@molgenis/vip-report-template 8.2.2 → 8.3.0

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Files changed (17) hide show
  1. package/package.json +1 -1
  2. package/scripts/validateConfig/schema.ts +2 -0
  3. package/src/components/field/composed/FieldComposed.tsx +10 -0
  4. package/src/components/field/composed/FieldConfidenceInterval.tsx +14 -0
  5. package/src/components/field/composed/FieldGenotypeStr.tsx +3 -1
  6. package/src/components/field/composed/FieldSpanningReads.tsx +14 -0
  7. package/src/mocks/GRCh38/field_metadata.json +11 -13
  8. package/src/mocks/GRCh38/vcf/str.db.blob +0 -0
  9. package/src/mocks/GRCh38/vcf/str.vcf +179 -177
  10. package/src/mocks/config_cram.json +9 -4
  11. package/src/mocks/config_default_values.json +6 -2
  12. package/src/mocks/config_vcf.json +4 -4
  13. package/src/types/config.d.ts +2 -0
  14. package/src/types/configCellComposed.d.ts +14 -2
  15. package/src/utils/config/configCellsComposed.ts +89 -15
  16. package/src/utils/config/configValidator.precompiled.ts +80 -0
  17. package/tests/utils/config/configCellsComposed.test.ts +44 -32
package/tests/utils/config/configCellsComposed.test.ts CHANGED
@@ -242,22 +242,23 @@ describe("config cells composed", () => {
242
242
  };
243
243
 
244
244
  const fieldGt = { id: "FORMAT/GT" };
245
- const fieldRepCn = { id: "FORMAT/REPCN" };
246
245
  const fieldViab = { id: "FORMAT/VIAB" };
247
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  const fieldSvType = { id: "INFO/SVTYPE" };
248
- const fieldRu = { id: "INFO/RU" };
247
+ const fieldRuCall = { id: "INFO/RU_CALL" };
248
+ const fieldRu = { id: "INFO/RU_NR" };
249
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  const fieldRuMatch = { id: "INFO/RUMATCH" };
250
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  const fieldDisplayRu = { id: "INFO/DisplayRU" };
251
- vi.mocked(getSampleFields).mockReturnValue([fieldGt, fieldRepCn, fieldViab] as FieldMetadataWrapper[]);
251
+ vi.mocked(getSampleFields).mockReturnValue([fieldGt, fieldViab] as FieldMetadataWrapper[]);
252
252
  vi.mocked(getInfoFields).mockReturnValue([
253
253
  fieldSvType,
254
254
  fieldRu,
255
255
  fieldRuMatch,
256
256
  fieldDisplayRu,
257
+ fieldRuCall
257
258
  ] as FieldMetadataWrapper[]);
258
259
  vi.mocked(getInfoValueCount).mockReturnValue(1);
259
- vi.mocked(getSampleValues).mockReturnValue([0, 1, 2]);
260
- vi.mocked(getInfoValues).mockReturnValue([3, 4, 5, 6]);
260
+ vi.mocked(getSampleValues).mockReturnValue([0, 1]);
261
+ vi.mocked(getInfoValues).mockReturnValue([2, 3, 4, 5, "6"]);
261
262
 
262
263
  const cell = initConfigCellComposed(config, variantType, metadata, sample) as ConfigCellCustom<CellValueCustom>;
263
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  expect(cell.type).toStrictEqual("composed");
@@ -267,20 +268,22 @@ describe("config cells composed", () => {
267
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  expect(cell.valueCount(record)).toStrictEqual(1);
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  expect(cell.value(record, 1)).toStrictEqual({
269
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  altAlleles: ["C", "T"],
270
- displayRepeatUnit: 6,
271
+ displayRepeatUnit: 5,
271
272
  genotype: 0,
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  refAllele: "A",
273
- repeatCount: 1,
274
- repeatUnitMatch: 5,
275
- repeatUnitValue: 4,
276
- svType: 3,
277
- viab: 2,
274
+ repeatCount: "6",
275
+ repeatUnitMatch: 4,
276
+ repeatUnitValue: 3,
277
+ svType: 2,
278
+ viab: 1,
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279
  });
279
280
 
280
- expect(getSampleFields).toHaveBeenCalledWith(vcfMetadata, "GT", "REPCN", "VIAB");
281
- expect(getInfoFields).toHaveBeenCalledWith(vcfMetadata, "SVTYPE", "RU", "RUMATCH", "DisplayRU");
282
- expect(getSampleValues).toHaveBeenCalledWith(sample, record, 1, fieldGt, fieldRepCn, fieldViab);
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- expect(getInfoValues).toHaveBeenCalledWith(record, 1, fieldSvType, fieldRu, fieldRuMatch, fieldDisplayRu);
281
+ expect(getSampleFields).toHaveBeenCalledWith(vcfMetadata, "GT", "VIAB");
282
+ expect(getInfoFields).toHaveBeenCalledWith(
283
+ vcfMetadata, "SVTYPE", "RU_CALL", "RU_MATCH", "DisplayRU", "RU_NR",
284
+ );
285
+ expect(getSampleValues).toHaveBeenCalledWith(sample, record, 1, fieldGt, fieldViab);
286
+ expect(getInfoValues).toHaveBeenCalledWith(record, 1, fieldSvType, fieldRu, fieldRuMatch, fieldDisplayRu, fieldRuCall);
284
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  });
285
288
 
286
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  test("genotype with required fields", () => {
@@ -314,16 +317,18 @@ describe("config cells composed", () => {
314
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  viab: undefined,
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  });
316
319
 
317
- expect(getSampleFields).toHaveBeenCalledWith(vcfMetadata, "GT", "REPCN", "VIAB");
318
- expect(getInfoFields).toHaveBeenCalledWith(vcfMetadata, "SVTYPE", "RU", "RUMATCH", "DisplayRU");
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- expect(getSampleValues).toHaveBeenCalledWith(sample, record, 1, fieldGt, undefined, undefined);
320
- expect(getInfoValues).toHaveBeenCalledWith(record, 1, undefined, undefined, undefined, undefined);
320
+ expect(getSampleFields).toHaveBeenCalledWith(vcfMetadata, "GT", "VIAB");
321
+ expect(getInfoFields).toHaveBeenCalledWith(
322
+ vcfMetadata, "SVTYPE", "RU_CALL", "RU_MATCH", "DisplayRU", "RU_NR",
323
+ );
324
+ expect(getSampleValues).toHaveBeenCalledWith(sample, record, 1, fieldGt, undefined);
325
+ expect(getInfoValues).toHaveBeenCalledWith(record, 1, undefined, undefined, undefined, undefined, undefined);
321
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  });
322
327
 
323
328
  test("genotype without required fields", () => {
324
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  vi.mocked(getSampleFields).mockReturnValue([undefined, undefined, undefined, undefined]);
325
330
  expect(initConfigCellComposed(configBase, variantType, metadata, sample)).toStrictEqual(null);
326
- expect(getSampleFields).toHaveBeenCalledWith(vcfMetadata, "GT", "REPCN", "VIAB");
331
+ expect(getSampleFields).toHaveBeenCalledWith(vcfMetadata, "GT", "VIAB");
327
332
  });
328
333
 
329
334
  test("genotype without sample", () => {
@@ -346,10 +351,10 @@ describe("config cells composed", () => {
346
351
 
347
352
  const fieldGt = { id: "FORMAT/GT" };
348
353
  vi.mocked(getSampleFields).mockReturnValue([fieldGt, undefined, undefined] as FieldMetadataWrapper[]);
349
- vi.mocked(getInfoFields).mockReturnValue([undefined, undefined, undefined, undefined]);
354
+ vi.mocked(getInfoFields).mockReturnValue([undefined, undefined, undefined, undefined, undefined]);
350
355
  vi.mocked(getInfoValueCount).mockReturnValue(1);
351
356
  vi.mocked(getSampleValues).mockReturnValue([0, undefined, undefined]);
352
- vi.mocked(getInfoValues).mockReturnValue([undefined, undefined, undefined, undefined]);
357
+ vi.mocked(getInfoValues).mockReturnValue([undefined, undefined, undefined, undefined, undefined]);
353
358
 
354
359
  const cell = initConfigCellComposed(
355
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  configBase,
@@ -374,8 +379,10 @@ describe("config cells composed", () => {
374
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  viab: undefined,
375
380
  });
376
381
 
377
- expect(getSampleFields).toHaveBeenCalledWith(vcfMetadata, "GT", "REPCN", "VIAB");
378
- expect(getInfoFields).toHaveBeenCalledWith(vcfMetadata, "SVTYPE", "RU", "RUMATCH", "DisplayRU");
382
+ expect(getSampleFields).toHaveBeenCalledWith(vcfMetadata, "GT", "VIAB");
383
+ expect(getInfoFields).toHaveBeenCalledWith(
384
+ vcfMetadata, "SVTYPE", "RU_CALL", "RU_MATCH", "DisplayRU", "RU_NR",
385
+ );
379
386
  expect(getSampleValues).toHaveBeenCalledWith(
380
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  {
381
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  item: {
@@ -392,9 +399,8 @@ describe("config cells composed", () => {
392
399
  1,
393
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  fieldGt,
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  undefined,
395
- undefined,
396
402
  );
397
- expect(getInfoValues).toHaveBeenCalledWith(record, 1, undefined, undefined, undefined, undefined);
403
+ expect(getInfoValues).toHaveBeenCalledWith(record, 1, undefined, undefined, undefined, undefined, undefined);
398
404
  });
399
405
 
400
406
  test("genotype_maternal no sample", () => {
@@ -425,10 +431,10 @@ describe("config cells composed", () => {
425
431
 
426
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  const fieldGt = { id: "FORMAT/GT" };
427
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  vi.mocked(getSampleFields).mockReturnValue([fieldGt, undefined, undefined] as FieldMetadataWrapper[]);
428
- vi.mocked(getInfoFields).mockReturnValue([undefined, undefined, undefined, undefined]);
434
+ vi.mocked(getInfoFields).mockReturnValue([undefined, undefined, undefined, undefined, undefined]);
429
435
  vi.mocked(getInfoValueCount).mockReturnValue(1);
430
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  vi.mocked(getSampleValues).mockReturnValue([0, undefined, undefined]);
431
- vi.mocked(getInfoValues).mockReturnValue([undefined, undefined, undefined, undefined]);
437
+ vi.mocked(getInfoValues).mockReturnValue([undefined, undefined, undefined, undefined, undefined]);
432
438
 
433
439
  const cell = initConfigCellComposed(
434
440
  configBase,
@@ -453,8 +459,15 @@ describe("config cells composed", () => {
453
459
  viab: undefined,
454
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  });
455
461
 
456
- expect(getSampleFields).toHaveBeenCalledWith(vcfMetadata, "GT", "REPCN", "VIAB");
457
- expect(getInfoFields).toHaveBeenCalledWith(vcfMetadata, "SVTYPE", "RU", "RUMATCH", "DisplayRU");
462
+ expect(getSampleFields).toHaveBeenCalledWith(vcfMetadata, "GT", "VIAB");
463
+ expect(getInfoFields).toHaveBeenCalledWith(
464
+ vcfMetadata,
465
+ "SVTYPE",
466
+ "RU_CALL",
467
+ "RU_MATCH",
468
+ "DisplayRU",
469
+ "RU_NR"
470
+ );
458
471
  expect(getSampleValues).toHaveBeenCalledWith(
459
472
  {
460
473
  item: {
@@ -471,9 +484,8 @@ describe("config cells composed", () => {
471
484
  1,
472
485
  fieldGt,
473
486
  undefined,
474
- undefined,
475
487
  );
476
- expect(getInfoValues).toHaveBeenCalledWith(record, 1, undefined, undefined, undefined, undefined);
488
+ expect(getInfoValues).toHaveBeenCalledWith(record, 1, undefined, undefined, undefined, undefined, undefined);
477
489
  });
478
490
 
479
491
  test("genotype_paternal no sample", () => {