|
+
"gap"
|
|
6476
|
+
],
|
|
6477
|
+
"title": "Base"
|
|
6478
|
+
},
|
|
6479
|
+
"identity": {
|
|
6480
|
+
"scale": "linear",
|
|
6481
|
+
"domainMin": 0,
|
|
6482
|
+
"domainMax": 1,
|
|
6483
|
+
"scheme": "redgreyblue",
|
|
6484
|
+
"title": "Per-base identity to reference"
|
|
6485
|
+
},
|
|
6486
|
+
"chromosome": {
|
|
6487
|
+
"scale": "categorical",
|
|
6488
|
+
"domain": [
|
|
6489
|
+
"0",
|
|
6490
|
+
"1",
|
|
6491
|
+
"2",
|
|
6492
|
+
"3",
|
|
6493
|
+
"4"
|
|
6494
|
+
],
|
|
6495
|
+
"range": [
|
|
6496
|
+
"hsl(210, 55%, 55%)",
|
|
6497
|
+
"hsl(28, 85%, 55%)",
|
|
6498
|
+
"hsl(350, 70%, 57%)",
|
|
6499
|
+
"hsl(275, 45%, 58%)",
|
|
6500
|
+
"hsl(150, 45%, 42%)"
|
|
6501
|
+
],
|
|
6502
|
+
"labels": [
|
|
6503
|
+
"Main chromosome",
|
|
6504
|
+
"2nd source",
|
|
6505
|
+
"3rd source",
|
|
6506
|
+
"4th source",
|
|
6507
|
+
"Other source"
|
|
6508
|
+
],
|
|
6509
|
+
"title": "Source chromosome"
|
|
6510
|
+
},
|
|
6511
|
+
"codon": {
|
|
6512
|
+
"scale": "categorical",
|
|
6513
|
+
"domain": [
|
|
6514
|
+
"nonsyn",
|
|
6515
|
+
"syn",
|
|
6516
|
+
"stop"
|
|
6517
|
+
],
|
|
6518
|
+
"labels": [
|
|
6519
|
+
"Nonsynonymous",
|
|
6520
|
+
"Synonymous",
|
|
6521
|
+
"Stop gained"
|
|
6522
|
+
],
|
|
6523
|
+
"title": "Codon change"
|
|
6524
|
+
}
|
|
6525
|
+
},
|
|
6526
|
+
"fieldDefault": "mismatch"
|
|
5745
6527
|
},
|
|
5746
6528
|
{
|
|
5747
6529
|
"name": "y",
|
|
@@ -5769,7 +6551,7 @@ export const configManifest = {
|
|
|
5769
6551
|
},
|
|
5770
6552
|
{
|
|
5771
6553
|
"name": "rows",
|
|
5772
|
-
"type": "
|
|
6554
|
+
"type": "SampleRowsConfigurationSchema",
|
|
5773
6555
|
"subSlots": [
|
|
5774
6556
|
{
|
|
5775
6557
|
"name": "domain",
|
|
@@ -5792,8 +6574,15 @@ export const configManifest = {
|
|
|
5792
6574
|
"name": "kept",
|
|
5793
6575
|
"type": "string[]",
|
|
5794
6576
|
"liftsNumbers": true
|
|
6577
|
+
},
|
|
6578
|
+
{
|
|
6579
|
+
"name": "field",
|
|
6580
|
+
"type": "SampleRowsField"
|
|
5795
6581
|
}
|
|
5796
|
-
]
|
|
6582
|
+
],
|
|
6583
|
+
"shorthand": {
|
|
6584
|
+
"string": "field"
|
|
6585
|
+
}
|
|
5797
6586
|
},
|
|
5798
6587
|
{
|
|
5799
6588
|
"name": "rowColor",
|
|
@@ -5803,10 +6592,6 @@ export const configManifest = {
|
|
|
5803
6592
|
"name": "field",
|
|
5804
6593
|
"type": "string"
|
|
5805
6594
|
},
|
|
5806
|
-
{
|
|
5807
|
-
"name": "scale",
|
|
5808
|
-
"type": "(RowColorScale | undefined)"
|
|
5809
|
-
},
|
|
5810
6595
|
{
|
|
5811
6596
|
"name": "domain",
|
|
5812
6597
|
"type": "string[]",
|
|
@@ -5815,6 +6600,10 @@ export const configManifest = {
|
|
|
5815
6600
|
{
|
|
5816
6601
|
"name": "range",
|
|
5817
6602
|
"type": "CssColorEntry[]"
|
|
6603
|
+
},
|
|
6604
|
+
{
|
|
6605
|
+
"name": "unknown",
|
|
6606
|
+
"type": "(CssColor | undefined)"
|
|
5818
6607
|
}
|
|
5819
6608
|
],
|
|
5820
6609
|
"shorthand": {
|
|
@@ -5837,6 +6626,87 @@ export const configManifest = {
|
|
|
5837
6626
|
"name": "coverageHeight",
|
|
5838
6627
|
"type": "number"
|
|
5839
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
|
+
},
|
|
5840
6710
|
{
|
|
5841
6711
|
"name": "showConservation",
|
|
5842
6712
|
"type": "boolean"
|
|
@@ -5866,6 +6736,18 @@ export const configManifest = {
|
|
|
5866
6736
|
"type": "boolean"
|
|
5867
6737
|
}
|
|
5868
6738
|
],
|
|
6739
|
+
"legacyKeys": [
|
|
6740
|
+
"maxFeatureScreenDensity",
|
|
6741
|
+
"maxDisplayedBpPerPx",
|
|
6742
|
+
"mouseover",
|
|
6743
|
+
"jexlFilters"
|
|
6744
|
+
],
|
|
6745
|
+
"droppedKeys": [
|
|
6746
|
+
"maxFeatureScreenDensity",
|
|
6747
|
+
"maxDisplayedBpPerPx",
|
|
6748
|
+
"fetchSizeLimit",
|
|
6749
|
+
"mouseover"
|
|
6750
|
+
],
|
|
5869
6751
|
"stateModelProps": [
|
|
5870
6752
|
"id",
|
|
5871
6753
|
"type",
|
|
@@ -5902,8 +6784,8 @@ export const configManifest = {
|
|
|
5902
6784
|
"type": "HicColorConfigurationSchema",
|
|
5903
6785
|
"subSlots": [
|
|
5904
6786
|
{
|
|
5905
|
-
"name": "
|
|
5906
|
-
"type": "
|
|
6787
|
+
"name": "field",
|
|
6788
|
+
"type": "HicColorField"
|
|
5907
6789
|
},
|
|
5908
6790
|
{
|
|
5909
6791
|
"name": "scheme",
|
|
@@ -5917,15 +6799,28 @@ export const configManifest = {
|
|
|
5917
6799
|
"name": "domainMin",
|
|
5918
6800
|
"type": "(number | undefined)"
|
|
5919
6801
|
},
|
|
5920
|
-
{
|
|
5921
|
-
"name": "domainMax",
|
|
5922
|
-
"type": "(number | undefined)"
|
|
5923
|
-
},
|
|
5924
6802
|
{
|
|
5925
6803
|
"name": "domainQuantile",
|
|
5926
6804
|
"type": "number"
|
|
6805
|
+
},
|
|
6806
|
+
{
|
|
6807
|
+
"name": "scale",
|
|
6808
|
+
"type": "(HicColorScale | undefined)"
|
|
6809
|
+
},
|
|
6810
|
+
{
|
|
6811
|
+
"name": "domainMax",
|
|
6812
|
+
"type": "(number | undefined)"
|
|
5927
6813
|
}
|
|
5928
|
-
]
|
|
6814
|
+
],
|
|
6815
|
+
"shorthand": {
|
|
6816
|
+
"string": "field"
|
|
6817
|
+
},
|
|
6818
|
+
"fieldPresets": {
|
|
6819
|
+
"count": {
|
|
6820
|
+
"scale": "linear"
|
|
6821
|
+
}
|
|
6822
|
+
},
|
|
6823
|
+
"fieldDefault": "count"
|
|
5929
6824
|
},
|
|
5930
6825
|
{
|
|
5931
6826
|
"name": "resolutionBias",
|
|
@@ -5941,7 +6836,19 @@ export const configManifest = {
|
|
|
5941
6836
|
}
|
|
5942
6837
|
],
|
|
5943
6838
|
"legacyKeys": [
|
|
5944
|
-
"
|
|
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"
|
|
5945
6852
|
],
|
|
5946
6853
|
"stateModelProps": [
|
|
5947
6854
|
"id",
|
|
@@ -5971,14 +6878,6 @@ export const configManifest = {
|
|
|
5971
6878
|
"name": "forceLoad",
|
|
5972
6879
|
"type": "boolean"
|
|
5973
6880
|
},
|
|
5974
|
-
{
|
|
5975
|
-
"name": "densityTier",
|
|
5976
|
-
"type": "Density tier"
|
|
5977
|
-
},
|
|
5978
|
-
{
|
|
5979
|
-
"name": "densityTierBpPerPx",
|
|
5980
|
-
"type": "number"
|
|
5981
|
-
},
|
|
5982
6881
|
{
|
|
5983
6882
|
"name": "marks",
|
|
5984
6883
|
"type": "MarkConfigurationSchema[]",
|
|
@@ -5991,6 +6890,10 @@ export const configManifest = {
|
|
|
5991
6890
|
"name": "interpolate",
|
|
5992
6891
|
"type": "LineInterpolation"
|
|
5993
6892
|
},
|
|
6893
|
+
{
|
|
6894
|
+
"name": "gapBp",
|
|
6895
|
+
"type": "(number | undefined)"
|
|
6896
|
+
},
|
|
5994
6897
|
{
|
|
5995
6898
|
"name": "linkShape",
|
|
5996
6899
|
"type": "LinkShape"
|
|
@@ -6097,7 +7000,7 @@ export const configManifest = {
|
|
|
6097
7000
|
},
|
|
6098
7001
|
{
|
|
6099
7002
|
"name": "descending",
|
|
6100
|
-
"type": "boolean"
|
|
7003
|
+
"type": "(boolean | undefined)"
|
|
6101
7004
|
},
|
|
6102
7005
|
{
|
|
6103
7006
|
"name": "missingLabel",
|
|
@@ -6207,11 +7110,7 @@ export const configManifest = {
|
|
|
6207
7110
|
},
|
|
6208
7111
|
{
|
|
6209
7112
|
"name": "transform",
|
|
6210
|
-
"type": "(filterConfigurationSchema | formulaConfigurationSchema | binConfigurationSchema | aggregateConfigurationSchema | coverageConfigurationSchema | flattenConfigurationSchema | cellsConfigurationSchema | pileupConfigurationSchema | mateConfigurationSchema)[]"
|
|
6211
|
-
},
|
|
6212
|
-
{
|
|
6213
|
-
"name": "source",
|
|
6214
|
-
"type": "MarkSource"
|
|
7113
|
+
"type": "(filterConfigurationSchema | formulaConfigurationSchema | binConfigurationSchema | aggregateConfigurationSchema | windowConfigurationSchema | coverageConfigurationSchema | flattenConfigurationSchema | cellsConfigurationSchema | pileupConfigurationSchema | mateConfigurationSchema)[]"
|
|
6215
7114
|
},
|
|
6216
7115
|
{
|
|
6217
7116
|
"name": "minBpPerPx",
|
|
@@ -6233,7 +7132,7 @@ export const configManifest = {
|
|
|
6233
7132
|
},
|
|
6234
7133
|
{
|
|
6235
7134
|
"name": "transform",
|
|
6236
|
-
"type": "(filterConfigurationSchema | formulaConfigurationSchema | binConfigurationSchema | aggregateConfigurationSchema | coverageConfigurationSchema | flattenConfigurationSchema | cellsConfigurationSchema | pileupConfigurationSchema | mateConfigurationSchema)[]"
|
|
7135
|
+
"type": "(filterConfigurationSchema | formulaConfigurationSchema | binConfigurationSchema | aggregateConfigurationSchema | windowConfigurationSchema | coverageConfigurationSchema | flattenConfigurationSchema | cellsConfigurationSchema | pileupConfigurationSchema | mateConfigurationSchema)[]"
|
|
6237
7136
|
},
|
|
6238
7137
|
{
|
|
6239
7138
|
"name": "facet",
|
|
@@ -6248,9 +7147,14 @@ export const configManifest = {
|
|
|
6248
7147
|
"type": "string[]",
|
|
6249
7148
|
"liftsNumbers": true
|
|
6250
7149
|
},
|
|
7150
|
+
{
|
|
7151
|
+
"name": "hidden",
|
|
7152
|
+
"type": "string[]",
|
|
7153
|
+
"liftsNumbers": true
|
|
7154
|
+
},
|
|
6251
7155
|
{
|
|
6252
7156
|
"name": "transform",
|
|
6253
|
-
"type": "(filterConfigurationSchema | formulaConfigurationSchema | binConfigurationSchema | aggregateConfigurationSchema | coverageConfigurationSchema | flattenConfigurationSchema | cellsConfigurationSchema | pileupConfigurationSchema | mateConfigurationSchema)[]"
|
|
7157
|
+
"type": "(filterConfigurationSchema | formulaConfigurationSchema | binConfigurationSchema | aggregateConfigurationSchema | windowConfigurationSchema | coverageConfigurationSchema | flattenConfigurationSchema | cellsConfigurationSchema | pileupConfigurationSchema | mateConfigurationSchema)[]"
|
|
6254
7158
|
}
|
|
6255
7159
|
],
|
|
6256
7160
|
"shorthand": {
|
|
@@ -6300,10 +7204,6 @@ export const configManifest = {
|
|
|
6300
7204
|
"name": "field",
|
|
6301
7205
|
"type": "string"
|
|
6302
7206
|
},
|
|
6303
|
-
{
|
|
6304
|
-
"name": "scale",
|
|
6305
|
-
"type": "(RowColorScale | undefined)"
|
|
6306
|
-
},
|
|
6307
7207
|
{
|
|
6308
7208
|
"name": "domain",
|
|
6309
7209
|
"type": "string[]",
|
|
@@ -6312,6 +7212,10 @@ export const configManifest = {
|
|
|
6312
7212
|
{
|
|
6313
7213
|
"name": "range",
|
|
6314
7214
|
"type": "CssColorEntry[]"
|
|
7215
|
+
},
|
|
7216
|
+
{
|
|
7217
|
+
"name": "unknown",
|
|
7218
|
+
"type": "(CssColor | undefined)"
|
|
6315
7219
|
}
|
|
6316
7220
|
],
|
|
6317
7221
|
"shorthand": {
|
|
@@ -6429,10 +7333,17 @@ export const configManifest = {
|
|
|
6429
7333
|
}
|
|
6430
7334
|
],
|
|
6431
7335
|
"legacyKeys": [
|
|
6432
|
-
"
|
|
6433
|
-
"
|
|
7336
|
+
"maxFeatureScreenDensity",
|
|
7337
|
+
"maxDisplayedBpPerPx",
|
|
7338
|
+
"mouseover",
|
|
6434
7339
|
"jexlFilters"
|
|
6435
7340
|
],
|
|
7341
|
+
"droppedKeys": [
|
|
7342
|
+
"maxFeatureScreenDensity",
|
|
7343
|
+
"maxDisplayedBpPerPx",
|
|
7344
|
+
"fetchSizeLimit",
|
|
7345
|
+
"mouseover"
|
|
7346
|
+
],
|
|
6436
7347
|
"stateModelProps": [
|
|
6437
7348
|
"id",
|
|
6438
7349
|
"type",
|
|
@@ -6440,8 +7351,7 @@ export const configManifest = {
|
|
|
6440
7351
|
"clusterRegion",
|
|
6441
7352
|
"sortRowsBy",
|
|
6442
7353
|
"configuration",
|
|
6443
|
-
"indexSnp"
|
|
6444
|
-
"indexSnpPinned"
|
|
7354
|
+
"indexSnp"
|
|
6445
7355
|
]
|
|
6446
7356
|
},
|
|
6447
7357
|
"LinearMarkDisplay": {
|
|
@@ -6466,14 +7376,6 @@ export const configManifest = {
|
|
|
6466
7376
|
"name": "forceLoad",
|
|
6467
7377
|
"type": "boolean"
|
|
6468
7378
|
},
|
|
6469
|
-
{
|
|
6470
|
-
"name": "densityTier",
|
|
6471
|
-
"type": "Density tier"
|
|
6472
|
-
},
|
|
6473
|
-
{
|
|
6474
|
-
"name": "densityTierBpPerPx",
|
|
6475
|
-
"type": "number"
|
|
6476
|
-
},
|
|
6477
7379
|
{
|
|
6478
7380
|
"name": "marks",
|
|
6479
7381
|
"type": "MarkConfigurationSchema[]",
|
|
@@ -6486,6 +7388,10 @@ export const configManifest = {
|
|
|
6486
7388
|
"name": "interpolate",
|
|
6487
7389
|
"type": "LineInterpolation"
|
|
6488
7390
|
},
|
|
7391
|
+
{
|
|
7392
|
+
"name": "gapBp",
|
|
7393
|
+
"type": "(number | undefined)"
|
|
7394
|
+
},
|
|
6489
7395
|
{
|
|
6490
7396
|
"name": "linkShape",
|
|
6491
7397
|
"type": "LinkShape"
|
|
@@ -6592,7 +7498,7 @@ export const configManifest = {
|
|
|
6592
7498
|
},
|
|
6593
7499
|
{
|
|
6594
7500
|
"name": "descending",
|
|
6595
|
-
"type": "boolean"
|
|
7501
|
+
"type": "(boolean | undefined)"
|
|
6596
7502
|
},
|
|
6597
7503
|
{
|
|
6598
7504
|
"name": "missingLabel",
|
|
@@ -6702,11 +7608,7 @@ export const configManifest = {
|
|
|
6702
7608
|
},
|
|
6703
7609
|
{
|
|
6704
7610
|
"name": "transform",
|
|
6705
|
-
"type": "(filterConfigurationSchema | formulaConfigurationSchema | binConfigurationSchema | aggregateConfigurationSchema | coverageConfigurationSchema | flattenConfigurationSchema | cellsConfigurationSchema | pileupConfigurationSchema | mateConfigurationSchema)[]"
|
|
6706
|
-
},
|
|
6707
|
-
{
|
|
6708
|
-
"name": "source",
|
|
6709
|
-
"type": "MarkSource"
|
|
7611
|
+
"type": "(filterConfigurationSchema | formulaConfigurationSchema | binConfigurationSchema | aggregateConfigurationSchema | windowConfigurationSchema | coverageConfigurationSchema | flattenConfigurationSchema | cellsConfigurationSchema | pileupConfigurationSchema | mateConfigurationSchema)[]"
|
|
6710
7612
|
},
|
|
6711
7613
|
{
|
|
6712
7614
|
"name": "minBpPerPx",
|
|
@@ -6720,7 +7622,7 @@ export const configManifest = {
|
|
|
6720
7622
|
},
|
|
6721
7623
|
{
|
|
6722
7624
|
"name": "transform",
|
|
6723
|
-
"type": "(filterConfigurationSchema | formulaConfigurationSchema | binConfigurationSchema | aggregateConfigurationSchema | coverageConfigurationSchema | flattenConfigurationSchema | cellsConfigurationSchema | pileupConfigurationSchema | mateConfigurationSchema)[]"
|
|
7625
|
+
"type": "(filterConfigurationSchema | formulaConfigurationSchema | binConfigurationSchema | aggregateConfigurationSchema | windowConfigurationSchema | coverageConfigurationSchema | flattenConfigurationSchema | cellsConfigurationSchema | pileupConfigurationSchema | mateConfigurationSchema)[]"
|
|
6724
7626
|
},
|
|
6725
7627
|
{
|
|
6726
7628
|
"name": "facet",
|
|
@@ -6735,9 +7637,14 @@ export const configManifest = {
|
|
|
6735
7637
|
"type": "string[]",
|
|
6736
7638
|
"liftsNumbers": true
|
|
6737
7639
|
},
|
|
7640
|
+
{
|
|
7641
|
+
"name": "hidden",
|
|
7642
|
+
"type": "string[]",
|
|
7643
|
+
"liftsNumbers": true
|
|
7644
|
+
},
|
|
6738
7645
|
{
|
|
6739
7646
|
"name": "transform",
|
|
6740
|
-
"type": "(filterConfigurationSchema | formulaConfigurationSchema | binConfigurationSchema | aggregateConfigurationSchema | coverageConfigurationSchema | flattenConfigurationSchema | cellsConfigurationSchema | pileupConfigurationSchema | mateConfigurationSchema)[]"
|
|
7647
|
+
"type": "(filterConfigurationSchema | formulaConfigurationSchema | binConfigurationSchema | aggregateConfigurationSchema | windowConfigurationSchema | coverageConfigurationSchema | flattenConfigurationSchema | cellsConfigurationSchema | pileupConfigurationSchema | mateConfigurationSchema)[]"
|
|
6741
7648
|
}
|
|
6742
7649
|
],
|
|
6743
7650
|
"shorthand": {
|
|
@@ -6787,10 +7694,6 @@ export const configManifest = {
|
|
|
6787
7694
|
"name": "field",
|
|
6788
7695
|
"type": "string"
|
|
6789
7696
|
},
|
|
6790
|
-
{
|
|
6791
|
-
"name": "scale",
|
|
6792
|
-
"type": "(RowColorScale | undefined)"
|
|
6793
|
-
},
|
|
6794
7697
|
{
|
|
6795
7698
|
"name": "domain",
|
|
6796
7699
|
"type": "string[]",
|
|
@@ -6799,6 +7702,10 @@ export const configManifest = {
|
|
|
6799
7702
|
{
|
|
6800
7703
|
"name": "range",
|
|
6801
7704
|
"type": "CssColorEntry[]"
|
|
7705
|
+
},
|
|
7706
|
+
{
|
|
7707
|
+
"name": "unknown",
|
|
7708
|
+
"type": "(CssColor | undefined)"
|
|
6802
7709
|
}
|
|
6803
7710
|
],
|
|
6804
7711
|
"shorthand": {
|
|
@@ -6916,10 +7823,17 @@ export const configManifest = {
|
|
|
6916
7823
|
}
|
|
6917
7824
|
],
|
|
6918
7825
|
"legacyKeys": [
|
|
6919
|
-
"
|
|
6920
|
-
"
|
|
7826
|
+
"maxFeatureScreenDensity",
|
|
7827
|
+
"maxDisplayedBpPerPx",
|
|
7828
|
+
"mouseover",
|
|
6921
7829
|
"jexlFilters"
|
|
6922
7830
|
],
|
|
7831
|
+
"droppedKeys": [
|
|
7832
|
+
"maxFeatureScreenDensity",
|
|
7833
|
+
"maxDisplayedBpPerPx",
|
|
7834
|
+
"fetchSizeLimit",
|
|
7835
|
+
"mouseover"
|
|
7836
|
+
],
|
|
6923
7837
|
"aliases": [
|
|
6924
7838
|
"LinearArcDisplay",
|
|
6925
7839
|
"LinearPairedArcDisplay"
|
|
@@ -6947,11 +7861,11 @@ export const configManifest = {
|
|
|
6947
7861
|
},
|
|
6948
7862
|
{
|
|
6949
7863
|
"name": "ixFilePath",
|
|
6950
|
-
"type": "(LocalPathLocation | UriLocation | BlobLocation | FileHandleLocation)"
|
|
7864
|
+
"type": "((LocalPathLocation | UriLocation | BlobLocation | FileHandleLocation) | undefined)"
|
|
6951
7865
|
},
|
|
6952
7866
|
{
|
|
6953
7867
|
"name": "ixxFilePath",
|
|
6954
|
-
"type": "(LocalPathLocation | UriLocation | BlobLocation | FileHandleLocation)"
|
|
7868
|
+
"type": "((LocalPathLocation | UriLocation | BlobLocation | FileHandleLocation) | undefined)"
|
|
6955
7869
|
},
|
|
6956
7870
|
{
|
|
6957
7871
|
"name": "assemblyNames",
|
|
@@ -7385,9 +8299,8 @@ export const configManifest = {
|
|
|
7385
8299
|
"color",
|
|
7386
8300
|
"trackColors",
|
|
7387
8301
|
"hideUnlabelled",
|
|
7388
|
-
"
|
|
8302
|
+
"opacity",
|
|
7389
8303
|
"minAlignmentLength",
|
|
7390
|
-
"opacityByIdentity",
|
|
7391
8304
|
"fadeThinAlignmentsMode",
|
|
7392
8305
|
"type",
|
|
7393
8306
|
"offsetRadians",
|
|
@@ -7422,7 +8335,7 @@ export const configManifest = {
|
|
|
7422
8335
|
"color",
|
|
7423
8336
|
"trackColors",
|
|
7424
8337
|
"hideUnlabelled",
|
|
7425
|
-
"
|
|
8338
|
+
"opacity",
|
|
7426
8339
|
"minAlignmentLength",
|
|
7427
8340
|
"lodMode",
|
|
7428
8341
|
"type",
|
|
@@ -7447,6 +8360,7 @@ export const configManifest = {
|
|
|
7447
8360
|
"views"
|
|
7448
8361
|
],
|
|
7449
8362
|
"passThrough": [
|
|
8363
|
+
"alpha",
|
|
7450
8364
|
"colorBy"
|
|
7451
8365
|
]
|
|
7452
8366
|
},
|
|
@@ -7458,10 +8372,9 @@ export const configManifest = {
|
|
|
7458
8372
|
"color",
|
|
7459
8373
|
"trackColors",
|
|
7460
8374
|
"hideUnlabelled",
|
|
7461
|
-
"
|
|
8375
|
+
"opacity",
|
|
7462
8376
|
"minAlignmentLength",
|
|
7463
8377
|
"lodMode",
|
|
7464
|
-
"opacityByIdentity",
|
|
7465
8378
|
"fadeThinAlignmentsMode",
|
|
7466
8379
|
"type",
|
|
7467
8380
|
"cigarMode",
|
|
@@ -7488,6 +8401,7 @@ export const configManifest = {
|
|
|
7488
8401
|
"views"
|
|
7489
8402
|
],
|
|
7490
8403
|
"passThrough": [
|
|
8404
|
+
"alpha",
|
|
7491
8405
|
"colorBy"
|
|
7492
8406
|
]
|
|
7493
8407
|
},
|
|
@@ -7570,6 +8484,7 @@ export const configManifest = {
|
|
|
7570
8484
|
"filterBy",
|
|
7571
8485
|
"filterBySetting",
|
|
7572
8486
|
"hideMismatchesSetting",
|
|
8487
|
+
"sortedBy",
|
|
7573
8488
|
"trackMaxHeight"
|
|
7574
8489
|
],
|
|
7575
8490
|
"LinearVariantDisplay": [
|
|
@@ -7579,6 +8494,7 @@ export const configManifest = {
|
|
|
7579
8494
|
"clusterTree",
|
|
7580
8495
|
"jexlFilters",
|
|
7581
8496
|
"layout",
|
|
8497
|
+
"renderingModeSetting",
|
|
7582
8498
|
"showSidebarLabelsSetting",
|
|
7583
8499
|
"showTreeSetting",
|
|
7584
8500
|
"subtreeFilter",
|