@jbrowse/plugin-alignments 1.5.0 → 1.5.4

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (58) hide show
  1. package/dist/AlignmentsFeatureDetail/index.d.ts +7 -4
  2. package/dist/AlignmentsTrack/index.d.ts +2 -0
  3. package/dist/BamAdapter/BamSlightlyLazyFeature.d.ts +1 -1
  4. package/dist/BamAdapter/index.d.ts +2 -4
  5. package/dist/CramAdapter/index.d.ts +1 -4
  6. package/dist/HtsgetBamAdapter/HtsgetBamAdapter.d.ts +2 -1
  7. package/dist/HtsgetBamAdapter/index.d.ts +2 -4
  8. package/dist/LinearAlignmentsDisplay/index.d.ts +2 -3
  9. package/dist/LinearPileupDisplay/index.d.ts +2 -2
  10. package/dist/LinearPileupDisplay/model.d.ts +1 -2
  11. package/dist/LinearSNPCoverageDisplay/components/Tooltip.d.ts +1 -1
  12. package/dist/LinearSNPCoverageDisplay/index.d.ts +2 -2
  13. package/dist/LinearSNPCoverageDisplay/models/model.d.ts +1 -0
  14. package/dist/PileupRenderer/PileupRenderer.d.ts +20 -7
  15. package/dist/PileupRenderer/index.d.ts +2 -3
  16. package/dist/SNPCoverageAdapter/SNPCoverageAdapter.d.ts +38 -26
  17. package/dist/SNPCoverageAdapter/index.d.ts +1 -5
  18. package/dist/SNPCoverageRenderer/index.d.ts +3 -3
  19. package/dist/plugin-alignments.cjs.development.js +3696 -3526
  20. package/dist/plugin-alignments.cjs.development.js.map +1 -1
  21. package/dist/plugin-alignments.cjs.production.min.js +1 -1
  22. package/dist/plugin-alignments.cjs.production.min.js.map +1 -1
  23. package/dist/plugin-alignments.esm.js +3690 -3520
  24. package/dist/plugin-alignments.esm.js.map +1 -1
  25. package/package.json +4 -4
  26. package/src/AlignmentsFeatureDetail/__snapshots__/index.test.js.snap +8 -0
  27. package/src/AlignmentsFeatureDetail/{index.js → index.ts} +19 -3
  28. package/src/AlignmentsTrack/index.ts +36 -0
  29. package/src/BamAdapter/BamSlightlyLazyFeature.ts +14 -30
  30. package/src/BamAdapter/MismatchParser.test.ts +20 -0
  31. package/src/BamAdapter/MismatchParser.ts +6 -5
  32. package/src/BamAdapter/index.ts +11 -5
  33. package/src/CramAdapter/CramSlightlyLazyFeature.ts +1 -5
  34. package/src/CramAdapter/index.ts +11 -4
  35. package/src/HtsgetBamAdapter/HtsgetBamAdapter.ts +2 -2
  36. package/src/HtsgetBamAdapter/index.ts +18 -5
  37. package/src/LinearAlignmentsDisplay/index.ts +20 -3
  38. package/src/LinearAlignmentsDisplay/models/configSchema.test.js +8 -68
  39. package/src/LinearPileupDisplay/configSchema.test.js +2 -13
  40. package/src/LinearPileupDisplay/index.ts +19 -2
  41. package/src/LinearPileupDisplay/model.ts +15 -20
  42. package/src/LinearSNPCoverageDisplay/components/Tooltip.tsx +17 -12
  43. package/src/LinearSNPCoverageDisplay/index.ts +19 -2
  44. package/src/LinearSNPCoverageDisplay/models/configSchema.test.js +2 -13
  45. package/src/LinearSNPCoverageDisplay/models/model.ts +21 -0
  46. package/src/PileupRenderer/PileupRenderer.tsx +154 -128
  47. package/src/PileupRenderer/components/PileupRendering.tsx +2 -0
  48. package/src/PileupRenderer/configSchema.ts +2 -2
  49. package/src/PileupRenderer/index.ts +16 -3
  50. package/src/SNPCoverageAdapter/SNPCoverageAdapter.ts +95 -25
  51. package/src/SNPCoverageAdapter/index.ts +17 -5
  52. package/src/SNPCoverageRenderer/SNPCoverageRenderer.ts +60 -13
  53. package/src/SNPCoverageRenderer/configSchema.js +5 -0
  54. package/src/SNPCoverageRenderer/index.ts +24 -0
  55. package/src/index.ts +91 -163
  56. package/src/SNPCoverageAdapter/SNPCoverageAdapter.test.ts +0 -275
  57. package/src/SNPCoverageAdapter/__snapshots__/SNPCoverageAdapter.test.ts.snap +0 -579
  58. package/src/SNPCoverageRenderer/index.js +0 -11
package/src/SNPCoverageAdapter/__snapshots__/SNPCoverageAdapter.test.ts.snap DELETED
@@ -1,579 +0,0 @@
1
- // Jest Snapshot v1, https://goo.gl/fbAQLP
2
-
3
- exports[`SNP adapter can fetch features from volvox.bam using bam subadapter 1`] = `
4
- Array [
5
- Object {
6
- "end": 1003,
7
- "refName": "ctgA",
8
- "score": 18,
9
- "snpinfo": Object {
10
- "cov": Object {
11
- "T": Object {
12
- "strands": Object {
13
- "-1": 1,
14
- "0": 0,
15
- "1": 0,
16
- },
17
- "total": 1,
18
- },
19
- },
20
- "delskips": Object {},
21
- "lowqual": Object {},
22
- "noncov": Object {},
23
- "ref": Object {
24
- "ref": Object {
25
- "strands": Object {
26
- "-1": 7,
27
- "0": 0,
28
- "1": 10,
29
- },
30
- "total": 17,
31
- },
32
- },
33
- "total": 18,
34
- },
35
- "start": 1002,
36
- "uniqueId": "test-0-1002",
37
- },
38
- Object {
39
- "end": 1004,
40
- "refName": "ctgA",
41
- "score": 18,
42
- "snpinfo": Object {
43
- "cov": Object {},
44
- "delskips": Object {},
45
- "lowqual": Object {},
46
- "noncov": Object {},
47
- "ref": Object {
48
- "ref": Object {
49
- "strands": Object {
50
- "-1": 8,
51
- "0": 0,
52
- "1": 10,
53
- },
54
- "total": 18,
55
- },
56
- },
57
- "total": 18,
58
- },
59
- "start": 1003,
60
- "uniqueId": "test-0-1003",
61
- },
62
- Object {
63
- "end": 1005,
64
- "refName": "ctgA",
65
- "score": 18,
66
- "snpinfo": Object {
67
- "cov": Object {
68
- "A": Object {
69
- "strands": Object {
70
- "-1": 1,
71
- "0": 0,
72
- "1": 0,
73
- },
74
- "total": 1,
75
- },
76
- },
77
- "delskips": Object {},
78
- "lowqual": Object {},
79
- "noncov": Object {},
80
- "ref": Object {
81
- "ref": Object {
82
- "strands": Object {
83
- "-1": 7,
84
- "0": 0,
85
- "1": 10,
86
- },
87
- "total": 17,
88
- },
89
- },
90
- "total": 18,
91
- },
92
- "start": 1004,
93
- "uniqueId": "test-0-1004",
94
- },
95
- Object {
96
- "end": 1006,
97
- "refName": "ctgA",
98
- "score": 19,
99
- "snpinfo": Object {
100
- "cov": Object {},
101
- "delskips": Object {},
102
- "lowqual": Object {},
103
- "noncov": Object {},
104
- "ref": Object {
105
- "ref": Object {
106
- "strands": Object {
107
- "-1": 9,
108
- "0": 0,
109
- "1": 10,
110
- },
111
- "total": 19,
112
- },
113
- },
114
- "total": 19,
115
- },
116
- "start": 1005,
117
- "uniqueId": "test-0-1005",
118
- },
119
- Object {
120
- "end": 1007,
121
- "refName": "ctgA",
122
- "score": 20,
123
- "snpinfo": Object {
124
- "cov": Object {
125
- "A": Object {
126
- "strands": Object {
127
- "-1": 0,
128
- "0": 0,
129
- "1": 2,
130
- },
131
- "total": 2,
132
- },
133
- "T": Object {
134
- "strands": Object {
135
- "-1": 0,
136
- "0": 0,
137
- "1": 1,
138
- },
139
- "total": 1,
140
- },
141
- },
142
- "delskips": Object {},
143
- "lowqual": Object {},
144
- "noncov": Object {},
145
- "ref": Object {
146
- "ref": Object {
147
- "strands": Object {
148
- "-1": 9,
149
- "0": 0,
150
- "1": 8,
151
- },
152
- "total": 17,
153
- },
154
- },
155
- "total": 20,
156
- },
157
- "start": 1006,
158
- "uniqueId": "test-0-1006",
159
- },
160
- Object {
161
- "end": 1008,
162
- "refName": "ctgA",
163
- "score": 20,
164
- "snpinfo": Object {
165
- "cov": Object {},
166
- "delskips": Object {},
167
- "lowqual": Object {},
168
- "noncov": Object {},
169
- "ref": Object {
170
- "ref": Object {
171
- "strands": Object {
172
- "-1": 9,
173
- "0": 0,
174
- "1": 11,
175
- },
176
- "total": 20,
177
- },
178
- },
179
- "total": 20,
180
- },
181
- "start": 1007,
182
- "uniqueId": "test-0-1007",
183
- },
184
- Object {
185
- "end": 1009,
186
- "refName": "ctgA",
187
- "score": 20,
188
- "snpinfo": Object {
189
- "cov": Object {
190
- "T": Object {
191
- "strands": Object {
192
- "-1": 0,
193
- "0": 0,
194
- "1": 1,
195
- },
196
- "total": 1,
197
- },
198
- },
199
- "delskips": Object {},
200
- "lowqual": Object {},
201
- "noncov": Object {},
202
- "ref": Object {
203
- "ref": Object {
204
- "strands": Object {
205
- "-1": 9,
206
- "0": 0,
207
- "1": 10,
208
- },
209
- "total": 19,
210
- },
211
- },
212
- "total": 20,
213
- },
214
- "start": 1008,
215
- "uniqueId": "test-0-1008",
216
- },
217
- Object {
218
- "end": 1010,
219
- "refName": "ctgA",
220
- "score": 20,
221
- "snpinfo": Object {
222
- "cov": Object {},
223
- "delskips": Object {},
224
- "lowqual": Object {},
225
- "noncov": Object {},
226
- "ref": Object {
227
- "ref": Object {
228
- "strands": Object {
229
- "-1": 9,
230
- "0": 0,
231
- "1": 11,
232
- },
233
- "total": 20,
234
- },
235
- },
236
- "total": 20,
237
- },
238
- "start": 1009,
239
- "uniqueId": "test-0-1009",
240
- },
241
- Object {
242
- "end": 1011,
243
- "refName": "ctgA",
244
- "score": 20,
245
- "snpinfo": Object {
246
- "cov": Object {},
247
- "delskips": Object {},
248
- "lowqual": Object {},
249
- "noncov": Object {},
250
- "ref": Object {
251
- "ref": Object {
252
- "strands": Object {
253
- "-1": 9,
254
- "0": 0,
255
- "1": 11,
256
- },
257
- "total": 20,
258
- },
259
- },
260
- "total": 20,
261
- },
262
- "start": 1010,
263
- "uniqueId": "test-0-1010",
264
- },
265
- Object {
266
- "end": 1012,
267
- "refName": "ctgA",
268
- "score": 19,
269
- "snpinfo": Object {
270
- "cov": Object {},
271
- "delskips": Object {},
272
- "lowqual": Object {},
273
- "noncov": Object {},
274
- "ref": Object {
275
- "ref": Object {
276
- "strands": Object {
277
- "-1": 9,
278
- "0": 0,
279
- "1": 10,
280
- },
281
- "total": 19,
282
- },
283
- },
284
- "total": 19,
285
- },
286
- "start": 1011,
287
- "uniqueId": "test-0-1011",
288
- },
289
- ]
290
- `;
291
-
292
- exports[`SNP adapter can fetch features from volvox.cram using cram subadapter 1`] = `
293
- Array [
294
- Object {
295
- "end": 1003,
296
- "refName": "ctgA",
297
- "score": 18,
298
- "snpinfo": Object {
299
- "cov": Object {
300
- "T": Object {
301
- "strands": Object {
302
- "-1": 1,
303
- "0": 0,
304
- "1": 0,
305
- },
306
- "total": 1,
307
- },
308
- },
309
- "delskips": Object {},
310
- "lowqual": Object {},
311
- "noncov": Object {},
312
- "ref": Object {
313
- "ref": Object {
314
- "strands": Object {
315
- "-1": 7,
316
- "0": 0,
317
- "1": 10,
318
- },
319
- "total": 17,
320
- },
321
- },
322
- "total": 18,
323
- },
324
- "start": 1002,
325
- "uniqueId": "test-0-1002",
326
- },
327
- Object {
328
- "end": 1004,
329
- "refName": "ctgA",
330
- "score": 18,
331
- "snpinfo": Object {
332
- "cov": Object {},
333
- "delskips": Object {},
334
- "lowqual": Object {},
335
- "noncov": Object {},
336
- "ref": Object {
337
- "ref": Object {
338
- "strands": Object {
339
- "-1": 8,
340
- "0": 0,
341
- "1": 10,
342
- },
343
- "total": 18,
344
- },
345
- },
346
- "total": 18,
347
- },
348
- "start": 1003,
349
- "uniqueId": "test-0-1003",
350
- },
351
- Object {
352
- "end": 1005,
353
- "refName": "ctgA",
354
- "score": 18,
355
- "snpinfo": Object {
356
- "cov": Object {
357
- "C": Object {
358
- "strands": Object {
359
- "-1": 1,
360
- "0": 0,
361
- "1": 0,
362
- },
363
- "total": 1,
364
- },
365
- },
366
- "delskips": Object {},
367
- "lowqual": Object {},
368
- "noncov": Object {},
369
- "ref": Object {
370
- "ref": Object {
371
- "strands": Object {
372
- "-1": 7,
373
- "0": 0,
374
- "1": 10,
375
- },
376
- "total": 17,
377
- },
378
- },
379
- "total": 18,
380
- },
381
- "start": 1004,
382
- "uniqueId": "test-0-1004",
383
- },
384
- Object {
385
- "end": 1006,
386
- "refName": "ctgA",
387
- "score": 19,
388
- "snpinfo": Object {
389
- "cov": Object {},
390
- "delskips": Object {},
391
- "lowqual": Object {},
392
- "noncov": Object {},
393
- "ref": Object {
394
- "ref": Object {
395
- "strands": Object {
396
- "-1": 9,
397
- "0": 0,
398
- "1": 10,
399
- },
400
- "total": 19,
401
- },
402
- },
403
- "total": 19,
404
- },
405
- "start": 1005,
406
- "uniqueId": "test-0-1005",
407
- },
408
- Object {
409
- "end": 1007,
410
- "refName": "ctgA",
411
- "score": 20,
412
- "snpinfo": Object {
413
- "cov": Object {
414
- "A": Object {
415
- "strands": Object {
416
- "-1": 0,
417
- "0": 0,
418
- "1": 2,
419
- },
420
- "total": 2,
421
- },
422
- "T": Object {
423
- "strands": Object {
424
- "-1": 0,
425
- "0": 0,
426
- "1": 1,
427
- },
428
- "total": 1,
429
- },
430
- },
431
- "delskips": Object {},
432
- "lowqual": Object {},
433
- "noncov": Object {},
434
- "ref": Object {
435
- "ref": Object {
436
- "strands": Object {
437
- "-1": 9,
438
- "0": 0,
439
- "1": 8,
440
- },
441
- "total": 17,
442
- },
443
- },
444
- "total": 20,
445
- },
446
- "start": 1006,
447
- "uniqueId": "test-0-1006",
448
- },
449
- Object {
450
- "end": 1008,
451
- "refName": "ctgA",
452
- "score": 20,
453
- "snpinfo": Object {
454
- "cov": Object {},
455
- "delskips": Object {},
456
- "lowqual": Object {},
457
- "noncov": Object {},
458
- "ref": Object {
459
- "ref": Object {
460
- "strands": Object {
461
- "-1": 9,
462
- "0": 0,
463
- "1": 11,
464
- },
465
- "total": 20,
466
- },
467
- },
468
- "total": 20,
469
- },
470
- "start": 1007,
471
- "uniqueId": "test-0-1007",
472
- },
473
- Object {
474
- "end": 1009,
475
- "refName": "ctgA",
476
- "score": 20,
477
- "snpinfo": Object {
478
- "cov": Object {
479
- "T": Object {
480
- "strands": Object {
481
- "-1": 0,
482
- "0": 0,
483
- "1": 1,
484
- },
485
- "total": 1,
486
- },
487
- },
488
- "delskips": Object {},
489
- "lowqual": Object {},
490
- "noncov": Object {},
491
- "ref": Object {
492
- "ref": Object {
493
- "strands": Object {
494
- "-1": 9,
495
- "0": 0,
496
- "1": 10,
497
- },
498
- "total": 19,
499
- },
500
- },
501
- "total": 20,
502
- },
503
- "start": 1008,
504
- "uniqueId": "test-0-1008",
505
- },
506
- Object {
507
- "end": 1010,
508
- "refName": "ctgA",
509
- "score": 20,
510
- "snpinfo": Object {
511
- "cov": Object {},
512
- "delskips": Object {},
513
- "lowqual": Object {},
514
- "noncov": Object {},
515
- "ref": Object {
516
- "ref": Object {
517
- "strands": Object {
518
- "-1": 9,
519
- "0": 0,
520
- "1": 11,
521
- },
522
- "total": 20,
523
- },
524
- },
525
- "total": 20,
526
- },
527
- "start": 1009,
528
- "uniqueId": "test-0-1009",
529
- },
530
- Object {
531
- "end": 1011,
532
- "refName": "ctgA",
533
- "score": 20,
534
- "snpinfo": Object {
535
- "cov": Object {},
536
- "delskips": Object {},
537
- "lowqual": Object {},
538
- "noncov": Object {},
539
- "ref": Object {
540
- "ref": Object {
541
- "strands": Object {
542
- "-1": 9,
543
- "0": 0,
544
- "1": 11,
545
- },
546
- "total": 20,
547
- },
548
- },
549
- "total": 20,
550
- },
551
- "start": 1010,
552
- "uniqueId": "test-0-1010",
553
- },
554
- Object {
555
- "end": 1012,
556
- "refName": "ctgA",
557
- "score": 19,
558
- "snpinfo": Object {
559
- "cov": Object {},
560
- "delskips": Object {},
561
- "lowqual": Object {},
562
- "noncov": Object {},
563
- "ref": Object {
564
- "ref": Object {
565
- "strands": Object {
566
- "-1": 9,
567
- "0": 0,
568
- "1": 10,
569
- },
570
- "total": 19,
571
- },
572
- },
573
- "total": 19,
574
- },
575
- "start": 1011,
576
- "uniqueId": "test-0-1011",
577
- },
578
- ]
579
- `;
package/src/SNPCoverageRenderer/index.js DELETED
@@ -1,11 +0,0 @@
1
- import { ConfigurationSchema } from '@jbrowse/core/configuration'
2
- import ConfigSchema from './configSchema'
3
-
4
- export { WiggleRendering as ReactComponent } from '@jbrowse/plugin-wiggle'
5
- export { default } from './SNPCoverageRenderer'
6
-
7
- export const configSchema = ConfigurationSchema(
8
- 'SNPCoverageRenderer',
9
- {},
10
- { baseConfiguration: ConfigSchema, explicitlyTyped: true },
11
- )