@molgenis/vip-report-template 5.8.0 → 6.0.1

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Files changed (11) hide show
  1. package/package.json +18 -18
  2. package/src/components/filter/FilterVariantType.tsx +3 -5
  3. package/src/mocks/GRCh37/field_metadata.json +454 -0
  4. package/src/mocks/GRCh37/static.ts +5 -1
  5. package/src/mocks/GRCh38/alignment.cram.blob +0 -0
  6. package/src/mocks/GRCh38/alignment.cram.crai.blob +0 -0
  7. package/src/mocks/GRCh38/field_metadata.json +454 -0
  8. package/src/mocks/GRCh38/static.ts +5 -1
  9. package/src/mocks/MockApiClient.ts +13 -1
  10. package/src/views/SampleVariants.tsx +1 -1
  11. package/vite.config.mts +1 -2
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@molgenis/vip-report-template",
3
- "version": "5.8.0",
3
+ "version": "6.0.1",
4
4
  "description": "Report Template for Variant Call Format (VCF) Report Generator",
5
5
  "scripts": {
6
6
  "build": "vite build",
@@ -15,33 +15,33 @@
15
15
  },
16
16
  "license": "LGPL-3.0",
17
17
  "devDependencies": {
18
- "@molgenis/vite-plugin-inline": "^1.0.19",
19
- "@typescript-eslint/eslint-plugin": "^6.13.2",
20
- "@typescript-eslint/parser": "^6.13.2",
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- "@vitest/coverage-v8": "^1.0.1",
18
+ "@molgenis/vite-plugin-inline": "^1.0.21",
19
+ "@typescript-eslint/eslint-plugin": "^6.19.1",
20
+ "@typescript-eslint/parser": "^6.19.1",
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+ "@vitest/coverage-v8": "^1.2.1",
22
22
  "bulma": "^0.9.4",
23
- "eslint": "^8.55.0",
23
+ "eslint": "^8.56.0",
24
24
  "eslint-config-prettier": "^9.1.0",
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- "eslint-plugin-prettier": "^5.0.1",
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- "eslint-plugin-solid": "^0.13.0",
27
- "husky": "^8.0.3",
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- "jsdom": "^23.0.1",
29
- "prettier": "^3.1.0",
30
- "sass": "^1.69.5",
25
+ "eslint-plugin-prettier": "^5.1.3",
26
+ "eslint-plugin-solid": "^0.13.1",
27
+ "husky": "^9.0.5",
28
+ "jsdom": "^24.0.0",
29
+ "prettier": "^3.2.4",
30
+ "sass": "^1.70.0",
31
31
  "typescript": "^5.3.3",
32
- "vite": "^5.0.6",
33
- "vite-plugin-solid": "^2.7.2",
34
- "vitest": "^1.0.1"
32
+ "vite": "^5.0.12",
33
+ "vite-plugin-solid": "^2.9.1",
34
+ "vitest": "^1.2.1"
35
35
  },
36
36
  "dependencies": {
37
37
  "@fortawesome/fontawesome-svg-core": "^6.5.1",
38
38
  "@fortawesome/free-solid-svg-icons": "^6.5.1",
39
- "@molgenis/vip-report-api": "^4.8.0",
40
- "@molgenis/vip-report-vcf": "^1.8.0",
39
+ "@molgenis/vip-report-api": "^5.0.2",
40
+ "@molgenis/vip-report-vcf": "^2.0.0",
41
41
  "@solidjs/router": "^0.9.1",
42
42
  "base64-js": "^1.5.1",
43
43
  "igv": "^2.15.11",
44
- "solid-js": "^1.8.7"
44
+ "solid-js": "^1.8.12"
45
45
  },
46
46
  "lint-staged": {
47
47
  "src/**/*.{tsx,ts}": [
package/src/components/filter/FilterVariantType.tsx CHANGED
@@ -66,14 +66,12 @@ export const FilterVariantType: Component<
66
66
  };
67
67
 
68
68
  if (props.query !== undefined && props.query.args.length > 0) {
69
- console.log(props.query);
70
- const query: Query = props.query.args[0] as Query;
71
- (query.args as Query[]).forEach((childQuery) => {
72
- if (childQuery.operator == "and") {
69
+ (props.query.args as Query[]).forEach((childQuery) => {
70
+ if (childQuery.operator == "or") {
73
71
  group["SNV"] = true;
74
72
  snvChecked = true;
75
73
  }
76
- if (childQuery.operator == "or") {
74
+ if (childQuery.operator == "and") {
77
75
  group["SV"] = true;
78
76
  svChecked = true;
79
77
  }
package/src/mocks/GRCh37/field_metadata.json ADDED
@@ -0,0 +1,454 @@
1
+ {
2
+ "format": {
3
+ "VI": {
4
+ "label": "Inheritance",
5
+ "description": "An enumeration of possible inheritance modes based on the pedigree of the sample. Potential values: AD, AD_IP, AR, AR_C, XLR, XLD, YL, MT",
6
+ "numberType": "OTHER",
7
+ "separator": ",",
8
+ "type": "CATEGORICAL",
9
+ "categories": [
10
+ "AD",
11
+ "AD_IP",
12
+ "AR",
13
+ "AR_C",
14
+ "XLD",
15
+ "XLR",
16
+ "YL",
17
+ "MT"
18
+ ]
19
+ }
20
+ },
21
+ "info": {
22
+ "CSQ": {
23
+ "nestedFields": {
24
+ "ALLELE_NUM": {
25
+ "label": "Allele Nr.",
26
+ "description": "Allele nr within the VCF file.",
27
+ "numberType": "NUMBER",
28
+ "numberCount": 1,
29
+ "type": "INTEGER"
30
+ },
31
+ "ALPHSCORE": {
32
+ "label": "AlphScore",
33
+ "description": "AlphScore pathogenicity score for missense variants",
34
+ "numberType": "NUMBER",
35
+ "numberCount": 1,
36
+ "type": "FLOAT"
37
+ },
38
+ "CAPICE_CL": {
39
+ "label": "CAPICE",
40
+ "description": "CAPICE classification",
41
+ "numberType": "NUMBER",
42
+ "numberCount": 1,
43
+ "type": "CATEGORICAL",
44
+ "categories": [
45
+ "B",
46
+ "LB",
47
+ "VUS",
48
+ "LP",
49
+ "P"
50
+ ]
51
+ },
52
+ "CAPICE_SC": {
53
+ "label": "CAPICE",
54
+ "description": "CAPICE pathogenicity score",
55
+ "numberType": "NUMBER",
56
+ "numberCount": 1,
57
+ "type": "FLOAT"
58
+ },
59
+ "cDNA_position": {
60
+ "label": "cDNA pos",
61
+ "description": "Position within the cDNA.",
62
+ "numberType": "NUMBER",
63
+ "numberCount": 1,
64
+ "type": "STRING"
65
+ },
66
+ "CDS_position": {
67
+ "label": "CDS pos",
68
+ "description": "Position within the coding sequence.",
69
+ "numberType": "NUMBER",
70
+ "numberCount": 1,
71
+ "type": "STRING"
72
+ },
73
+ "CLIN_SIG": {
74
+ "label": "ClinVar",
75
+ "description": "ClinVar classification(s)",
76
+ "numberType": "OTHER",
77
+ "separator": "&",
78
+ "type": "STRING"
79
+ },
80
+ "clinVar": {
81
+ "label": "ClinVar ID",
82
+ "description": "ClinVar Variation ID",
83
+ "numberType": "OTHER",
84
+ "type": "INTEGER"
85
+ },
86
+ "clinVar_CLNID": {
87
+ "label": "ClinVar ID",
88
+ "description": "ClinVar Variation ID",
89
+ "numberType": "OTHER",
90
+ "type": "INTEGER"
91
+ },
92
+ "clinVar_CLNSIG": {
93
+ "label": "ClinVar variant",
94
+ "description": "Clinical significance for this single variant",
95
+ "numberType": "OTHER",
96
+ "separator": "/",
97
+ "type": "CATEGORICAL",
98
+ "categories": [
99
+ "Benign",
100
+ "Likely_benign",
101
+ "Uncertain_significance",
102
+ "Likely_pathogenic",
103
+ "Pathogenic",
104
+ "Conflicting_interpretations_of_pathogenicity"
105
+ ]
106
+ },
107
+ "clinVar_CLNSIGINCL": {
108
+ "label": "ClinVar variant combination",
109
+ "description": "Clinical significance for a haplotype or genotype that includes this variant",
110
+ "numberType": "OTHER",
111
+ "separator": "&",
112
+ "type": "CATEGORICAL",
113
+ "categories": [
114
+ "Benign",
115
+ "Likely_benign",
116
+ "Uncertain_significance",
117
+ "Likely_pathogenic",
118
+ "Pathogenic",
119
+ "Conflicting_interpretations_of_pathogenicity"
120
+ ]
121
+ },
122
+ "clinVar_CLNREVSTAT": {
123
+ "label": "ClinVar status",
124
+ "description": "ClinVar review status",
125
+ "numberType": "OTHER",
126
+ "separator": "&",
127
+ "type": "CATEGORICAL",
128
+ "categories": [
129
+ "practice_guideline",
130
+ "reviewed_by_expert_panel",
131
+ "criteria_provided",
132
+ "_multiple_submitters",
133
+ "_no_conflicts",
134
+ "_single_submitter",
135
+ "_conflicting_interpretations",
136
+ "no_assertion_criteria_provided",
137
+ "no_assertion_provided"
138
+ ]
139
+ },
140
+ "Consequence": {
141
+ "label": "Effect",
142
+ "description": "Effect(s) described as Sequence Ontology term(s)",
143
+ "numberType": "OTHER",
144
+ "separator": "&",
145
+ "type": "STRING"
146
+ },
147
+ "Existing_variation": {
148
+ "label": "Ex. var.",
149
+ "description": "Existing variation.",
150
+ "numberType": "OTHER",
151
+ "separator": "&",
152
+ "type": "STRING"
153
+ },
154
+ "Feature_type": {
155
+ "label": "Feature Type.",
156
+ "description": "The VEP feature type",
157
+ "numberType": "NUMBER",
158
+ "numberCount": 1,
159
+ "type": "CATEGORICAL",
160
+ "categories": [
161
+ "Transcript",
162
+ "RegulatoryFeature",
163
+ "MotifFeature"
164
+ ],
165
+ "required": true
166
+ },
167
+ "FLAGS": {
168
+ "label": "Flags",
169
+ "description": "Flags",
170
+ "numberType": "OTHER",
171
+ "separator": "&",
172
+ "type": "STRING"
173
+ },
174
+ "GADO_PD": {
175
+ "label": "GADO_PD",
176
+ "description": "The GADO prediction for the relation between the HPO terms of the proband(s) and the gene, HC: high confidence, LC: low confidence.",
177
+ "numberType": "NUMBER",
178
+ "numberCount": 1,
179
+ "type": "CATEGORICAL",
180
+ "categories": [
181
+ "LC",
182
+ "HC"
183
+ ]
184
+ },
185
+ "GADO_SC": {
186
+ "label": "GADO_SC",
187
+ "description": "The combined prioritization GADO Z-score over the HPO of the proband(s) terms for this case.",
188
+ "numberType": "NUMBER",
189
+ "numberCount": 1,
190
+ "type": "FLOAT"
191
+ },
192
+ "gnomAD_AF": {
193
+ "label": "gnomAD AF",
194
+ "description": "gnomAD allele frequency",
195
+ "numberType": "NUMBER",
196
+ "numberCount": 1,
197
+ "type": "FLOAT"
198
+ },
199
+ "gnomAD_COV": {
200
+ "label": "gnomAD COV",
201
+ "description": "gnomAD coverage (percent of individuals in gnomAD source)",
202
+ "numberType": "NUMBER",
203
+ "numberCount": 1,
204
+ "type": "FLOAT"
205
+ },
206
+ "gnomAD_FAF95": {
207
+ "label": "gnomAD FAF95",
208
+ "description": "gnomAD filter allele frequency (95% confidence)",
209
+ "numberType": "NUMBER",
210
+ "numberCount": 1,
211
+ "type": "FLOAT"
212
+ },
213
+ "gnomAD_FAF99": {
214
+ "label": "gnomAD FAF99",
215
+ "description": "gnomAD filter allele frequency (99% confidence)",
216
+ "numberType": "NUMBER",
217
+ "numberCount": 1,
218
+ "type": "FLOAT"
219
+ },
220
+ "gnomAD_HN": {
221
+ "label": "gnomAD HN",
222
+ "description": "gnomAD number of homozygotes",
223
+ "numberType": "NUMBER",
224
+ "numberCount": 1,
225
+ "type": "INTEGER"
226
+ },
227
+ "gnomAD_SRC": {
228
+ "label": "gnomAD SRC",
229
+ "description": "gnomAD source (E=exomes, G=genomes, T=total)",
230
+ "numberType": "NUMBER",
231
+ "numberCount": 1,
232
+ "type": "CATEGORICAL",
233
+ "categories": [
234
+ "E",
235
+ "G",
236
+ "T"
237
+ ]
238
+ },
239
+ "gnomAD_QC": {
240
+ "label": "gnomAD QC",
241
+ "description": "gnomAD quality control filters that failed",
242
+ "numberType": "OTHER",
243
+ "separator": "&",
244
+ "type": "STRING"
245
+ },
246
+ "HGNC_ID": {
247
+ "label": "HGNC ID",
248
+ "description": "The HGNC gene ID",
249
+ "numberType": "NUMBER",
250
+ "numberCount": 1,
251
+ "type": "INTEGER"
252
+ },
253
+ "HGVSc": {
254
+ "label": "HGVS C",
255
+ "description": "HGVS nomenclature: coding DNA reference sequence",
256
+ "numberType": "NUMBER",
257
+ "numberCount": 1,
258
+ "type": "STRING"
259
+ },
260
+ "HGVSp": {
261
+ "label": "HGVS P",
262
+ "description": "HGVS nomenclature: protein reference sequence",
263
+ "numberType": "NUMBER",
264
+ "numberCount": 1,
265
+ "type": "STRING"
266
+ },
267
+ "HPO": {
268
+ "label": "HPO",
269
+ "description": "Human phenotype ontology matches.",
270
+ "numberType": "OTHER",
271
+ "separator": "&",
272
+ "type": "STRING"
273
+ },
274
+ "IMPACT": {
275
+ "label": "Impact",
276
+ "description": "The Impact as predicted by VEP",
277
+ "numberType": "NUMBER",
278
+ "numberCount": 1,
279
+ "type": "CATEGORICAL",
280
+ "categories": [
281
+ "LOW",
282
+ "MODERATE",
283
+ "HIGH",
284
+ "MODIFIER"
285
+ ],
286
+ "required": true
287
+ },
288
+ "IncompletePenetrance": {
289
+ "label": "Gene: Inc.Pen.",
290
+ "description": "The gene is associated with Incomplete Penetrance (1:true)",
291
+ "numberType": "NUMBER",
292
+ "numberCount": 1,
293
+ "type": "STRING"
294
+ },
295
+ "InheritanceModesGene": {
296
+ "label": "Inh.Pat.",
297
+ "description": "Inheritance pattern",
298
+ "numberType": "OTHER",
299
+ "separator": "&",
300
+ "type": "STRING"
301
+ },
302
+ "ncER": {
303
+ "label": "ncER",
304
+ "description": "Non-coding essential regulation, from: 0(probably not essential for regulation) to 100 (probably essential for regulation).",
305
+ "numberType": "NUMBER",
306
+ "numberCount": 1,
307
+ "type": "FLOAT"
308
+ },
309
+ "PHENO": {
310
+ "label": "Pheno",
311
+ "description": "Phenotype match.",
312
+ "numberType": "OTHER",
313
+ "separator": "&",
314
+ "type": "INTEGER"
315
+ },
316
+ "PICK": {
317
+ "label": "PICK",
318
+ "description": "Boolean indicating if this is the VEP picked transcript.",
319
+ "numberType": "NUMBER",
320
+ "numberCount": 1,
321
+ "type": "INTEGER"
322
+ },
323
+ "PolyPhen": {
324
+ "label": "PolyPhen",
325
+ "description": "PolyPhen score.",
326
+ "numberType": "NUMBER",
327
+ "numberCount": 1,
328
+ "type": "FLOAT"
329
+ },
330
+ "Protein_position": {
331
+ "label": "Protein pos",
332
+ "description": "Position within the protein.",
333
+ "numberType": "NUMBER",
334
+ "numberCount": 1,
335
+ "type": "STRING"
336
+ },
337
+ "PUBMED": {
338
+ "label": "PubMed",
339
+ "description": "PubMed citations",
340
+ "numberType": "OTHER",
341
+ "separator": "&",
342
+ "type": "INTEGER"
343
+ },
344
+ "SIFT": {
345
+ "label": "SIFT",
346
+ "description": "SIFT score.",
347
+ "numberType": "NUMBER",
348
+ "numberCount": 1,
349
+ "type": "FLOAT"
350
+ },
351
+ "SOMATIC": {
352
+ "label": "Somatic",
353
+ "description": "Somatic.",
354
+ "numberType": "OTHER",
355
+ "separator": "&",
356
+ "type": "INTEGER"
357
+ },
358
+ "SpliceAI_pred_DS_AG": {
359
+ "label": "SpliceAI AG",
360
+ "description": "SpliceAI Delta score (acceptor gain).",
361
+ "numberType": "NUMBER",
362
+ "numberCount": 1,
363
+ "type": "FLOAT"
364
+ },
365
+ "SpliceAI_pred_DS_AL": {
366
+ "label": "SpliceAI AL",
367
+ "description": "SpliceAI Delta score (acceptor loss).",
368
+ "numberType": "NUMBER",
369
+ "numberCount": 1,
370
+ "type": "FLOAT"
371
+ },
372
+ "SpliceAI_pred_DS_DG": {
373
+ "label": "SpliceAI DG",
374
+ "description": "SpliceAI Delta score (donor gain).",
375
+ "numberType": "NUMBER",
376
+ "numberCount": 1,
377
+ "type": "FLOAT"
378
+ },
379
+ "SpliceAI_pred_DS_DL": {
380
+ "label": "SpliceAI DL",
381
+ "description": "SpliceAI Delta score (donor loss).",
382
+ "numberType": "NUMBER",
383
+ "numberCount": 1,
384
+ "type": "FLOAT"
385
+ },
386
+ "STRAND": {
387
+ "label": "Strand",
388
+ "description": "The strand of the gene (0=- 1=+).",
389
+ "numberType": "NUMBER",
390
+ "numberCount": 1,
391
+ "type": "INTEGER"
392
+ },
393
+ "SYMBOL": {
394
+ "label": "Gene",
395
+ "description": "Gene symbol",
396
+ "numberType": "NUMBER",
397
+ "numberCount": 1,
398
+ "type": "STRING"
399
+ },
400
+ "VIPC": {
401
+ "label": "VIP",
402
+ "description": "VIP classification",
403
+ "numberType": "NUMBER",
404
+ "numberCount": 1,
405
+ "type": "STRING",
406
+ "required": true
407
+ },
408
+ "VIPL": {
409
+ "label": "VIP labels",
410
+ "description": "VIP decision tree labels",
411
+ "numberType": "NUMBER",
412
+ "numberCount": 1,
413
+ "type": "STRING"
414
+ },
415
+ "VIPP": {
416
+ "label": "VIP path",
417
+ "description": "VIP decision tree path",
418
+ "numberType": "OTHER",
419
+ "separator": "&",
420
+ "type": "STRING",
421
+ "required": true
422
+ },
423
+ "VKGL_CL": {
424
+ "label": "VKGL",
425
+ "description": "VKGL consensus classification",
426
+ "numberType": "NUMBER",
427
+ "numberCount": 1,
428
+ "type": "CATEGORICAL",
429
+ "categories": [
430
+ "B",
431
+ "LB",
432
+ "VUS",
433
+ "LP",
434
+ "P"
435
+ ]
436
+ },
437
+ "VKGL_UMCG": {
438
+ "label": "MVL",
439
+ "description": "UMCG managed variant list classification",
440
+ "numberType": "NUMBER",
441
+ "numberCount": 1,
442
+ "type": "CATEGORICAL",
443
+ "categories": [
444
+ "B",
445
+ "LB",
446
+ "VUS",
447
+ "LP",
448
+ "P"
449
+ ]
450
+ }
451
+ }
452
+ }
453
+ }
454
+ }
package/src/mocks/GRCh37/static.ts CHANGED
@@ -39,6 +39,7 @@ import fastaUrlX_48932771_48933271 from "./fasta/X-48932771-48933271.fasta.gz.bl
39
39
  import fastaUrlY_2655391_2655891 from "./fasta/Y-2655391-2655891.fasta.gz.blob";
40
40
  import fastaUrlMT_15076_15576 from "./fasta/MT-15076-15576.fasta.gz.blob";
41
41
  import genesUrl from "./genes.gff.gz.blob";
42
+ import vcfMetaJson from "./field_metadata.json";
42
43
  import vcfUrlFamily from "./vcf/family.vcf.blob";
43
44
  import vcfUrlNoVep from "./vcf/no_vep.vcf.blob";
44
45
  import vcfUrlSamples0 from "./vcf/samples_0.vcf.blob";
@@ -47,11 +48,12 @@ import vcfUrlSamples100 from "./vcf/samples_100.vcf.blob";
47
48
 
48
49
  import { fetchAsBytes } from "../utils";
49
50
  import { DecisionTree } from "@molgenis/vip-report-api/src/Api";
51
+ import { Metadata } from "@molgenis/vip-report-vcf/src/FieldMetadata";
50
52
 
51
53
  export const cram = await fetchAsBytes(cramUrl as string);
52
54
  export const crai = await fetchAsBytes(craiUrl as string);
53
55
 
54
- export const decisionTree: DecisionTree = decisionTreeJson as DecisionTree;
56
+ export const decisionTree: DecisionTree = decisionTreeJson as unknown as DecisionTree;
55
57
 
56
58
  export const fastaGz = {
57
59
  "1:10042288-10042788": await fetchAsBytes(fastaUrl1_10042288_10042788 as string),
@@ -95,6 +97,8 @@ export const fastaGz = {
95
97
 
96
98
  export const genesGz = await fetchAsBytes(genesUrl as string);
97
99
 
100
+ export const vcfMeta = vcfMetaJson as unknown as Metadata;
101
+
98
102
  export const vcfFamily = await fetchAsBytes(vcfUrlFamily as string);
99
103
 
100
104
  export const vcfNoVep = await fetchAsBytes(vcfUrlNoVep as string);
package/src/mocks/GRCh38/field_metadata.json ADDED
@@ -0,0 +1,454 @@
1
+ {
2
+ "format": {
3
+ "VI": {
4
+ "label": "Inheritance",
5
+ "description": "An enumeration of possible inheritance modes based on the pedigree of the sample. Potential values: AD, AD_IP, AR, AR_C, XLR, XLD, YL, MT",
6
+ "numberType": "OTHER",
7
+ "separator": ",",
8
+ "type": "CATEGORICAL",
9
+ "categories": [
10
+ "AD",
11
+ "AD_IP",
12
+ "AR",
13
+ "AR_C",
14
+ "XLD",
15
+ "XLR",
16
+ "YL",
17
+ "MT"
18
+ ]
19
+ }
20
+ },
21
+ "info": {
22
+ "CSQ": {
23
+ "nestedFields": {
24
+ "ALLELE_NUM": {
25
+ "label": "Allele Nr.",
26
+ "description": "Allele nr within the VCF file.",
27
+ "numberType": "NUMBER",
28
+ "numberCount": 1,
29
+ "type": "INTEGER"
30
+ },
31
+ "ALPHSCORE": {
32
+ "label": "AlphScore",
33
+ "description": "AlphScore pathogenicity score for missense variants",
34
+ "numberType": "NUMBER",
35
+ "numberCount": 1,
36
+ "type": "FLOAT"
37
+ },
38
+ "CAPICE_CL": {
39
+ "label": "CAPICE",
40
+ "description": "CAPICE classification",
41
+ "numberType": "NUMBER",
42
+ "numberCount": 1,
43
+ "type": "CATEGORICAL",
44
+ "categories": [
45
+ "B",
46
+ "LB",
47
+ "VUS",
48
+ "LP",
49
+ "P"
50
+ ]
51
+ },
52
+ "CAPICE_SC": {
53
+ "label": "CAPICE",
54
+ "description": "CAPICE pathogenicity score",
55
+ "numberType": "NUMBER",
56
+ "numberCount": 1,
57
+ "type": "FLOAT"
58
+ },
59
+ "cDNA_position": {
60
+ "label": "cDNA pos",
61
+ "description": "Position within the cDNA.",
62
+ "numberType": "NUMBER",
63
+ "numberCount": 1,
64
+ "type": "STRING"
65
+ },
66
+ "CDS_position": {
67
+ "label": "CDS pos",
68
+ "description": "Position within the coding sequence.",
69
+ "numberType": "NUMBER",
70
+ "numberCount": 1,
71
+ "type": "STRING"
72
+ },
73
+ "CLIN_SIG": {
74
+ "label": "ClinVar",
75
+ "description": "ClinVar classification(s)",
76
+ "numberType": "OTHER",
77
+ "separator": "&",
78
+ "type": "STRING"
79
+ },
80
+ "clinVar": {
81
+ "label": "ClinVar ID",
82
+ "description": "ClinVar Variation ID",
83
+ "numberType": "OTHER",
84
+ "type": "INTEGER"
85
+ },
86
+ "clinVar_CLNID": {
87
+ "label": "ClinVar ID",
88
+ "description": "ClinVar Variation ID",
89
+ "numberType": "OTHER",
90
+ "type": "INTEGER"
91
+ },
92
+ "clinVar_CLNSIG": {
93
+ "label": "ClinVar variant",
94
+ "description": "Clinical significance for this single variant",
95
+ "numberType": "OTHER",
96
+ "separator": "/",
97
+ "type": "CATEGORICAL",
98
+ "categories": [
99
+ "Benign",
100
+ "Likely_benign",
101
+ "Uncertain_significance",
102
+ "Likely_pathogenic",
103
+ "Pathogenic",
104
+ "Conflicting_interpretations_of_pathogenicity"
105
+ ]
106
+ },
107
+ "clinVar_CLNSIGINCL": {
108
+ "label": "ClinVar variant combination",
109
+ "description": "Clinical significance for a haplotype or genotype that includes this variant",
110
+ "numberType": "OTHER",
111
+ "separator": "&",
112
+ "type": "CATEGORICAL",
113
+ "categories": [
114
+ "Benign",
115
+ "Likely_benign",
116
+ "Uncertain_significance",
117
+ "Likely_pathogenic",
118
+ "Pathogenic",
119
+ "Conflicting_interpretations_of_pathogenicity"
120
+ ]
121
+ },
122
+ "clinVar_CLNREVSTAT": {
123
+ "label": "ClinVar status",
124
+ "description": "ClinVar review status",
125
+ "numberType": "OTHER",
126
+ "separator": "&",
127
+ "type": "CATEGORICAL",
128
+ "categories": [
129
+ "practice_guideline",
130
+ "reviewed_by_expert_panel",
131
+ "criteria_provided",
132
+ "_multiple_submitters",
133
+ "_no_conflicts",
134
+ "_single_submitter",
135
+ "_conflicting_interpretations",
136
+ "no_assertion_criteria_provided",
137
+ "no_assertion_provided"
138
+ ]
139
+ },
140
+ "Consequence": {
141
+ "label": "Effect",
142
+ "description": "Effect(s) described as Sequence Ontology term(s)",
143
+ "numberType": "OTHER",
144
+ "separator": "&",
145
+ "type": "STRING"
146
+ },
147
+ "Existing_variation": {
148
+ "label": "Ex. var.",
149
+ "description": "Existing variation.",
150
+ "numberType": "OTHER",
151
+ "separator": "&",
152
+ "type": "STRING"
153
+ },
154
+ "Feature_type": {
155
+ "label": "Feature Type.",
156
+ "description": "The VEP feature type",
157
+ "numberType": "NUMBER",
158
+ "numberCount": 1,
159
+ "type": "CATEGORICAL",
160
+ "categories": [
161
+ "Transcript",
162
+ "RegulatoryFeature",
163
+ "MotifFeature"
164
+ ],
165
+ "required": true
166
+ },
167
+ "FLAGS": {
168
+ "label": "Flags",
169
+ "description": "Flags",
170
+ "numberType": "OTHER",
171
+ "separator": "&",
172
+ "type": "STRING"
173
+ },
174
+ "GADO_PD": {
175
+ "label": "GADO_PD",
176
+ "description": "The GADO prediction for the relation between the HPO terms of the proband(s) and the gene, HC: high confidence, LC: low confidence.",
177
+ "numberType": "NUMBER",
178
+ "numberCount": 1,
179
+ "type": "CATEGORICAL",
180
+ "categories": [
181
+ "LC",
182
+ "HC"
183
+ ]
184
+ },
185
+ "GADO_SC": {
186
+ "label": "GADO_SC",
187
+ "description": "The combined prioritization GADO Z-score over the HPO of the proband(s) terms for this case.",
188
+ "numberType": "NUMBER",
189
+ "numberCount": 1,
190
+ "type": "FLOAT"
191
+ },
192
+ "gnomAD_AF": {
193
+ "label": "gnomAD AF",
194
+ "description": "gnomAD allele frequency",
195
+ "numberType": "NUMBER",
196
+ "numberCount": 1,
197
+ "type": "FLOAT"
198
+ },
199
+ "gnomAD_COV": {
200
+ "label": "gnomAD COV",
201
+ "description": "gnomAD coverage (percent of individuals in gnomAD source)",
202
+ "numberType": "NUMBER",
203
+ "numberCount": 1,
204
+ "type": "FLOAT"
205
+ },
206
+ "gnomAD_FAF95": {
207
+ "label": "gnomAD FAF95",
208
+ "description": "gnomAD filter allele frequency (95% confidence)",
209
+ "numberType": "NUMBER",
210
+ "numberCount": 1,
211
+ "type": "FLOAT"
212
+ },
213
+ "gnomAD_FAF99": {
214
+ "label": "gnomAD FAF99",
215
+ "description": "gnomAD filter allele frequency (99% confidence)",
216
+ "numberType": "NUMBER",
217
+ "numberCount": 1,
218
+ "type": "FLOAT"
219
+ },
220
+ "gnomAD_HN": {
221
+ "label": "gnomAD HN",
222
+ "description": "gnomAD number of homozygotes",
223
+ "numberType": "NUMBER",
224
+ "numberCount": 1,
225
+ "type": "INTEGER"
226
+ },
227
+ "gnomAD_SRC": {
228
+ "label": "gnomAD SRC",
229
+ "description": "gnomAD source (E=exomes, G=genomes, T=total)",
230
+ "numberType": "NUMBER",
231
+ "numberCount": 1,
232
+ "type": "CATEGORICAL",
233
+ "categories": [
234
+ "E",
235
+ "G",
236
+ "T"
237
+ ]
238
+ },
239
+ "gnomAD_QC": {
240
+ "label": "gnomAD QC",
241
+ "description": "gnomAD quality control filters that failed",
242
+ "numberType": "OTHER",
243
+ "separator": "&",
244
+ "type": "STRING"
245
+ },
246
+ "HGNC_ID": {
247
+ "label": "HGNC ID",
248
+ "description": "The HGNC gene ID",
249
+ "numberType": "NUMBER",
250
+ "numberCount": 1,
251
+ "type": "INTEGER"
252
+ },
253
+ "HGVSc": {
254
+ "label": "HGVS C",
255
+ "description": "HGVS nomenclature: coding DNA reference sequence",
256
+ "numberType": "NUMBER",
257
+ "numberCount": 1,
258
+ "type": "STRING"
259
+ },
260
+ "HGVSp": {
261
+ "label": "HGVS P",
262
+ "description": "HGVS nomenclature: protein reference sequence",
263
+ "numberType": "NUMBER",
264
+ "numberCount": 1,
265
+ "type": "STRING"
266
+ },
267
+ "HPO": {
268
+ "label": "HPO",
269
+ "description": "Human phenotype ontology matches.",
270
+ "numberType": "OTHER",
271
+ "separator": "&",
272
+ "type": "STRING"
273
+ },
274
+ "IMPACT": {
275
+ "label": "Impact",
276
+ "description": "The Impact as predicted by VEP",
277
+ "numberType": "NUMBER",
278
+ "numberCount": 1,
279
+ "type": "CATEGORICAL",
280
+ "categories": [
281
+ "LOW",
282
+ "MODERATE",
283
+ "HIGH",
284
+ "MODIFIER"
285
+ ],
286
+ "required": true
287
+ },
288
+ "IncompletePenetrance": {
289
+ "label": "Gene: Inc.Pen.",
290
+ "description": "The gene is associated with Incomplete Penetrance (1:true)",
291
+ "numberType": "NUMBER",
292
+ "numberCount": 1,
293
+ "type": "STRING"
294
+ },
295
+ "InheritanceModesGene": {
296
+ "label": "Inh.Pat.",
297
+ "description": "Inheritance pattern",
298
+ "numberType": "OTHER",
299
+ "separator": "&",
300
+ "type": "STRING"
301
+ },
302
+ "ncER": {
303
+ "label": "ncER",
304
+ "description": "Non-coding essential regulation, from: 0(probably not essential for regulation) to 100 (probably essential for regulation).",
305
+ "numberType": "NUMBER",
306
+ "numberCount": 1,
307
+ "type": "FLOAT"
308
+ },
309
+ "PHENO": {
310
+ "label": "Pheno",
311
+ "description": "Phenotype match.",
312
+ "numberType": "OTHER",
313
+ "separator": "&",
314
+ "type": "INTEGER"
315
+ },
316
+ "PICK": {
317
+ "label": "PICK",
318
+ "description": "Boolean indicating if this is the VEP picked transcript.",
319
+ "numberType": "NUMBER",
320
+ "numberCount": 1,
321
+ "type": "INTEGER"
322
+ },
323
+ "PolyPhen": {
324
+ "label": "PolyPhen",
325
+ "description": "PolyPhen score.",
326
+ "numberType": "NUMBER",
327
+ "numberCount": 1,
328
+ "type": "FLOAT"
329
+ },
330
+ "Protein_position": {
331
+ "label": "Protein pos",
332
+ "description": "Position within the protein.",
333
+ "numberType": "NUMBER",
334
+ "numberCount": 1,
335
+ "type": "STRING"
336
+ },
337
+ "PUBMED": {
338
+ "label": "PubMed",
339
+ "description": "PubMed citations",
340
+ "numberType": "OTHER",
341
+ "separator": "&",
342
+ "type": "INTEGER"
343
+ },
344
+ "SIFT": {
345
+ "label": "SIFT",
346
+ "description": "SIFT score.",
347
+ "numberType": "NUMBER",
348
+ "numberCount": 1,
349
+ "type": "FLOAT"
350
+ },
351
+ "SOMATIC": {
352
+ "label": "Somatic",
353
+ "description": "Somatic.",
354
+ "numberType": "OTHER",
355
+ "separator": "&",
356
+ "type": "INTEGER"
357
+ },
358
+ "SpliceAI_pred_DS_AG": {
359
+ "label": "SpliceAI AG",
360
+ "description": "SpliceAI Delta score (acceptor gain).",
361
+ "numberType": "NUMBER",
362
+ "numberCount": 1,
363
+ "type": "FLOAT"
364
+ },
365
+ "SpliceAI_pred_DS_AL": {
366
+ "label": "SpliceAI AL",
367
+ "description": "SpliceAI Delta score (acceptor loss).",
368
+ "numberType": "NUMBER",
369
+ "numberCount": 1,
370
+ "type": "FLOAT"
371
+ },
372
+ "SpliceAI_pred_DS_DG": {
373
+ "label": "SpliceAI DG",
374
+ "description": "SpliceAI Delta score (donor gain).",
375
+ "numberType": "NUMBER",
376
+ "numberCount": 1,
377
+ "type": "FLOAT"
378
+ },
379
+ "SpliceAI_pred_DS_DL": {
380
+ "label": "SpliceAI DL",
381
+ "description": "SpliceAI Delta score (donor loss).",
382
+ "numberType": "NUMBER",
383
+ "numberCount": 1,
384
+ "type": "FLOAT"
385
+ },
386
+ "STRAND": {
387
+ "label": "Strand",
388
+ "description": "The strand of the gene (0=- 1=+).",
389
+ "numberType": "NUMBER",
390
+ "numberCount": 1,
391
+ "type": "INTEGER"
392
+ },
393
+ "SYMBOL": {
394
+ "label": "Gene",
395
+ "description": "Gene symbol",
396
+ "numberType": "NUMBER",
397
+ "numberCount": 1,
398
+ "type": "STRING"
399
+ },
400
+ "VIPC": {
401
+ "label": "VIP",
402
+ "description": "VIP classification",
403
+ "numberType": "NUMBER",
404
+ "numberCount": 1,
405
+ "type": "STRING",
406
+ "required": true
407
+ },
408
+ "VIPL": {
409
+ "label": "VIP labels",
410
+ "description": "VIP decision tree labels",
411
+ "numberType": "NUMBER",
412
+ "numberCount": 1,
413
+ "type": "STRING"
414
+ },
415
+ "VIPP": {
416
+ "label": "VIP path",
417
+ "description": "VIP decision tree path",
418
+ "numberType": "OTHER",
419
+ "separator": "&",
420
+ "type": "STRING",
421
+ "required": true
422
+ },
423
+ "VKGL_CL": {
424
+ "label": "VKGL",
425
+ "description": "VKGL consensus classification",
426
+ "numberType": "NUMBER",
427
+ "numberCount": 1,
428
+ "type": "CATEGORICAL",
429
+ "categories": [
430
+ "B",
431
+ "LB",
432
+ "VUS",
433
+ "LP",
434
+ "P"
435
+ ]
436
+ },
437
+ "VKGL_UMCG": {
438
+ "label": "MVL",
439
+ "description": "UMCG managed variant list classification",
440
+ "numberType": "NUMBER",
441
+ "numberCount": 1,
442
+ "type": "CATEGORICAL",
443
+ "categories": [
444
+ "B",
445
+ "LB",
446
+ "VUS",
447
+ "LP",
448
+ "P"
449
+ ]
450
+ }
451
+ }
452
+ }
453
+ }
454
+ }
package/src/mocks/GRCh38/static.ts CHANGED
@@ -27,6 +27,7 @@ import fastaUrl_chrM_15075_15575 from "./fasta/chrM-15075-15575.fasta.gz.blob";
27
27
  import fastaUrl_chrX_49075112_49075612 from "./fasta/chrX-49075112-49075612.fasta.gz.blob";
28
28
  import fastaUrl_chrY_2787350_2787850 from "./fasta/chrY-2787350-2787850.fasta.gz.blob";
29
29
  import genesUrl from "./genes.gff.gz.blob";
30
+ import vcfMetaJson from "./field_metadata.json";
30
31
  import vcfUrlFamily from "./vcf/family.vcf.blob";
31
32
  import vcfUrlNoVep from "./vcf/no_vep.vcf.blob";
32
33
  import vcfUrlSamples0 from "./vcf/samples_0.vcf.blob";
@@ -36,11 +37,12 @@ import vcfUrlSamples100 from "./vcf/samples_100.vcf.blob";
36
37
  import { fetchAsBytes } from "../utils";
37
38
  import decisionTreeJson from "./decisionTree.json";
38
39
  import { DecisionTree } from "@molgenis/vip-report-api/src/Api";
40
+ import { Metadata } from "@molgenis/vip-report-vcf/src/FieldMetadata";
39
41
 
40
42
  export const cram = await fetchAsBytes(cramUrl as string);
41
43
  export const crai = await fetchAsBytes(craiUrl as string);
42
44
 
43
- export const decisionTree: DecisionTree = decisionTreeJson as DecisionTree;
45
+ export const decisionTree: DecisionTree = decisionTreeJson as unknown as DecisionTree;
44
46
 
45
47
  export const fastaGz = {
46
48
  "chr1:9982230-9982730": await fetchAsBytes(fastaUrl_chr1_9982230_9982730 as string),
@@ -73,6 +75,8 @@ export const fastaGz = {
73
75
 
74
76
  export const genesGz = await fetchAsBytes(genesUrl as string);
75
77
 
78
+ export const vcfMeta = vcfMetaJson as unknown as Metadata;
79
+
76
80
  export const vcfFamily = await fetchAsBytes(vcfUrlFamily as string);
77
81
 
78
82
  export const vcfNoVep = await fetchAsBytes(vcfUrlNoVep as string);
package/src/mocks/MockApiClient.ts CHANGED
@@ -21,6 +21,7 @@ import {
21
21
  fastaGz as fastaGzGRCh37,
22
22
  genesGz as genesGzGRCh37,
23
23
  samplesFamily as samplesFamilyGRCh37,
24
+ vcfMeta as vcfMetaGRCh37,
24
25
  vcfFamily as vcfFamilyGRCh37,
25
26
  vcfNoVep as vcfNoVepGRCh37,
26
27
  vcfSamples0 as vcfSamples0GRCh37,
@@ -35,6 +36,7 @@ import {
35
36
  fastaGz as fastaGzGRCh38,
36
37
  genesGz as genesGzGRCh38,
37
38
  samplesFamily as samplesFamilyGRCh38,
39
+ vcfMeta as vcfMetaGRCh38,
38
40
  vcfFamily as vcfFamilyGRCh38,
39
41
  vcfNoVep as vcfNoVepGRCh38,
40
42
  vcfSamples0 as vcfSamples0GRCh38,
@@ -142,6 +144,7 @@ export class MockApiClient implements Api {
142
144
  },
143
145
  },
144
146
  decisionTree: decisionTreeGRCh37,
147
+ vcfMeta: vcfMetaGRCh37,
145
148
  };
146
149
 
147
150
  const mockReportDataNoVep: ReportData = {
@@ -170,6 +173,7 @@ export class MockApiClient implements Api {
170
173
  },
171
174
  },
172
175
  decisionTree: decisionTreeGRCh37,
176
+ vcfMeta: vcfMetaGRCh37,
173
177
  };
174
178
 
175
179
  const mockReportData1Sample: ReportData = {
@@ -198,6 +202,7 @@ export class MockApiClient implements Api {
198
202
  },
199
203
  },
200
204
  decisionTree: decisionTreeGRCh37,
205
+ vcfMeta: vcfMetaGRCh37,
201
206
  };
202
207
 
203
208
  const mockReportData100Samples: ReportData = {
@@ -220,6 +225,7 @@ export class MockApiClient implements Api {
220
225
  genesGz: genesGzGRCh37,
221
226
  },
222
227
  decisionTree: decisionTreeGRCh37,
228
+ vcfMeta: vcfMetaGRCh37,
223
229
  };
224
230
 
225
231
  const mockReportDataNoSample: ReportData = {
@@ -242,6 +248,7 @@ export class MockApiClient implements Api {
242
248
  genesGz: genesGzGRCh37,
243
249
  },
244
250
  decisionTree: decisionTreeGRCh37,
251
+ vcfMeta: vcfMetaGRCh37,
245
252
  };
246
253
 
247
254
  const mockReportDataFamilyGRCh38: ReportData = {
@@ -270,6 +277,7 @@ export class MockApiClient implements Api {
270
277
  },
271
278
  },
272
279
  decisionTree: decisionTreeGRCh38,
280
+ vcfMeta: vcfMetaGRCh38,
273
281
  };
274
282
 
275
283
  const mockReportDataNoVepGRCh38: ReportData = {
@@ -298,6 +306,7 @@ export class MockApiClient implements Api {
298
306
  },
299
307
  },
300
308
  decisionTree: decisionTreeGRCh38,
309
+ vcfMeta: vcfMetaGRCh38,
301
310
  };
302
311
 
303
312
  const mockReportData1SampleGRCh38: ReportData = {
@@ -326,6 +335,7 @@ export class MockApiClient implements Api {
326
335
  },
327
336
  },
328
337
  decisionTree: decisionTreeGRCh38,
338
+ vcfMeta: vcfMetaGRCh38,
329
339
  };
330
340
 
331
341
  const mockReportData100SamplesGRCh38: ReportData = {
@@ -348,6 +358,7 @@ export class MockApiClient implements Api {
348
358
  genesGz: genesGzGRCh38,
349
359
  },
350
360
  decisionTree: decisionTreeGRCh38,
361
+ vcfMeta: vcfMetaGRCh38,
351
362
  };
352
363
 
353
364
  const mockReportDataNoSampleGRCh38: ReportData = {
@@ -370,6 +381,7 @@ export class MockApiClient implements Api {
370
381
  genesGz: genesGzGRCh38,
371
382
  },
372
383
  decisionTree: decisionTreeGRCh38,
384
+ vcfMeta: vcfMetaGRCh38,
373
385
  };
374
386
 
375
387
  const datasets: { [key: string]: ReportData } = {};
@@ -388,7 +400,7 @@ export class MockApiClient implements Api {
388
400
 
389
401
  private createApiClient(id: string): Api {
390
402
  const reportData = this.datasets[id];
391
- const vcf = parseVcf(new TextDecoder().decode(reportData.binary.vcf));
403
+ const vcf = parseVcf(new TextDecoder().decode(reportData.binary.vcf), reportData.vcfMeta);
392
404
  reportData.metadata.records = vcf.metadata;
393
405
  reportData.data.records = vcf.data;
394
406
 
package/src/views/SampleVariants.tsx CHANGED
@@ -196,7 +196,7 @@ export const SampleVariants: Component<{
196
196
  {
197
197
  selector: selectorVi,
198
198
  operator: "has_any",
199
- args: ["AD", "AR", "AR_C", "XLD", "XLR"],
199
+ args: ["AD", "AR", "AR_C", "XLD", "XLR", "YL", "MT"],
200
200
  },
201
201
  selectorKey(selectorVi),
202
202
  );
package/vite.config.mts CHANGED
@@ -9,10 +9,9 @@ export default defineConfig({
9
9
  charset: "ascii",
10
10
  },
11
11
  build: {
12
- polyfillDynamicImport: false,
13
12
  // inline plugin build options
14
13
  rollupOptions: {
15
- input: ["./index.html", "./node_modules/@molgenis/vite-plugin-inline/dist/loader.js"],
14
+ input: ["./index.html", "./node_modules/@molgenis/vite-plugin-inline/dist/loader.mjs"],
16
15
  output: {
17
16
  manualChunks: undefined,
18
17
  },