@jbrowse/cli 2.5.0 → 2.6.2

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 (27) hide show
  1. package/README.md +30 -31
  2. package/lib/base.js +16 -26
  3. package/lib/commands/add-connection.js +31 -78
  4. package/lib/commands/create.js +4 -3
  5. package/lib/commands/upgrade.js +2 -2
  6. package/lib/fetchWithProxy.js +4 -2
  7. package/lib/types/gff3Adapter.js +35 -37
  8. package/lib/types/vcfAdapter.js +36 -41
  9. package/oclif.manifest.json +1 -1
  10. package/package.json +6 -6
  11. package/lib/base.d.ts +0 -129
  12. package/lib/commands/add-assembly.d.ts +0 -35
  13. package/lib/commands/add-connection.d.ts +0 -29
  14. package/lib/commands/add-track-json.d.ts +0 -18
  15. package/lib/commands/add-track.d.ts +0 -819
  16. package/lib/commands/admin-server.d.ts +0 -13
  17. package/lib/commands/create.d.ts +0 -23
  18. package/lib/commands/remove-track.d.ts +0 -17
  19. package/lib/commands/set-default-session.d.ts +0 -22
  20. package/lib/commands/text-index.d.ts +0 -52
  21. package/lib/commands/upgrade.d.ts +0 -22
  22. package/lib/fetchWithProxy.d.ts +0 -2
  23. package/lib/index.d.ts +0 -1
  24. package/lib/types/common.d.ts +0 -13
  25. package/lib/types/gff3Adapter.d.ts +0 -9
  26. package/lib/types/vcfAdapter.d.ts +0 -9
  27. package/lib/util.d.ts +0 -7
package/lib/commands/add-track.d.ts DELETED
@@ -1,819 +0,0 @@
1
- import { flags } from '@oclif/command';
2
- import JBrowseCommand from '../base';
3
- interface UriLocation {
4
- uri: string;
5
- locationType: 'UriLocation';
6
- }
7
- interface LocalPathLocation {
8
- localPath: string;
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- locationType: 'LocalPathLocation';
10
- }
11
- export default class AddTrack extends JBrowseCommand {
12
- target: string;
13
- static description: string;
14
- static examples: string[];
15
- static args: {
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- name: string;
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- required: boolean;
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- description: string;
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- }[];
20
- static flags: {
21
- trackType: flags.IOptionFlag<string | undefined>;
22
- name: flags.IOptionFlag<string | undefined>;
23
- indexFile: flags.IOptionFlag<string | undefined>;
24
- description: flags.IOptionFlag<string | undefined>;
25
- assemblyNames: flags.IOptionFlag<string | undefined>;
26
- category: flags.IOptionFlag<string | undefined>;
27
- config: flags.IOptionFlag<string | undefined>;
28
- target: flags.IOptionFlag<string | undefined>;
29
- out: flags.IOptionFlag<string | undefined>;
30
- subDir: flags.IOptionFlag<string>;
31
- help: import("@oclif/parser/lib/flags").IBooleanFlag<void>;
32
- trackId: flags.IOptionFlag<string | undefined>;
33
- load: flags.IOptionFlag<string | undefined>;
34
- skipCheck: import("@oclif/parser/lib/flags").IBooleanFlag<boolean>;
35
- overwrite: import("@oclif/parser/lib/flags").IBooleanFlag<boolean>;
36
- force: import("@oclif/parser/lib/flags").IBooleanFlag<boolean>;
37
- protocol: flags.IOptionFlag<string>;
38
- bed1: flags.IOptionFlag<string | undefined>;
39
- bed2: flags.IOptionFlag<string | undefined>;
40
- };
41
- run(): Promise<void>;
42
- guessFileNames({ location, index, bed1, bed2, }: {
43
- location: string;
44
- index?: string;
45
- bed1?: string;
46
- bed2?: string;
47
- }): {
48
- file: string;
49
- bed1: string;
50
- bed2: string;
51
- index?: undefined;
52
- index2?: undefined;
53
- } | {
54
- file: string;
55
- index: string;
56
- bed1?: undefined;
57
- bed2?: undefined;
58
- index2?: undefined;
59
- } | {
60
- file: string;
61
- index: string;
62
- index2: string;
63
- bed1?: undefined;
64
- bed2?: undefined;
65
- } | {
66
- file: string;
67
- bed1?: undefined;
68
- bed2?: undefined;
69
- index?: undefined;
70
- index2?: undefined;
71
- } | {
72
- file?: undefined;
73
- bed1?: undefined;
74
- bed2?: undefined;
75
- index?: undefined;
76
- index2?: undefined;
77
- };
78
- guessAdapter({ location, protocol, index, bed1, bed2, }: {
79
- location: string;
80
- protocol: string;
81
- index?: string;
82
- bed1?: string;
83
- bed2?: string;
84
- }): {
85
- type: string;
86
- bamLocation: UriLocation | LocalPathLocation;
87
- index: {
88
- location: UriLocation | LocalPathLocation;
89
- indexType: string;
90
- };
91
- cramLocation?: undefined;
92
- craiLocation?: undefined;
93
- gffLocation?: undefined;
94
- gffGzLocation?: undefined;
95
- gtfLocation?: undefined;
96
- vcfLocation?: undefined;
97
- vcfGzLocation?: undefined;
98
- bedGzLocation?: undefined;
99
- bedLocation?: undefined;
100
- bigBedLocation?: undefined;
101
- bigWigLocation?: undefined;
102
- fastaLocation?: undefined;
103
- faiLocation?: undefined;
104
- gziLocation?: undefined;
105
- twoBitLocation?: undefined;
106
- rootUrlTemplate?: undefined;
107
- endpoint?: undefined;
108
- hicLocation?: undefined;
109
- pafLocation?: undefined;
110
- outLocation?: undefined;
111
- chainLocation?: undefined;
112
- deltaLocation?: undefined;
113
- mcscanAnchorsLocation?: undefined;
114
- bed1Location?: undefined;
115
- bed2Location?: undefined;
116
- mcscanSimpleAnchorsLocation?: undefined;
117
- } | {
118
- type: string;
119
- cramLocation: UriLocation | LocalPathLocation;
120
- craiLocation: UriLocation | LocalPathLocation;
121
- bamLocation?: undefined;
122
- index?: undefined;
123
- gffLocation?: undefined;
124
- gffGzLocation?: undefined;
125
- gtfLocation?: undefined;
126
- vcfLocation?: undefined;
127
- vcfGzLocation?: undefined;
128
- bedGzLocation?: undefined;
129
- bedLocation?: undefined;
130
- bigBedLocation?: undefined;
131
- bigWigLocation?: undefined;
132
- fastaLocation?: undefined;
133
- faiLocation?: undefined;
134
- gziLocation?: undefined;
135
- twoBitLocation?: undefined;
136
- rootUrlTemplate?: undefined;
137
- endpoint?: undefined;
138
- hicLocation?: undefined;
139
- pafLocation?: undefined;
140
- outLocation?: undefined;
141
- chainLocation?: undefined;
142
- deltaLocation?: undefined;
143
- mcscanAnchorsLocation?: undefined;
144
- bed1Location?: undefined;
145
- bed2Location?: undefined;
146
- mcscanSimpleAnchorsLocation?: undefined;
147
- } | {
148
- type: string;
149
- gffLocation: UriLocation | LocalPathLocation;
150
- bamLocation?: undefined;
151
- index?: undefined;
152
- cramLocation?: undefined;
153
- craiLocation?: undefined;
154
- gffGzLocation?: undefined;
155
- gtfLocation?: undefined;
156
- vcfLocation?: undefined;
157
- vcfGzLocation?: undefined;
158
- bedGzLocation?: undefined;
159
- bedLocation?: undefined;
160
- bigBedLocation?: undefined;
161
- bigWigLocation?: undefined;
162
- fastaLocation?: undefined;
163
- faiLocation?: undefined;
164
- gziLocation?: undefined;
165
- twoBitLocation?: undefined;
166
- rootUrlTemplate?: undefined;
167
- endpoint?: undefined;
168
- hicLocation?: undefined;
169
- pafLocation?: undefined;
170
- outLocation?: undefined;
171
- chainLocation?: undefined;
172
- deltaLocation?: undefined;
173
- mcscanAnchorsLocation?: undefined;
174
- bed1Location?: undefined;
175
- bed2Location?: undefined;
176
- mcscanSimpleAnchorsLocation?: undefined;
177
- } | {
178
- type: string;
179
- gffGzLocation: UriLocation | LocalPathLocation;
180
- index: {
181
- location: UriLocation | LocalPathLocation;
182
- indexType: string;
183
- };
184
- bamLocation?: undefined;
185
- cramLocation?: undefined;
186
- craiLocation?: undefined;
187
- gffLocation?: undefined;
188
- gtfLocation?: undefined;
189
- vcfLocation?: undefined;
190
- vcfGzLocation?: undefined;
191
- bedGzLocation?: undefined;
192
- bedLocation?: undefined;
193
- bigBedLocation?: undefined;
194
- bigWigLocation?: undefined;
195
- fastaLocation?: undefined;
196
- faiLocation?: undefined;
197
- gziLocation?: undefined;
198
- twoBitLocation?: undefined;
199
- rootUrlTemplate?: undefined;
200
- endpoint?: undefined;
201
- hicLocation?: undefined;
202
- pafLocation?: undefined;
203
- outLocation?: undefined;
204
- chainLocation?: undefined;
205
- deltaLocation?: undefined;
206
- mcscanAnchorsLocation?: undefined;
207
- bed1Location?: undefined;
208
- bed2Location?: undefined;
209
- mcscanSimpleAnchorsLocation?: undefined;
210
- } | {
211
- type: string;
212
- gtfLocation: UriLocation | LocalPathLocation;
213
- bamLocation?: undefined;
214
- index?: undefined;
215
- cramLocation?: undefined;
216
- craiLocation?: undefined;
217
- gffLocation?: undefined;
218
- gffGzLocation?: undefined;
219
- vcfLocation?: undefined;
220
- vcfGzLocation?: undefined;
221
- bedGzLocation?: undefined;
222
- bedLocation?: undefined;
223
- bigBedLocation?: undefined;
224
- bigWigLocation?: undefined;
225
- fastaLocation?: undefined;
226
- faiLocation?: undefined;
227
- gziLocation?: undefined;
228
- twoBitLocation?: undefined;
229
- rootUrlTemplate?: undefined;
230
- endpoint?: undefined;
231
- hicLocation?: undefined;
232
- pafLocation?: undefined;
233
- outLocation?: undefined;
234
- chainLocation?: undefined;
235
- deltaLocation?: undefined;
236
- mcscanAnchorsLocation?: undefined;
237
- bed1Location?: undefined;
238
- bed2Location?: undefined;
239
- mcscanSimpleAnchorsLocation?: undefined;
240
- } | {
241
- type: string;
242
- vcfLocation: UriLocation | LocalPathLocation;
243
- bamLocation?: undefined;
244
- index?: undefined;
245
- cramLocation?: undefined;
246
- craiLocation?: undefined;
247
- gffLocation?: undefined;
248
- gffGzLocation?: undefined;
249
- gtfLocation?: undefined;
250
- vcfGzLocation?: undefined;
251
- bedGzLocation?: undefined;
252
- bedLocation?: undefined;
253
- bigBedLocation?: undefined;
254
- bigWigLocation?: undefined;
255
- fastaLocation?: undefined;
256
- faiLocation?: undefined;
257
- gziLocation?: undefined;
258
- twoBitLocation?: undefined;
259
- rootUrlTemplate?: undefined;
260
- endpoint?: undefined;
261
- hicLocation?: undefined;
262
- pafLocation?: undefined;
263
- outLocation?: undefined;
264
- chainLocation?: undefined;
265
- deltaLocation?: undefined;
266
- mcscanAnchorsLocation?: undefined;
267
- bed1Location?: undefined;
268
- bed2Location?: undefined;
269
- mcscanSimpleAnchorsLocation?: undefined;
270
- } | {
271
- type: string;
272
- vcfGzLocation: UriLocation | LocalPathLocation;
273
- index: {
274
- location: UriLocation | LocalPathLocation;
275
- indexType: string;
276
- };
277
- bamLocation?: undefined;
278
- cramLocation?: undefined;
279
- craiLocation?: undefined;
280
- gffLocation?: undefined;
281
- gffGzLocation?: undefined;
282
- gtfLocation?: undefined;
283
- vcfLocation?: undefined;
284
- bedGzLocation?: undefined;
285
- bedLocation?: undefined;
286
- bigBedLocation?: undefined;
287
- bigWigLocation?: undefined;
288
- fastaLocation?: undefined;
289
- faiLocation?: undefined;
290
- gziLocation?: undefined;
291
- twoBitLocation?: undefined;
292
- rootUrlTemplate?: undefined;
293
- endpoint?: undefined;
294
- hicLocation?: undefined;
295
- pafLocation?: undefined;
296
- outLocation?: undefined;
297
- chainLocation?: undefined;
298
- deltaLocation?: undefined;
299
- mcscanAnchorsLocation?: undefined;
300
- bed1Location?: undefined;
301
- bed2Location?: undefined;
302
- mcscanSimpleAnchorsLocation?: undefined;
303
- } | {
304
- type: string;
305
- bamLocation?: undefined;
306
- index?: undefined;
307
- cramLocation?: undefined;
308
- craiLocation?: undefined;
309
- gffLocation?: undefined;
310
- gffGzLocation?: undefined;
311
- gtfLocation?: undefined;
312
- vcfLocation?: undefined;
313
- vcfGzLocation?: undefined;
314
- bedGzLocation?: undefined;
315
- bedLocation?: undefined;
316
- bigBedLocation?: undefined;
317
- bigWigLocation?: undefined;
318
- fastaLocation?: undefined;
319
- faiLocation?: undefined;
320
- gziLocation?: undefined;
321
- twoBitLocation?: undefined;
322
- rootUrlTemplate?: undefined;
323
- endpoint?: undefined;
324
- hicLocation?: undefined;
325
- pafLocation?: undefined;
326
- outLocation?: undefined;
327
- chainLocation?: undefined;
328
- deltaLocation?: undefined;
329
- mcscanAnchorsLocation?: undefined;
330
- bed1Location?: undefined;
331
- bed2Location?: undefined;
332
- mcscanSimpleAnchorsLocation?: undefined;
333
- } | {
334
- type: string;
335
- bedGzLocation: UriLocation | LocalPathLocation;
336
- index: {
337
- location: UriLocation | LocalPathLocation;
338
- indexType: string;
339
- };
340
- bamLocation?: undefined;
341
- cramLocation?: undefined;
342
- craiLocation?: undefined;
343
- gffLocation?: undefined;
344
- gffGzLocation?: undefined;
345
- gtfLocation?: undefined;
346
- vcfLocation?: undefined;
347
- vcfGzLocation?: undefined;
348
- bedLocation?: undefined;
349
- bigBedLocation?: undefined;
350
- bigWigLocation?: undefined;
351
- fastaLocation?: undefined;
352
- faiLocation?: undefined;
353
- gziLocation?: undefined;
354
- twoBitLocation?: undefined;
355
- rootUrlTemplate?: undefined;
356
- endpoint?: undefined;
357
- hicLocation?: undefined;
358
- pafLocation?: undefined;
359
- outLocation?: undefined;
360
- chainLocation?: undefined;
361
- deltaLocation?: undefined;
362
- mcscanAnchorsLocation?: undefined;
363
- bed1Location?: undefined;
364
- bed2Location?: undefined;
365
- mcscanSimpleAnchorsLocation?: undefined;
366
- } | {
367
- type: string;
368
- bedLocation: UriLocation | LocalPathLocation;
369
- bamLocation?: undefined;
370
- index?: undefined;
371
- cramLocation?: undefined;
372
- craiLocation?: undefined;
373
- gffLocation?: undefined;
374
- gffGzLocation?: undefined;
375
- gtfLocation?: undefined;
376
- vcfLocation?: undefined;
377
- vcfGzLocation?: undefined;
378
- bedGzLocation?: undefined;
379
- bigBedLocation?: undefined;
380
- bigWigLocation?: undefined;
381
- fastaLocation?: undefined;
382
- faiLocation?: undefined;
383
- gziLocation?: undefined;
384
- twoBitLocation?: undefined;
385
- rootUrlTemplate?: undefined;
386
- endpoint?: undefined;
387
- hicLocation?: undefined;
388
- pafLocation?: undefined;
389
- outLocation?: undefined;
390
- chainLocation?: undefined;
391
- deltaLocation?: undefined;
392
- mcscanAnchorsLocation?: undefined;
393
- bed1Location?: undefined;
394
- bed2Location?: undefined;
395
- mcscanSimpleAnchorsLocation?: undefined;
396
- } | {
397
- type: string;
398
- bigBedLocation: UriLocation | LocalPathLocation;
399
- bamLocation?: undefined;
400
- index?: undefined;
401
- cramLocation?: undefined;
402
- craiLocation?: undefined;
403
- gffLocation?: undefined;
404
- gffGzLocation?: undefined;
405
- gtfLocation?: undefined;
406
- vcfLocation?: undefined;
407
- vcfGzLocation?: undefined;
408
- bedGzLocation?: undefined;
409
- bedLocation?: undefined;
410
- bigWigLocation?: undefined;
411
- fastaLocation?: undefined;
412
- faiLocation?: undefined;
413
- gziLocation?: undefined;
414
- twoBitLocation?: undefined;
415
- rootUrlTemplate?: undefined;
416
- endpoint?: undefined;
417
- hicLocation?: undefined;
418
- pafLocation?: undefined;
419
- outLocation?: undefined;
420
- chainLocation?: undefined;
421
- deltaLocation?: undefined;
422
- mcscanAnchorsLocation?: undefined;
423
- bed1Location?: undefined;
424
- bed2Location?: undefined;
425
- mcscanSimpleAnchorsLocation?: undefined;
426
- } | {
427
- type: string;
428
- bigWigLocation: UriLocation | LocalPathLocation;
429
- bamLocation?: undefined;
430
- index?: undefined;
431
- cramLocation?: undefined;
432
- craiLocation?: undefined;
433
- gffLocation?: undefined;
434
- gffGzLocation?: undefined;
435
- gtfLocation?: undefined;
436
- vcfLocation?: undefined;
437
- vcfGzLocation?: undefined;
438
- bedGzLocation?: undefined;
439
- bedLocation?: undefined;
440
- bigBedLocation?: undefined;
441
- fastaLocation?: undefined;
442
- faiLocation?: undefined;
443
- gziLocation?: undefined;
444
- twoBitLocation?: undefined;
445
- rootUrlTemplate?: undefined;
446
- endpoint?: undefined;
447
- hicLocation?: undefined;
448
- pafLocation?: undefined;
449
- outLocation?: undefined;
450
- chainLocation?: undefined;
451
- deltaLocation?: undefined;
452
- mcscanAnchorsLocation?: undefined;
453
- bed1Location?: undefined;
454
- bed2Location?: undefined;
455
- mcscanSimpleAnchorsLocation?: undefined;
456
- } | {
457
- type: string;
458
- fastaLocation: UriLocation | LocalPathLocation;
459
- faiLocation: UriLocation | LocalPathLocation;
460
- bamLocation?: undefined;
461
- index?: undefined;
462
- cramLocation?: undefined;
463
- craiLocation?: undefined;
464
- gffLocation?: undefined;
465
- gffGzLocation?: undefined;
466
- gtfLocation?: undefined;
467
- vcfLocation?: undefined;
468
- vcfGzLocation?: undefined;
469
- bedGzLocation?: undefined;
470
- bedLocation?: undefined;
471
- bigBedLocation?: undefined;
472
- bigWigLocation?: undefined;
473
- gziLocation?: undefined;
474
- twoBitLocation?: undefined;
475
- rootUrlTemplate?: undefined;
476
- endpoint?: undefined;
477
- hicLocation?: undefined;
478
- pafLocation?: undefined;
479
- outLocation?: undefined;
480
- chainLocation?: undefined;
481
- deltaLocation?: undefined;
482
- mcscanAnchorsLocation?: undefined;
483
- bed1Location?: undefined;
484
- bed2Location?: undefined;
485
- mcscanSimpleAnchorsLocation?: undefined;
486
- } | {
487
- type: string;
488
- fastaLocation: UriLocation | LocalPathLocation;
489
- faiLocation: UriLocation | LocalPathLocation;
490
- gziLocation: UriLocation | LocalPathLocation;
491
- bamLocation?: undefined;
492
- index?: undefined;
493
- cramLocation?: undefined;
494
- craiLocation?: undefined;
495
- gffLocation?: undefined;
496
- gffGzLocation?: undefined;
497
- gtfLocation?: undefined;
498
- vcfLocation?: undefined;
499
- vcfGzLocation?: undefined;
500
- bedGzLocation?: undefined;
501
- bedLocation?: undefined;
502
- bigBedLocation?: undefined;
503
- bigWigLocation?: undefined;
504
- twoBitLocation?: undefined;
505
- rootUrlTemplate?: undefined;
506
- endpoint?: undefined;
507
- hicLocation?: undefined;
508
- pafLocation?: undefined;
509
- outLocation?: undefined;
510
- chainLocation?: undefined;
511
- deltaLocation?: undefined;
512
- mcscanAnchorsLocation?: undefined;
513
- bed1Location?: undefined;
514
- bed2Location?: undefined;
515
- mcscanSimpleAnchorsLocation?: undefined;
516
- } | {
517
- type: string;
518
- twoBitLocation: UriLocation | LocalPathLocation;
519
- bamLocation?: undefined;
520
- index?: undefined;
521
- cramLocation?: undefined;
522
- craiLocation?: undefined;
523
- gffLocation?: undefined;
524
- gffGzLocation?: undefined;
525
- gtfLocation?: undefined;
526
- vcfLocation?: undefined;
527
- vcfGzLocation?: undefined;
528
- bedGzLocation?: undefined;
529
- bedLocation?: undefined;
530
- bigBedLocation?: undefined;
531
- bigWigLocation?: undefined;
532
- fastaLocation?: undefined;
533
- faiLocation?: undefined;
534
- gziLocation?: undefined;
535
- rootUrlTemplate?: undefined;
536
- endpoint?: undefined;
537
- hicLocation?: undefined;
538
- pafLocation?: undefined;
539
- outLocation?: undefined;
540
- chainLocation?: undefined;
541
- deltaLocation?: undefined;
542
- mcscanAnchorsLocation?: undefined;
543
- bed1Location?: undefined;
544
- bed2Location?: undefined;
545
- mcscanSimpleAnchorsLocation?: undefined;
546
- } | {
547
- type: string;
548
- rootUrlTemplate: UriLocation | LocalPathLocation;
549
- bamLocation?: undefined;
550
- index?: undefined;
551
- cramLocation?: undefined;
552
- craiLocation?: undefined;
553
- gffLocation?: undefined;
554
- gffGzLocation?: undefined;
555
- gtfLocation?: undefined;
556
- vcfLocation?: undefined;
557
- vcfGzLocation?: undefined;
558
- bedGzLocation?: undefined;
559
- bedLocation?: undefined;
560
- bigBedLocation?: undefined;
561
- bigWigLocation?: undefined;
562
- fastaLocation?: undefined;
563
- faiLocation?: undefined;
564
- gziLocation?: undefined;
565
- twoBitLocation?: undefined;
566
- endpoint?: undefined;
567
- hicLocation?: undefined;
568
- pafLocation?: undefined;
569
- outLocation?: undefined;
570
- chainLocation?: undefined;
571
- deltaLocation?: undefined;
572
- mcscanAnchorsLocation?: undefined;
573
- bed1Location?: undefined;
574
- bed2Location?: undefined;
575
- mcscanSimpleAnchorsLocation?: undefined;
576
- } | {
577
- type: string;
578
- endpoint: string;
579
- bamLocation?: undefined;
580
- index?: undefined;
581
- cramLocation?: undefined;
582
- craiLocation?: undefined;
583
- gffLocation?: undefined;
584
- gffGzLocation?: undefined;
585
- gtfLocation?: undefined;
586
- vcfLocation?: undefined;
587
- vcfGzLocation?: undefined;
588
- bedGzLocation?: undefined;
589
- bedLocation?: undefined;
590
- bigBedLocation?: undefined;
591
- bigWigLocation?: undefined;
592
- fastaLocation?: undefined;
593
- faiLocation?: undefined;
594
- gziLocation?: undefined;
595
- twoBitLocation?: undefined;
596
- rootUrlTemplate?: undefined;
597
- hicLocation?: undefined;
598
- pafLocation?: undefined;
599
- outLocation?: undefined;
600
- chainLocation?: undefined;
601
- deltaLocation?: undefined;
602
- mcscanAnchorsLocation?: undefined;
603
- bed1Location?: undefined;
604
- bed2Location?: undefined;
605
- mcscanSimpleAnchorsLocation?: undefined;
606
- } | {
607
- type: string;
608
- hicLocation: UriLocation | LocalPathLocation;
609
- bamLocation?: undefined;
610
- index?: undefined;
611
- cramLocation?: undefined;
612
- craiLocation?: undefined;
613
- gffLocation?: undefined;
614
- gffGzLocation?: undefined;
615
- gtfLocation?: undefined;
616
- vcfLocation?: undefined;
617
- vcfGzLocation?: undefined;
618
- bedGzLocation?: undefined;
619
- bedLocation?: undefined;
620
- bigBedLocation?: undefined;
621
- bigWigLocation?: undefined;
622
- fastaLocation?: undefined;
623
- faiLocation?: undefined;
624
- gziLocation?: undefined;
625
- twoBitLocation?: undefined;
626
- rootUrlTemplate?: undefined;
627
- endpoint?: undefined;
628
- pafLocation?: undefined;
629
- outLocation?: undefined;
630
- chainLocation?: undefined;
631
- deltaLocation?: undefined;
632
- mcscanAnchorsLocation?: undefined;
633
- bed1Location?: undefined;
634
- bed2Location?: undefined;
635
- mcscanSimpleAnchorsLocation?: undefined;
636
- } | {
637
- type: string;
638
- pafLocation: UriLocation | LocalPathLocation;
639
- bamLocation?: undefined;
640
- index?: undefined;
641
- cramLocation?: undefined;
642
- craiLocation?: undefined;
643
- gffLocation?: undefined;
644
- gffGzLocation?: undefined;
645
- gtfLocation?: undefined;
646
- vcfLocation?: undefined;
647
- vcfGzLocation?: undefined;
648
- bedGzLocation?: undefined;
649
- bedLocation?: undefined;
650
- bigBedLocation?: undefined;
651
- bigWigLocation?: undefined;
652
- fastaLocation?: undefined;
653
- faiLocation?: undefined;
654
- gziLocation?: undefined;
655
- twoBitLocation?: undefined;
656
- rootUrlTemplate?: undefined;
657
- endpoint?: undefined;
658
- hicLocation?: undefined;
659
- outLocation?: undefined;
660
- chainLocation?: undefined;
661
- deltaLocation?: undefined;
662
- mcscanAnchorsLocation?: undefined;
663
- bed1Location?: undefined;
664
- bed2Location?: undefined;
665
- mcscanSimpleAnchorsLocation?: undefined;
666
- } | {
667
- type: string;
668
- outLocation: UriLocation | LocalPathLocation;
669
- bamLocation?: undefined;
670
- index?: undefined;
671
- cramLocation?: undefined;
672
- craiLocation?: undefined;
673
- gffLocation?: undefined;
674
- gffGzLocation?: undefined;
675
- gtfLocation?: undefined;
676
- vcfLocation?: undefined;
677
- vcfGzLocation?: undefined;
678
- bedGzLocation?: undefined;
679
- bedLocation?: undefined;
680
- bigBedLocation?: undefined;
681
- bigWigLocation?: undefined;
682
- fastaLocation?: undefined;
683
- faiLocation?: undefined;
684
- gziLocation?: undefined;
685
- twoBitLocation?: undefined;
686
- rootUrlTemplate?: undefined;
687
- endpoint?: undefined;
688
- hicLocation?: undefined;
689
- pafLocation?: undefined;
690
- chainLocation?: undefined;
691
- deltaLocation?: undefined;
692
- mcscanAnchorsLocation?: undefined;
693
- bed1Location?: undefined;
694
- bed2Location?: undefined;
695
- mcscanSimpleAnchorsLocation?: undefined;
696
- } | {
697
- type: string;
698
- chainLocation: UriLocation | LocalPathLocation;
699
- bamLocation?: undefined;
700
- index?: undefined;
701
- cramLocation?: undefined;
702
- craiLocation?: undefined;
703
- gffLocation?: undefined;
704
- gffGzLocation?: undefined;
705
- gtfLocation?: undefined;
706
- vcfLocation?: undefined;
707
- vcfGzLocation?: undefined;
708
- bedGzLocation?: undefined;
709
- bedLocation?: undefined;
710
- bigBedLocation?: undefined;
711
- bigWigLocation?: undefined;
712
- fastaLocation?: undefined;
713
- faiLocation?: undefined;
714
- gziLocation?: undefined;
715
- twoBitLocation?: undefined;
716
- rootUrlTemplate?: undefined;
717
- endpoint?: undefined;
718
- hicLocation?: undefined;
719
- pafLocation?: undefined;
720
- outLocation?: undefined;
721
- deltaLocation?: undefined;
722
- mcscanAnchorsLocation?: undefined;
723
- bed1Location?: undefined;
724
- bed2Location?: undefined;
725
- mcscanSimpleAnchorsLocation?: undefined;
726
- } | {
727
- type: string;
728
- deltaLocation: UriLocation | LocalPathLocation;
729
- bamLocation?: undefined;
730
- index?: undefined;
731
- cramLocation?: undefined;
732
- craiLocation?: undefined;
733
- gffLocation?: undefined;
734
- gffGzLocation?: undefined;
735
- gtfLocation?: undefined;
736
- vcfLocation?: undefined;
737
- vcfGzLocation?: undefined;
738
- bedGzLocation?: undefined;
739
- bedLocation?: undefined;
740
- bigBedLocation?: undefined;
741
- bigWigLocation?: undefined;
742
- fastaLocation?: undefined;
743
- faiLocation?: undefined;
744
- gziLocation?: undefined;
745
- twoBitLocation?: undefined;
746
- rootUrlTemplate?: undefined;
747
- endpoint?: undefined;
748
- hicLocation?: undefined;
749
- pafLocation?: undefined;
750
- outLocation?: undefined;
751
- chainLocation?: undefined;
752
- mcscanAnchorsLocation?: undefined;
753
- bed1Location?: undefined;
754
- bed2Location?: undefined;
755
- mcscanSimpleAnchorsLocation?: undefined;
756
- } | {
757
- type: string;
758
- mcscanAnchorsLocation: UriLocation | LocalPathLocation;
759
- bed1Location: UriLocation | LocalPathLocation | undefined;
760
- bed2Location: UriLocation | LocalPathLocation | undefined;
761
- bamLocation?: undefined;
762
- index?: undefined;
763
- cramLocation?: undefined;
764
- craiLocation?: undefined;
765
- gffLocation?: undefined;
766
- gffGzLocation?: undefined;
767
- gtfLocation?: undefined;
768
- vcfLocation?: undefined;
769
- vcfGzLocation?: undefined;
770
- bedGzLocation?: undefined;
771
- bedLocation?: undefined;
772
- bigBedLocation?: undefined;
773
- bigWigLocation?: undefined;
774
- fastaLocation?: undefined;
775
- faiLocation?: undefined;
776
- gziLocation?: undefined;
777
- twoBitLocation?: undefined;
778
- rootUrlTemplate?: undefined;
779
- endpoint?: undefined;
780
- hicLocation?: undefined;
781
- pafLocation?: undefined;
782
- outLocation?: undefined;
783
- chainLocation?: undefined;
784
- deltaLocation?: undefined;
785
- mcscanSimpleAnchorsLocation?: undefined;
786
- } | {
787
- type: string;
788
- mcscanSimpleAnchorsLocation: UriLocation | LocalPathLocation;
789
- bed1Location: UriLocation | LocalPathLocation | undefined;
790
- bed2Location: UriLocation | LocalPathLocation | undefined;
791
- bamLocation?: undefined;
792
- index?: undefined;
793
- cramLocation?: undefined;
794
- craiLocation?: undefined;
795
- gffLocation?: undefined;
796
- gffGzLocation?: undefined;
797
- gtfLocation?: undefined;
798
- vcfLocation?: undefined;
799
- vcfGzLocation?: undefined;
800
- bedGzLocation?: undefined;
801
- bedLocation?: undefined;
802
- bigBedLocation?: undefined;
803
- bigWigLocation?: undefined;
804
- fastaLocation?: undefined;
805
- faiLocation?: undefined;
806
- gziLocation?: undefined;
807
- twoBitLocation?: undefined;
808
- rootUrlTemplate?: undefined;
809
- endpoint?: undefined;
810
- hicLocation?: undefined;
811
- pafLocation?: undefined;
812
- outLocation?: undefined;
813
- chainLocation?: undefined;
814
- deltaLocation?: undefined;
815
- mcscanAnchorsLocation?: undefined;
816
- };
817
- guessTrackType(adapterType: string): string;
818
- }
819
- export {};