@molgenis/vip-report-template 8.2.2 → 8.3.1

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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 +4 -2
  6. package/src/components/field/composed/FieldSpanningReads.tsx +18 -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 +71 -238
  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 +15 -3
  15. package/src/utils/config/configCellsComposed.ts +94 -19
  16. package/src/utils/config/configValidator.precompiled.ts +80 -0
  17. package/tests/utils/config/configCellsComposed.test.ts +70 -35
package/tests/utils/config/configCellsComposed.test.ts CHANGED
@@ -242,22 +242,20 @@ 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" };
246
+ const fieldRuCall = { id: "FORMAT/RU_CALL" };
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+ const fieldRu = { id: "FORMAT/RU_NR" };
248
+ const fieldRuMatch = { id: "FORMAT/RUMATCH" };
247
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  const fieldSvType = { id: "INFO/SVTYPE" };
248
- const fieldRu = { id: "INFO/RU" };
249
- const fieldRuMatch = { id: "INFO/RUMATCH" };
250
250
  const fieldDisplayRu = { id: "INFO/DisplayRU" };
251
- vi.mocked(getSampleFields).mockReturnValue([fieldGt, fieldRepCn, fieldViab] as FieldMetadataWrapper[]);
251
+ vi.mocked(getSampleFields).mockReturnValue([fieldGt, fieldViab, fieldRu, fieldRuMatch, fieldRuCall] as FieldMetadataWrapper[]);
252
252
  vi.mocked(getInfoFields).mockReturnValue([
253
253
  fieldSvType,
254
- fieldRu,
255
- fieldRuMatch,
256
254
  fieldDisplayRu,
257
255
  ] as FieldMetadataWrapper[]);
258
256
  vi.mocked(getInfoValueCount).mockReturnValue(1);
259
- vi.mocked(getSampleValues).mockReturnValue([0, 1, 2]);
260
- vi.mocked(getInfoValues).mockReturnValue([3, 4, 5, 6]);
257
+ vi.mocked(getSampleValues).mockReturnValue([0, 1, 3, 4, "6"]);
258
+ vi.mocked(getInfoValues).mockReturnValue([2, 5]);
261
259
 
262
260
  const cell = initConfigCellComposed(config, variantType, metadata, sample) as ConfigCellCustom<CellValueCustom>;
263
261
  expect(cell.type).toStrictEqual("composed");
@@ -267,20 +265,29 @@ describe("config cells composed", () => {
267
265
  expect(cell.valueCount(record)).toStrictEqual(1);
268
266
  expect(cell.value(record, 1)).toStrictEqual({
269
267
  altAlleles: ["C", "T"],
270
- displayRepeatUnit: 6,
268
+ displayRepeatUnit: 5,
271
269
  genotype: 0,
272
270
  refAllele: "A",
273
- repeatCount: 1,
274
- repeatUnitMatch: 5,
275
- repeatUnitValue: 4,
276
- svType: 3,
277
- viab: 2,
271
+ repeatCount: "6",
272
+ repeatUnitMatch: 4,
273
+ repeatUnitValue: 3,
274
+ svType: 2,
275
+ viab: 1,
278
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  });
279
277
 
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);
283
- expect(getInfoValues).toHaveBeenCalledWith(record, 1, fieldSvType, fieldRu, fieldRuMatch, fieldDisplayRu);
278
+ expect(getSampleFields).toHaveBeenCalledWith(vcfMetadata, "GT", "VIAB","RU_CALL", "RU_MATCH", "RU_NR");
279
+ expect(getInfoFields).toHaveBeenCalledWith(vcfMetadata, "SVTYPE", "DisplayRU");
280
+ expect(getSampleValues).toHaveBeenCalledWith(
281
+ sample,
282
+ record,
283
+ 1,
284
+ fieldGt,
285
+ fieldViab,
286
+ fieldRu,
287
+ fieldRuMatch,
288
+ fieldRuCall,
289
+ );
290
+ expect(getInfoValues).toHaveBeenCalledWith(record, 1, fieldSvType, fieldDisplayRu);
284
291
  });
285
292
 
286
293
  test("genotype with required fields", () => {
@@ -314,16 +321,27 @@ describe("config cells composed", () => {
314
321
  viab: undefined,
315
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  });
316
323
 
317
- expect(getSampleFields).toHaveBeenCalledWith(vcfMetadata, "GT", "REPCN", "VIAB");
318
- expect(getInfoFields).toHaveBeenCalledWith(vcfMetadata, "SVTYPE", "RU", "RUMATCH", "DisplayRU");
319
- expect(getSampleValues).toHaveBeenCalledWith(sample, record, 1, fieldGt, undefined, undefined);
320
- expect(getInfoValues).toHaveBeenCalledWith(record, 1, undefined, undefined, undefined, undefined);
324
+ expect(getSampleFields).toHaveBeenCalledWith(vcfMetadata, "GT", "VIAB", "RU_CALL", "RU_MATCH", "RU_NR");
325
+ expect(getInfoFields).toHaveBeenCalledWith(
326
+ vcfMetadata, "SVTYPE", "DisplayRU"
327
+ );
328
+ expect(getSampleValues).toHaveBeenCalledWith(
329
+ sample,
330
+ record,
331
+ 1,
332
+ fieldGt,
333
+ undefined,
334
+ undefined,
335
+ undefined,
336
+ undefined,
337
+ );
338
+ expect(getInfoValues).toHaveBeenCalledWith(record, 1, undefined, undefined);
321
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  });
322
340
 
323
341
  test("genotype without required fields", () => {
324
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  vi.mocked(getSampleFields).mockReturnValue([undefined, undefined, undefined, undefined]);
325
343
  expect(initConfigCellComposed(configBase, variantType, metadata, sample)).toStrictEqual(null);
326
- expect(getSampleFields).toHaveBeenCalledWith(vcfMetadata, "GT", "REPCN", "VIAB");
344
+ expect(getSampleFields).toHaveBeenCalledWith(vcfMetadata, "GT", "VIAB", "RU_CALL", "RU_MATCH", "RU_NR");
327
345
  });
328
346
 
329
347
  test("genotype without sample", () => {
@@ -345,11 +363,18 @@ describe("config cells composed", () => {
345
363
  } as SampleContainer;
346
364
 
347
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  const fieldGt = { id: "FORMAT/GT" };
348
- vi.mocked(getSampleFields).mockReturnValue([fieldGt, undefined, undefined] as FieldMetadataWrapper[]);
349
- vi.mocked(getInfoFields).mockReturnValue([undefined, undefined, undefined, undefined]);
366
+ vi.mocked(getSampleFields).mockReturnValue([
367
+ fieldGt,
368
+ undefined,
369
+ undefined,
370
+ undefined,
371
+ undefined,
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+ undefined,
373
+ ] as FieldMetadataWrapper[]);
374
+ vi.mocked(getInfoFields).mockReturnValue([undefined, undefined]);
350
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  vi.mocked(getInfoValueCount).mockReturnValue(1);
351
- vi.mocked(getSampleValues).mockReturnValue([0, undefined, undefined]);
352
- vi.mocked(getInfoValues).mockReturnValue([undefined, undefined, undefined, undefined]);
376
+ vi.mocked(getSampleValues).mockReturnValue([0, undefined, undefined, undefined, undefined, undefined]);
377
+ vi.mocked(getInfoValues).mockReturnValue([undefined, undefined]);
353
378
 
354
379
  const cell = initConfigCellComposed(
355
380
  configBase,
@@ -374,8 +399,10 @@ describe("config cells composed", () => {
374
399
  viab: undefined,
375
400
  });
376
401
 
377
- expect(getSampleFields).toHaveBeenCalledWith(vcfMetadata, "GT", "REPCN", "VIAB");
378
- expect(getInfoFields).toHaveBeenCalledWith(vcfMetadata, "SVTYPE", "RU", "RUMATCH", "DisplayRU");
402
+ expect(getSampleFields).toHaveBeenCalledWith(vcfMetadata, "GT", "VIAB", "RU_CALL", "RU_MATCH", "RU_NR");
403
+ expect(getInfoFields).toHaveBeenCalledWith(
404
+ vcfMetadata, "SVTYPE", "DisplayRU",
405
+ );
379
406
  expect(getSampleValues).toHaveBeenCalledWith(
380
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  {
381
408
  item: {
@@ -393,8 +420,10 @@ describe("config cells composed", () => {
393
420
  fieldGt,
394
421
  undefined,
395
422
  undefined,
423
+ undefined,
424
+ undefined,
396
425
  );
397
- expect(getInfoValues).toHaveBeenCalledWith(record, 1, undefined, undefined, undefined, undefined);
426
+ expect(getInfoValues).toHaveBeenCalledWith(record, 1, undefined, undefined);
398
427
  });
399
428
 
400
429
  test("genotype_maternal no sample", () => {
@@ -425,10 +454,10 @@ describe("config cells composed", () => {
425
454
 
426
455
  const fieldGt = { id: "FORMAT/GT" };
427
456
  vi.mocked(getSampleFields).mockReturnValue([fieldGt, undefined, undefined] as FieldMetadataWrapper[]);
428
- vi.mocked(getInfoFields).mockReturnValue([undefined, undefined, undefined, undefined]);
457
+ vi.mocked(getInfoFields).mockReturnValue([undefined, undefined, undefined, undefined, undefined]);
429
458
  vi.mocked(getInfoValueCount).mockReturnValue(1);
430
459
  vi.mocked(getSampleValues).mockReturnValue([0, undefined, undefined]);
431
- vi.mocked(getInfoValues).mockReturnValue([undefined, undefined, undefined, undefined]);
460
+ vi.mocked(getInfoValues).mockReturnValue([undefined, undefined, undefined, undefined, undefined]);
432
461
 
433
462
  const cell = initConfigCellComposed(
434
463
  configBase,
@@ -453,8 +482,12 @@ describe("config cells composed", () => {
453
482
  viab: undefined,
454
483
  });
455
484
 
456
- expect(getSampleFields).toHaveBeenCalledWith(vcfMetadata, "GT", "REPCN", "VIAB");
457
- expect(getInfoFields).toHaveBeenCalledWith(vcfMetadata, "SVTYPE", "RU", "RUMATCH", "DisplayRU");
485
+ expect(getSampleFields).toHaveBeenCalledWith(vcfMetadata, "GT", "VIAB", "RU_CALL", "RU_MATCH", "RU_NR");
486
+ expect(getInfoFields).toHaveBeenCalledWith(
487
+ vcfMetadata,
488
+ "SVTYPE",
489
+ "DisplayRU",
490
+ );
458
491
  expect(getSampleValues).toHaveBeenCalledWith(
459
492
  {
460
493
  item: {
@@ -472,8 +505,10 @@ describe("config cells composed", () => {
472
505
  fieldGt,
473
506
  undefined,
474
507
  undefined,
508
+ undefined,
509
+ undefined,
475
510
  );
476
- expect(getInfoValues).toHaveBeenCalledWith(record, 1, undefined, undefined, undefined, undefined);
511
+ expect(getInfoValues).toHaveBeenCalledWith(record, 1, undefined, undefined);
477
512
  });
478
513
 
479
514
  test("genotype_paternal no sample", () => {