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Issue 1078053002: Roll of googleapis as of 4/7/2015. (Closed) Base URL: https://github.com/dart-lang/googleapis.git@master
Patch Set: Created 5 years, 8 months ago
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1 {
2 "auth": {
3 "oauth2": {
4 "scopes": {
5 "https://www.googleapis.com/auth/bigquery": {
6 "description": "View and manage your data in Google BigQuery "
7 },
8 "https://www.googleapis.com/auth/devstorage.read_write": {
9 "description": "Manage your data in Google Cloud Storage"
10 },
11 "https://www.googleapis.com/auth/genomics": {
12 "description": "View and manage Genomics data"
13 },
14 "https://www.googleapis.com/auth/genomics.readonly": {
15 "description": "View Genomics data"
16 }
17 }
18 }
19 },
20 "basePath": "/genomics/v1beta/",
21 "baseUrl": "https://www.googleapis.com/genomics/v1beta/",
22 "batchPath": "batch",
23 "description": "Provides access to Genomics data.",
24 "discoveryVersion": "v1",
25 "documentationLink": "https://developers.google.com/genomics/v1beta/referenc e",
26 "etag": "\"ye6orv2F-1npMW3u9suM3a7C5Bo/G-sV_bAsBb-PJ30JMzI-mn4mHc4\"",
27 "icons": {
28 "x16": "http://www.google.com/images/icons/product/search-16.gif",
29 "x32": "http://www.google.com/images/icons/product/search-32.gif"
30 },
31 "id": "genomics:v1beta",
32 "kind": "discovery#restDescription",
33 "name": "genomics",
34 "ownerDomain": "google.com",
35 "ownerName": "Google",
36 "parameters": {
37 "alt": {
38 "default": "json",
39 "description": "Data format for the response.",
40 "enum": [
41 "json"
42 ],
43 "enumDescriptions": [
44 "Responses with Content-Type of application/json"
45 ],
46 "location": "query",
47 "type": "string"
48 },
49 "fields": {
50 "description": "Selector specifying which fields to include in a par tial response.",
51 "location": "query",
52 "type": "string"
53 },
54 "key": {
55 "description": "API key. Your API key identifies your project and pr ovides you with API access, quota, and reports. Required unless you provide an O Auth 2.0 token.",
56 "location": "query",
57 "type": "string"
58 },
59 "oauth_token": {
60 "description": "OAuth 2.0 token for the current user.",
61 "location": "query",
62 "type": "string"
63 },
64 "prettyPrint": {
65 "default": "true",
66 "description": "Returns response with indentations and line breaks." ,
67 "location": "query",
68 "type": "boolean"
69 },
70 "quotaUser": {
71 "description": "Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exc eed 40 characters. Overrides userIp if both are provided.",
72 "location": "query",
73 "type": "string"
74 },
75 "userIp": {
76 "description": "IP address of the site where the request originates. Use this if you want to enforce per-user limits.",
77 "location": "query",
78 "type": "string"
79 }
80 },
81 "protocol": "rest",
82 "resources": {
83 "callsets": {
84 "methods": {
85 "create": {
86 "description": "Creates a new call set.",
87 "httpMethod": "POST",
88 "id": "genomics.callsets.create",
89 "path": "callsets",
90 "request": {
91 "$ref": "CallSet"
92 },
93 "response": {
94 "$ref": "CallSet"
95 },
96 "scopes": [
97 "https://www.googleapis.com/auth/genomics"
98 ]
99 },
100 "delete": {
101 "description": "Deletes a call set.",
102 "httpMethod": "DELETE",
103 "id": "genomics.callsets.delete",
104 "parameterOrder": [
105 "callSetId"
106 ],
107 "parameters": {
108 "callSetId": {
109 "description": "The ID of the call set to be deleted .",
110 "location": "path",
111 "required": true,
112 "type": "string"
113 }
114 },
115 "path": "callsets/{callSetId}",
116 "scopes": [
117 "https://www.googleapis.com/auth/genomics"
118 ]
119 },
120 "get": {
121 "description": "Gets a call set by ID.",
122 "httpMethod": "GET",
123 "id": "genomics.callsets.get",
124 "parameterOrder": [
125 "callSetId"
126 ],
127 "parameters": {
128 "callSetId": {
129 "description": "The ID of the call set.",
130 "location": "path",
131 "required": true,
132 "type": "string"
133 }
134 },
135 "path": "callsets/{callSetId}",
136 "response": {
137 "$ref": "CallSet"
138 },
139 "scopes": [
140 "https://www.googleapis.com/auth/genomics",
141 "https://www.googleapis.com/auth/genomics.readonly"
142 ]
143 },
144 "patch": {
145 "description": "Updates a call set. This method supports pat ch semantics.",
146 "httpMethod": "PATCH",
147 "id": "genomics.callsets.patch",
148 "parameterOrder": [
149 "callSetId"
150 ],
151 "parameters": {
152 "callSetId": {
153 "description": "The ID of the call set to be updated .",
154 "location": "path",
155 "required": true,
156 "type": "string"
157 }
158 },
159 "path": "callsets/{callSetId}",
160 "request": {
161 "$ref": "CallSet"
162 },
163 "response": {
164 "$ref": "CallSet"
165 },
166 "scopes": [
167 "https://www.googleapis.com/auth/genomics"
168 ]
169 },
170 "search": {
171 "description": "Gets a list of call sets matching the criter ia.\n\nImplements GlobalAllianceApi.searchCallSets.",
172 "httpMethod": "POST",
173 "id": "genomics.callsets.search",
174 "path": "callsets/search",
175 "request": {
176 "$ref": "SearchCallSetsRequest"
177 },
178 "response": {
179 "$ref": "SearchCallSetsResponse"
180 },
181 "scopes": [
182 "https://www.googleapis.com/auth/genomics",
183 "https://www.googleapis.com/auth/genomics.readonly"
184 ]
185 },
186 "update": {
187 "description": "Updates a call set.",
188 "httpMethod": "PUT",
189 "id": "genomics.callsets.update",
190 "parameterOrder": [
191 "callSetId"
192 ],
193 "parameters": {
194 "callSetId": {
195 "description": "The ID of the call set to be updated .",
196 "location": "path",
197 "required": true,
198 "type": "string"
199 }
200 },
201 "path": "callsets/{callSetId}",
202 "request": {
203 "$ref": "CallSet"
204 },
205 "response": {
206 "$ref": "CallSet"
207 },
208 "scopes": [
209 "https://www.googleapis.com/auth/genomics"
210 ]
211 }
212 }
213 },
214 "datasets": {
215 "methods": {
216 "create": {
217 "description": "Creates a new dataset.",
218 "httpMethod": "POST",
219 "id": "genomics.datasets.create",
220 "path": "datasets",
221 "request": {
222 "$ref": "Dataset"
223 },
224 "response": {
225 "$ref": "Dataset"
226 },
227 "scopes": [
228 "https://www.googleapis.com/auth/genomics"
229 ]
230 },
231 "delete": {
232 "description": "Deletes a dataset.",
233 "httpMethod": "DELETE",
234 "id": "genomics.datasets.delete",
235 "parameterOrder": [
236 "datasetId"
237 ],
238 "parameters": {
239 "datasetId": {
240 "description": "The ID of the dataset to be deleted. ",
241 "location": "path",
242 "required": true,
243 "type": "string"
244 }
245 },
246 "path": "datasets/{datasetId}",
247 "scopes": [
248 "https://www.googleapis.com/auth/genomics"
249 ]
250 },
251 "get": {
252 "description": "Gets a dataset by ID.",
253 "httpMethod": "GET",
254 "id": "genomics.datasets.get",
255 "parameterOrder": [
256 "datasetId"
257 ],
258 "parameters": {
259 "datasetId": {
260 "description": "The ID of the dataset.",
261 "location": "path",
262 "required": true,
263 "type": "string"
264 }
265 },
266 "path": "datasets/{datasetId}",
267 "response": {
268 "$ref": "Dataset"
269 },
270 "scopes": [
271 "https://www.googleapis.com/auth/genomics",
272 "https://www.googleapis.com/auth/genomics.readonly"
273 ]
274 },
275 "list": {
276 "description": "Lists all datasets.",
277 "httpMethod": "GET",
278 "id": "genomics.datasets.list",
279 "parameters": {
280 "maxResults": {
281 "default": "50",
282 "description": "The maximum number of results return ed by this request.",
283 "format": "uint64",
284 "location": "query",
285 "type": "string"
286 },
287 "pageToken": {
288 "description": "The continuation token, which is use d to page through large result sets. To get the next page of results, set this p arameter to the value of nextPageToken from the previous response.",
289 "location": "query",
290 "type": "string"
291 },
292 "projectId": {
293 "description": "Only return datasets which belong to this Google Developers Console project. Only accepts project numbers. Returns a ll public projects if no project number is specified.",
294 "format": "int64",
295 "location": "query",
296 "type": "string"
297 }
298 },
299 "path": "datasets",
300 "response": {
301 "$ref": "ListDatasetsResponse"
302 },
303 "scopes": [
304 "https://www.googleapis.com/auth/genomics",
305 "https://www.googleapis.com/auth/genomics.readonly"
306 ]
307 },
308 "patch": {
309 "description": "Updates a dataset. This method supports patc h semantics.",
310 "httpMethod": "PATCH",
311 "id": "genomics.datasets.patch",
312 "parameterOrder": [
313 "datasetId"
314 ],
315 "parameters": {
316 "datasetId": {
317 "description": "The ID of the dataset to be updated. ",
318 "location": "path",
319 "required": true,
320 "type": "string"
321 }
322 },
323 "path": "datasets/{datasetId}",
324 "request": {
325 "$ref": "Dataset"
326 },
327 "response": {
328 "$ref": "Dataset"
329 },
330 "scopes": [
331 "https://www.googleapis.com/auth/genomics"
332 ]
333 },
334 "undelete": {
335 "description": "Undeletes a dataset by restoring a dataset w hich was deleted via this API. This operation is only possible for a week after the deletion occurred.",
336 "httpMethod": "POST",
337 "id": "genomics.datasets.undelete",
338 "parameterOrder": [
339 "datasetId"
340 ],
341 "parameters": {
342 "datasetId": {
343 "description": "The ID of the dataset to be undelete d.",
344 "location": "path",
345 "required": true,
346 "type": "string"
347 }
348 },
349 "path": "datasets/{datasetId}/undelete",
350 "response": {
351 "$ref": "Dataset"
352 },
353 "scopes": [
354 "https://www.googleapis.com/auth/genomics"
355 ]
356 },
357 "update": {
358 "description": "Updates a dataset.",
359 "httpMethod": "PUT",
360 "id": "genomics.datasets.update",
361 "parameterOrder": [
362 "datasetId"
363 ],
364 "parameters": {
365 "datasetId": {
366 "description": "The ID of the dataset to be updated. ",
367 "location": "path",
368 "required": true,
369 "type": "string"
370 }
371 },
372 "path": "datasets/{datasetId}",
373 "request": {
374 "$ref": "Dataset"
375 },
376 "response": {
377 "$ref": "Dataset"
378 },
379 "scopes": [
380 "https://www.googleapis.com/auth/genomics"
381 ]
382 }
383 }
384 },
385 "experimental": {
386 "resources": {
387 "jobs": {
388 "methods": {
389 "create": {
390 "description": "Creates and asynchronously runs an a d-hoc job. This is an experimental call and may be removed or changed at any tim e.",
391 "httpMethod": "POST",
392 "id": "genomics.experimental.jobs.create",
393 "path": "experimental/jobs/create",
394 "request": {
395 "$ref": "ExperimentalCreateJobRequest"
396 },
397 "response": {
398 "$ref": "ExperimentalCreateJobResponse"
399 },
400 "scopes": [
401 "https://www.googleapis.com/auth/devstorage.read _write",
402 "https://www.googleapis.com/auth/genomics"
403 ]
404 }
405 }
406 }
407 }
408 },
409 "jobs": {
410 "methods": {
411 "cancel": {
412 "description": "Cancels a job by ID. Note that it is possibl e for partial results to be generated and stored for cancelled jobs.",
413 "httpMethod": "POST",
414 "id": "genomics.jobs.cancel",
415 "parameterOrder": [
416 "jobId"
417 ],
418 "parameters": {
419 "jobId": {
420 "description": "Required. The ID of the job.",
421 "location": "path",
422 "required": true,
423 "type": "string"
424 }
425 },
426 "path": "jobs/{jobId}/cancel",
427 "scopes": [
428 "https://www.googleapis.com/auth/genomics"
429 ]
430 },
431 "get": {
432 "description": "Gets a job by ID.",
433 "httpMethod": "GET",
434 "id": "genomics.jobs.get",
435 "parameterOrder": [
436 "jobId"
437 ],
438 "parameters": {
439 "jobId": {
440 "description": "Required. The ID of the job.",
441 "location": "path",
442 "required": true,
443 "type": "string"
444 }
445 },
446 "path": "jobs/{jobId}",
447 "response": {
448 "$ref": "Job"
449 },
450 "scopes": [
451 "https://www.googleapis.com/auth/genomics",
452 "https://www.googleapis.com/auth/genomics.readonly"
453 ]
454 },
455 "search": {
456 "description": "Gets a list of jobs matching the criteria.",
457 "httpMethod": "POST",
458 "id": "genomics.jobs.search",
459 "path": "jobs/search",
460 "request": {
461 "$ref": "SearchJobsRequest"
462 },
463 "response": {
464 "$ref": "SearchJobsResponse"
465 },
466 "scopes": [
467 "https://www.googleapis.com/auth/genomics",
468 "https://www.googleapis.com/auth/genomics.readonly"
469 ]
470 }
471 }
472 },
473 "reads": {
474 "methods": {
475 "search": {
476 "description": "Gets a list of reads for one or more readset s. Reads search operates over a genomic coordinate space of reference sequence & position defined over the reference sequences to which the requested readsets a re aligned. If a target positional range is specified, search returns all reads whose alignment to the reference genome overlap the range. A query which specifi es only readset IDs yields all reads in those readsets, including unmapped reads . All reads returned (including reads on subsequent pages) are ordered by genomi c coordinate (reference sequence & position). Reads with equivalent genomic coor dinates are returned in a deterministic order.",
477 "httpMethod": "POST",
478 "id": "genomics.reads.search",
479 "path": "reads/search",
480 "request": {
481 "$ref": "SearchReadsRequest"
482 },
483 "response": {
484 "$ref": "SearchReadsResponse"
485 },
486 "scopes": [
487 "https://www.googleapis.com/auth/genomics",
488 "https://www.googleapis.com/auth/genomics.readonly"
489 ]
490 }
491 }
492 },
493 "readsets": {
494 "methods": {
495 "delete": {
496 "description": "Deletes a readset.",
497 "httpMethod": "DELETE",
498 "id": "genomics.readsets.delete",
499 "parameterOrder": [
500 "readsetId"
501 ],
502 "parameters": {
503 "readsetId": {
504 "description": "The ID of the readset to be deleted. The caller must have WRITE permissions to the dataset associated with this read set.",
505 "location": "path",
506 "required": true,
507 "type": "string"
508 }
509 },
510 "path": "readsets/{readsetId}",
511 "scopes": [
512 "https://www.googleapis.com/auth/genomics"
513 ]
514 },
515 "export": {
516 "description": "Exports readsets to a BAM file in Google Clo ud Storage. Note that currently there may be some differences between exported B AM files and the original BAM file at the time of import. In particular, comment s in the input file header will not be preserved, and some custom tags will be c onverted to strings.",
517 "httpMethod": "POST",
518 "id": "genomics.readsets.export",
519 "path": "readsets/export",
520 "request": {
521 "$ref": "ExportReadsetsRequest"
522 },
523 "response": {
524 "$ref": "ExportReadsetsResponse"
525 },
526 "scopes": [
527 "https://www.googleapis.com/auth/devstorage.read_write",
528 "https://www.googleapis.com/auth/genomics"
529 ]
530 },
531 "get": {
532 "description": "Gets a readset by ID.",
533 "httpMethod": "GET",
534 "id": "genomics.readsets.get",
535 "parameterOrder": [
536 "readsetId"
537 ],
538 "parameters": {
539 "readsetId": {
540 "description": "The ID of the readset.",
541 "location": "path",
542 "required": true,
543 "type": "string"
544 }
545 },
546 "path": "readsets/{readsetId}",
547 "response": {
548 "$ref": "Readset"
549 },
550 "scopes": [
551 "https://www.googleapis.com/auth/genomics",
552 "https://www.googleapis.com/auth/genomics.readonly"
553 ]
554 },
555 "import": {
556 "description": "Creates readsets by asynchronously importing the provided information. Note that currently comments in the input file header are not imported and some custom tags will be converted to strings, rather than preserving tag types. The caller must have WRITE permissions to the dataset.",
557 "httpMethod": "POST",
558 "id": "genomics.readsets.import",
559 "path": "readsets/import",
560 "request": {
561 "$ref": "ImportReadsetsRequest"
562 },
563 "response": {
564 "$ref": "ImportReadsetsResponse"
565 },
566 "scopes": [
567 "https://www.googleapis.com/auth/devstorage.read_write",
568 "https://www.googleapis.com/auth/genomics"
569 ]
570 },
571 "patch": {
572 "description": "Updates a readset. This method supports patc h semantics.",
573 "httpMethod": "PATCH",
574 "id": "genomics.readsets.patch",
575 "parameterOrder": [
576 "readsetId"
577 ],
578 "parameters": {
579 "readsetId": {
580 "description": "The ID of the readset to be updated. The caller must have WRITE permissions to the dataset associated with this read set.",
581 "location": "path",
582 "required": true,
583 "type": "string"
584 }
585 },
586 "path": "readsets/{readsetId}",
587 "request": {
588 "$ref": "Readset"
589 },
590 "response": {
591 "$ref": "Readset"
592 },
593 "scopes": [
594 "https://www.googleapis.com/auth/genomics"
595 ]
596 },
597 "search": {
598 "description": "Gets a list of readsets matching the criteri a.",
599 "httpMethod": "POST",
600 "id": "genomics.readsets.search",
601 "path": "readsets/search",
602 "request": {
603 "$ref": "SearchReadsetsRequest"
604 },
605 "response": {
606 "$ref": "SearchReadsetsResponse"
607 },
608 "scopes": [
609 "https://www.googleapis.com/auth/genomics",
610 "https://www.googleapis.com/auth/genomics.readonly"
611 ]
612 },
613 "update": {
614 "description": "Updates a readset.",
615 "httpMethod": "PUT",
616 "id": "genomics.readsets.update",
617 "parameterOrder": [
618 "readsetId"
619 ],
620 "parameters": {
621 "readsetId": {
622 "description": "The ID of the readset to be updated. The caller must have WRITE permissions to the dataset associated with this read set.",
623 "location": "path",
624 "required": true,
625 "type": "string"
626 }
627 },
628 "path": "readsets/{readsetId}",
629 "request": {
630 "$ref": "Readset"
631 },
632 "response": {
633 "$ref": "Readset"
634 },
635 "scopes": [
636 "https://www.googleapis.com/auth/genomics"
637 ]
638 }
639 },
640 "resources": {
641 "coveragebuckets": {
642 "methods": {
643 "list": {
644 "description": "Lists fixed width coverage buckets f or a readset, each of which correspond to a range of a reference sequence. Each bucket summarizes coverage information across its corresponding genomic range. C overage is defined as the number of reads which are aligned to a given base in t he reference sequence. Coverage buckets are available at various bucket widths, enabling various coverage \"zoom levels\". The caller must have READ permissions for the target readset.",
645 "httpMethod": "GET",
646 "id": "genomics.readsets.coveragebuckets.list",
647 "parameterOrder": [
648 "readsetId"
649 ],
650 "parameters": {
651 "maxResults": {
652 "default": "1024",
653 "description": "The maximum number of result s to return in a single page. If unspecified, defaults to 1024. The maximum valu e is 2048.",
654 "format": "uint64",
655 "location": "query",
656 "type": "string"
657 },
658 "pageToken": {
659 "description": "The continuation token, whic h is used to page through large result sets. To get the next page of results, se t this parameter to the value of nextPageToken from the previous response.",
660 "location": "query",
661 "type": "string"
662 },
663 "range.sequenceEnd": {
664 "description": "The end position of the rang e on the reference, 1-based exclusive. If specified, sequenceName must also be s pecified.",
665 "format": "uint64",
666 "location": "query",
667 "type": "string"
668 },
669 "range.sequenceName": {
670 "description": "The reference sequence name, for example chr1, 1, or chrX.",
671 "location": "query",
672 "type": "string"
673 },
674 "range.sequenceStart": {
675 "description": "The start position of the ra nge on the reference, 1-based inclusive. If specified, sequenceName must also be specified.",
676 "format": "uint64",
677 "location": "query",
678 "type": "string"
679 },
680 "readsetId": {
681 "description": "Required. The ID of the read set over which coverage is requested.",
682 "location": "path",
683 "required": true,
684 "type": "string"
685 },
686 "targetBucketWidth": {
687 "description": "The desired width of each re ported coverage bucket in base pairs. This will be rounded down to the nearest p recomputed bucket width; the value of which is returned as bucketWidth in the re sponse. Defaults to infinity (each bucket spans an entire reference sequence) or the length of the target range, if specified. The smallest precomputed bucketWi dth is currently 2048 base pairs; this is subject to change.",
688 "format": "uint64",
689 "location": "query",
690 "type": "string"
691 }
692 },
693 "path": "readsets/{readsetId}/coveragebuckets",
694 "response": {
695 "$ref": "ListCoverageBucketsResponse"
696 },
697 "scopes": [
698 "https://www.googleapis.com/auth/genomics",
699 "https://www.googleapis.com/auth/genomics.readon ly"
700 ]
701 }
702 }
703 }
704 }
705 },
706 "variants": {
707 "methods": {
708 "create": {
709 "description": "Creates a new variant.",
710 "httpMethod": "POST",
711 "id": "genomics.variants.create",
712 "path": "variants",
713 "request": {
714 "$ref": "Variant"
715 },
716 "response": {
717 "$ref": "Variant"
718 },
719 "scopes": [
720 "https://www.googleapis.com/auth/genomics"
721 ]
722 },
723 "delete": {
724 "description": "Deletes a variant.",
725 "httpMethod": "DELETE",
726 "id": "genomics.variants.delete",
727 "parameterOrder": [
728 "variantId"
729 ],
730 "parameters": {
731 "variantId": {
732 "description": "The ID of the variant to be deleted. ",
733 "location": "path",
734 "required": true,
735 "type": "string"
736 }
737 },
738 "path": "variants/{variantId}",
739 "scopes": [
740 "https://www.googleapis.com/auth/genomics"
741 ]
742 },
743 "export": {
744 "description": "Exports variant data to an external destinat ion.",
745 "httpMethod": "POST",
746 "id": "genomics.variants.export",
747 "path": "variants/export",
748 "request": {
749 "$ref": "ExportVariantsRequest"
750 },
751 "response": {
752 "$ref": "ExportVariantsResponse"
753 },
754 "scopes": [
755 "https://www.googleapis.com/auth/bigquery",
756 "https://www.googleapis.com/auth/genomics"
757 ]
758 },
759 "get": {
760 "description": "Gets a variant by ID.",
761 "httpMethod": "GET",
762 "id": "genomics.variants.get",
763 "parameterOrder": [
764 "variantId"
765 ],
766 "parameters": {
767 "variantId": {
768 "description": "The ID of the variant.",
769 "location": "path",
770 "required": true,
771 "type": "string"
772 }
773 },
774 "path": "variants/{variantId}",
775 "response": {
776 "$ref": "Variant"
777 },
778 "scopes": [
779 "https://www.googleapis.com/auth/genomics",
780 "https://www.googleapis.com/auth/genomics.readonly"
781 ]
782 },
783 "import": {
784 "description": "Creates variant data by asynchronously impor ting the provided information. The variants for import will be merged with any e xisting data and each other according to the behavior of mergeVariants. In parti cular, this means for merged VCF variants that have conflicting INFO fields, som e data will be arbitrarily discarded. As a special case, for single-sample VCF f iles, QUAL and FILTER fields will be moved to the call level; these are sometime s interpreted in a call-specific context. Imported VCF headers are appended to t he metadata already in a variant set.",
785 "httpMethod": "POST",
786 "id": "genomics.variants.import",
787 "path": "variants/import",
788 "request": {
789 "$ref": "ImportVariantsRequest"
790 },
791 "response": {
792 "$ref": "ImportVariantsResponse"
793 },
794 "scopes": [
795 "https://www.googleapis.com/auth/devstorage.read_write",
796 "https://www.googleapis.com/auth/genomics"
797 ]
798 },
799 "search": {
800 "description": "Gets a list of variants matching the criteri a.\n\nImplements GlobalAllianceApi.searchVariants.",
801 "httpMethod": "POST",
802 "id": "genomics.variants.search",
803 "path": "variants/search",
804 "request": {
805 "$ref": "SearchVariantsRequest"
806 },
807 "response": {
808 "$ref": "SearchVariantsResponse"
809 },
810 "scopes": [
811 "https://www.googleapis.com/auth/genomics",
812 "https://www.googleapis.com/auth/genomics.readonly"
813 ]
814 },
815 "update": {
816 "description": "Updates a variant's names and info fields. A ll other modifications are silently ignored. Returns the modified variant withou t its calls.",
817 "httpMethod": "PUT",
818 "id": "genomics.variants.update",
819 "parameterOrder": [
820 "variantId"
821 ],
822 "parameters": {
823 "variantId": {
824 "description": "The ID of the variant to be updated. ",
825 "location": "path",
826 "required": true,
827 "type": "string"
828 }
829 },
830 "path": "variants/{variantId}",
831 "request": {
832 "$ref": "Variant"
833 },
834 "response": {
835 "$ref": "Variant"
836 },
837 "scopes": [
838 "https://www.googleapis.com/auth/genomics"
839 ]
840 }
841 }
842 },
843 "variantsets": {
844 "methods": {
845 "delete": {
846 "description": "Deletes the contents of a variant set. The v ariant set object is not deleted.",
847 "httpMethod": "DELETE",
848 "id": "genomics.variantsets.delete",
849 "parameterOrder": [
850 "variantSetId"
851 ],
852 "parameters": {
853 "variantSetId": {
854 "description": "The ID of the variant set to be dele ted.",
855 "location": "path",
856 "required": true,
857 "type": "string"
858 }
859 },
860 "path": "variantsets/{variantSetId}",
861 "scopes": [
862 "https://www.googleapis.com/auth/genomics"
863 ]
864 },
865 "get": {
866 "description": "Gets a variant set by ID.",
867 "httpMethod": "GET",
868 "id": "genomics.variantsets.get",
869 "parameterOrder": [
870 "variantSetId"
871 ],
872 "parameters": {
873 "variantSetId": {
874 "description": "Required. The ID of the variant set. ",
875 "location": "path",
876 "required": true,
877 "type": "string"
878 }
879 },
880 "path": "variantsets/{variantSetId}",
881 "response": {
882 "$ref": "VariantSet"
883 },
884 "scopes": [
885 "https://www.googleapis.com/auth/genomics",
886 "https://www.googleapis.com/auth/genomics.readonly"
887 ]
888 },
889 "mergeVariants": {
890 "description": "Merges the given variants with existing vari ants. Each variant will be merged with an existing variant that matches its refe rence sequence, start, end, reference bases, and alternative bases. If no such v ariant exists, a new one will be created.\n\nWhen variants are merged, the call information from the new variant is added to the existing variant, and other fie lds (such as key/value pairs) are discarded.",
891 "httpMethod": "POST",
892 "id": "genomics.variantsets.mergeVariants",
893 "parameterOrder": [
894 "variantSetId"
895 ],
896 "parameters": {
897 "variantSetId": {
898 "description": "The destination variant set.",
899 "location": "path",
900 "required": true,
901 "type": "string"
902 }
903 },
904 "path": "variantsets/{variantSetId}/mergeVariants",
905 "request": {
906 "$ref": "MergeVariantsRequest"
907 }
908 },
909 "patch": {
910 "description": "Updates a variant set's metadata. All other modifications are silently ignored. This method supports patch semantics.",
911 "httpMethod": "PATCH",
912 "id": "genomics.variantsets.patch",
913 "parameterOrder": [
914 "variantSetId"
915 ],
916 "parameters": {
917 "variantSetId": {
918 "description": "The ID of the variant to be updated. ",
919 "location": "path",
920 "required": true,
921 "type": "string"
922 }
923 },
924 "path": "variantsets/{variantSetId}",
925 "request": {
926 "$ref": "VariantSet"
927 },
928 "response": {
929 "$ref": "VariantSet"
930 },
931 "scopes": [
932 "https://www.googleapis.com/auth/genomics"
933 ]
934 },
935 "search": {
936 "description": "Returns a list of all variant sets matching search criteria.\n\nImplements GlobalAllianceApi.searchVariantSets.",
937 "httpMethod": "POST",
938 "id": "genomics.variantsets.search",
939 "path": "variantsets/search",
940 "request": {
941 "$ref": "SearchVariantSetsRequest"
942 },
943 "response": {
944 "$ref": "SearchVariantSetsResponse"
945 },
946 "scopes": [
947 "https://www.googleapis.com/auth/genomics",
948 "https://www.googleapis.com/auth/genomics.readonly"
949 ]
950 },
951 "update": {
952 "description": "Updates a variant set's metadata. All other modifications are silently ignored.",
953 "httpMethod": "PUT",
954 "id": "genomics.variantsets.update",
955 "parameterOrder": [
956 "variantSetId"
957 ],
958 "parameters": {
959 "variantSetId": {
960 "description": "The ID of the variant to be updated. ",
961 "location": "path",
962 "required": true,
963 "type": "string"
964 }
965 },
966 "path": "variantsets/{variantSetId}",
967 "request": {
968 "$ref": "VariantSet"
969 },
970 "response": {
971 "$ref": "VariantSet"
972 },
973 "scopes": [
974 "https://www.googleapis.com/auth/genomics"
975 ]
976 }
977 }
978 }
979 },
980 "revision": "20150223",
981 "rootUrl": "https://www.googleapis.com/",
982 "schemas": {
983 "Call": {
984 "description": "A call represents the determination of genotype with respect to a particular variant. It may include associated information such as quality and phasing. For example, a call might assign a probability of 0.32 to t he occurrence of a SNP named rs1234 in a call set with the name NA12345.",
985 "id": "Call",
986 "properties": {
987 "callSetId": {
988 "description": "The ID of the call set this variant call bel ongs to.",
989 "type": "string"
990 },
991 "callSetName": {
992 "description": "The name of the call set this variant call b elongs to.",
993 "type": "string"
994 },
995 "genotype": {
996 "description": "The genotype of this variant call. Each valu e represents either the value of the referenceBases field or a 1-based index int o alternateBases. If a variant had a referenceBases value of T and an alternateB ases value of [\"A\", \"C\"], and the genotype was [2, 1], that would mean the c all represented the heterozygous value CA for this variant. If the genotype was instead [0, 1], the represented value would be TA. Ordering of the genotype valu es is important if the phaseset is present. If a genotype is not called (that is , a . is present in the GT string) -1 is returned.",
997 "items": {
998 "format": "int32",
999 "type": "integer"
1000 },
1001 "type": "array"
1002 },
1003 "genotypeLikelihood": {
1004 "description": "The genotype likelihoods for this variant ca ll. Each array entry represents how likely a specific genotype is for this call. The value ordering is defined by the GL tag in the VCF spec. If Phred-scaled ge notype likelihood scores (PL) are available and log10(P) genotype likelihood sco res (GL) are not, PL scores are converted to GL scores. If both are available, P L scores are stored in info.",
1005 "items": {
1006 "format": "double",
1007 "type": "number"
1008 },
1009 "type": "array"
1010 },
1011 "info": {
1012 "additionalProperties": {
1013 "description": "A string which maps to an array of value s.",
1014 "items": {
1015 "type": "string"
1016 },
1017 "type": "array"
1018 },
1019 "description": "A map of additional variant call information .",
1020 "type": "object"
1021 },
1022 "phaseset": {
1023 "description": "If this field is present, this variant call' s genotype ordering implies the phase of the bases and is consistent with any ot her variant calls in the same reference sequence which have the same phaseset va lue. When importing data from VCF, if the genotype data was phased but no phase set was specified this field will be set to *.",
1024 "type": "string"
1025 }
1026 },
1027 "type": "object"
1028 },
1029 "CallSet": {
1030 "description": "A call set is a collection of variant calls, typical ly for one sample. It belongs to a variant set.",
1031 "id": "CallSet",
1032 "properties": {
1033 "created": {
1034 "description": "The date this call set was created in millis econds from the epoch.",
1035 "format": "int64",
1036 "type": "string"
1037 },
1038 "id": {
1039 "description": "The Google generated ID of the call set, imm utable.",
1040 "type": "string"
1041 },
1042 "info": {
1043 "additionalProperties": {
1044 "description": "A string which maps to an array of value s.",
1045 "items": {
1046 "type": "string"
1047 },
1048 "type": "array"
1049 },
1050 "description": "A map of additional call set information.",
1051 "type": "object"
1052 },
1053 "name": {
1054 "description": "The call set name.",
1055 "type": "string"
1056 },
1057 "sampleId": {
1058 "description": "The sample ID this call set corresponds to." ,
1059 "type": "string"
1060 },
1061 "variantSetIds": {
1062 "description": "The IDs of the variant sets this call set be longs to.",
1063 "items": {
1064 "type": "string"
1065 },
1066 "type": "array"
1067 }
1068 },
1069 "type": "object"
1070 },
1071 "CoverageBucket": {
1072 "description": "A bucket over which read coverage has been precomput ed. A bucket corresponds to a specific range of the reference sequence.",
1073 "id": "CoverageBucket",
1074 "properties": {
1075 "meanCoverage": {
1076 "description": "The average number of reads which are aligne d to each individual reference base in this bucket.",
1077 "format": "float",
1078 "type": "number"
1079 },
1080 "range": {
1081 "$ref": "GenomicRange",
1082 "description": "The genomic coordinate range spanned by this bucket."
1083 }
1084 },
1085 "type": "object"
1086 },
1087 "Dataset": {
1088 "description": "A Dataset is a collection of genomic data.",
1089 "id": "Dataset",
1090 "properties": {
1091 "id": {
1092 "description": "The Google generated ID of the dataset, immu table.",
1093 "type": "string"
1094 },
1095 "isPublic": {
1096 "description": "Flag indicating whether or not a dataset is publicly viewable. If a dataset is not public, it inherits viewing permissions f rom its project.",
1097 "type": "boolean"
1098 },
1099 "name": {
1100 "description": "The dataset name.",
1101 "type": "string"
1102 },
1103 "projectId": {
1104 "description": "The Google Developers Console project number that this dataset belongs to.",
1105 "format": "int64",
1106 "type": "string"
1107 }
1108 },
1109 "type": "object"
1110 },
1111 "ExperimentalCreateJobRequest": {
1112 "description": "The job creation request.",
1113 "id": "ExperimentalCreateJobRequest",
1114 "properties": {
1115 "align": {
1116 "description": "Specifies whether or not to run the alignmen t pipeline. Either align or callVariants must be set.",
1117 "type": "boolean"
1118 },
1119 "callVariants": {
1120 "description": "Specifies whether or not to run the variant calling pipeline. Either align or callVariants must be set.",
1121 "type": "boolean"
1122 },
1123 "gcsOutputPath": {
1124 "description": "Specifies where to copy the results of certa in pipelines. This should be in the form of gs://bucket/path.",
1125 "type": "string"
1126 },
1127 "pairedSourceUris": {
1128 "description": "A list of Google Cloud Storage URIs of paire d end .fastq files to operate upon. If specified, this represents the second fil e of each paired .fastq file. The first file of each pair should be specified in sourceUris.",
1129 "items": {
1130 "type": "string"
1131 },
1132 "type": "array"
1133 },
1134 "projectId": {
1135 "description": "Required. The Google Cloud Project ID with w hich to associate the request.",
1136 "format": "int64",
1137 "type": "string"
1138 },
1139 "sourceUris": {
1140 "description": "A list of Google Cloud Storage URIs of data files to operate upon. These can be .bam, interleaved .fastq, or paired .fastq. If specifying paired .fastq files, the first of each pair of files should be lis ted here, and the second of each pair should be listed in pairedSourceUris.",
1141 "items": {
1142 "type": "string"
1143 },
1144 "type": "array"
1145 }
1146 },
1147 "type": "object"
1148 },
1149 "ExperimentalCreateJobResponse": {
1150 "description": "The job creation response.",
1151 "id": "ExperimentalCreateJobResponse",
1152 "properties": {
1153 "jobId": {
1154 "description": "A job ID that can be used to get status info rmation.",
1155 "type": "string"
1156 }
1157 },
1158 "type": "object"
1159 },
1160 "ExportReadsetsRequest": {
1161 "description": "The readset export request.",
1162 "id": "ExportReadsetsRequest",
1163 "properties": {
1164 "exportUri": {
1165 "description": "A Google Cloud Storage URI where the exporte d BAM file will be created. The currently authenticated user must have write acc ess to the new file location. An error will be returned if the URI already conta ins data.",
1166 "type": "string"
1167 },
1168 "projectId": {
1169 "description": "The Google Developers Console project number that owns this export.",
1170 "format": "int64",
1171 "type": "string"
1172 },
1173 "readsetIds": {
1174 "description": "The IDs of the readsets to export.",
1175 "items": {
1176 "type": "string"
1177 },
1178 "type": "array"
1179 },
1180 "referenceNames": {
1181 "description": "The reference names to export. If this is no t specified, all reference sequences, including unmapped reads, are exported. Us e * to export only unmapped reads.",
1182 "items": {
1183 "type": "string"
1184 },
1185 "type": "array"
1186 }
1187 },
1188 "type": "object"
1189 },
1190 "ExportReadsetsResponse": {
1191 "description": "The readset export response.",
1192 "id": "ExportReadsetsResponse",
1193 "properties": {
1194 "jobId": {
1195 "description": "A job ID that can be used to get status info rmation.",
1196 "type": "string"
1197 }
1198 },
1199 "type": "object"
1200 },
1201 "ExportVariantsRequest": {
1202 "description": "The variant data export request.",
1203 "id": "ExportVariantsRequest",
1204 "properties": {
1205 "bigqueryDataset": {
1206 "description": "The BigQuery dataset to export data to. Note that this is distinct from the Genomics concept of \"dataset\".",
1207 "type": "string"
1208 },
1209 "bigqueryTable": {
1210 "description": "The BigQuery table to export data to. If the table doesn't exist, it will be created. If it already exists, it will be overw ritten.",
1211 "type": "string"
1212 },
1213 "callSetIds": {
1214 "description": "If provided, only variant call information f rom the specified call sets will be exported. By default all variant calls are e xported.",
1215 "items": {
1216 "type": "string"
1217 },
1218 "type": "array"
1219 },
1220 "format": {
1221 "description": "The format for the exported data.",
1222 "enum": [
1223 "bigquery"
1224 ],
1225 "enumDescriptions": [
1226 ""
1227 ],
1228 "type": "string"
1229 },
1230 "projectId": {
1231 "description": "The Google Cloud project number that owns th e destination BigQuery dataset. The caller must have WRITE access to this projec t. This project will also own the resulting export job.",
1232 "format": "int64",
1233 "type": "string"
1234 },
1235 "variantSetId": {
1236 "description": "Required. The ID of the variant set that con tains variant data which should be exported. The caller must have READ access to this variant set.",
1237 "type": "string"
1238 }
1239 },
1240 "type": "object"
1241 },
1242 "ExportVariantsResponse": {
1243 "description": "The variant data export response.",
1244 "id": "ExportVariantsResponse",
1245 "properties": {
1246 "jobId": {
1247 "description": "A job ID that can be used to get status info rmation.",
1248 "type": "string"
1249 }
1250 },
1251 "type": "object"
1252 },
1253 "GenomicRange": {
1254 "description": "An inclusive, exclusive genomic coordinate range ove r a reference sequence.",
1255 "id": "GenomicRange",
1256 "properties": {
1257 "sequenceEnd": {
1258 "description": "The end position of the range on the referen ce, 1-based exclusive. If specified, sequenceName must also be specified.",
1259 "format": "uint64",
1260 "type": "string"
1261 },
1262 "sequenceName": {
1263 "description": "The reference sequence name, for example chr 1, 1, or chrX.",
1264 "type": "string"
1265 },
1266 "sequenceStart": {
1267 "description": "The start position of the range on the refer ence, 1-based inclusive. If specified, sequenceName must also be specified.",
1268 "format": "uint64",
1269 "type": "string"
1270 }
1271 },
1272 "type": "object"
1273 },
1274 "Header": {
1275 "id": "Header",
1276 "properties": {
1277 "sortingOrder": {
1278 "description": "(SO) Sorting order of alignments.",
1279 "type": "string"
1280 },
1281 "version": {
1282 "description": "(VN) BAM format version.",
1283 "type": "string"
1284 }
1285 },
1286 "type": "object"
1287 },
1288 "HeaderSection": {
1289 "description": "The header section of the BAM/SAM file.",
1290 "id": "HeaderSection",
1291 "properties": {
1292 "comments": {
1293 "description": "(@CO) One-line text comments.",
1294 "items": {
1295 "type": "string"
1296 },
1297 "type": "array"
1298 },
1299 "fileUri": {
1300 "description": "[Deprecated] This field is deprecated and wi ll no longer be populated. Please use filename instead.",
1301 "type": "string"
1302 },
1303 "filename": {
1304 "description": "The name of the file from which this data wa s imported.",
1305 "type": "string"
1306 },
1307 "headers": {
1308 "description": "(@HD) The header line.",
1309 "items": {
1310 "$ref": "Header"
1311 },
1312 "type": "array"
1313 },
1314 "programs": {
1315 "description": "(@PG) Programs.",
1316 "items": {
1317 "$ref": "Program"
1318 },
1319 "type": "array"
1320 },
1321 "readGroups": {
1322 "description": "(@RG) Read group.",
1323 "items": {
1324 "$ref": "ReadGroup"
1325 },
1326 "type": "array"
1327 },
1328 "refSequences": {
1329 "description": "(@SQ) Reference sequence dictionary.",
1330 "items": {
1331 "$ref": "ReferenceSequence"
1332 },
1333 "type": "array"
1334 }
1335 },
1336 "type": "object"
1337 },
1338 "ImportReadsetsRequest": {
1339 "description": "The readset import request.",
1340 "id": "ImportReadsetsRequest",
1341 "properties": {
1342 "datasetId": {
1343 "description": "Required. The ID of the dataset these readse ts will belong to. The caller must have WRITE permissions to this dataset.",
1344 "type": "string"
1345 },
1346 "sourceUris": {
1347 "description": "A list of URIs pointing at BAM files in Goog le Cloud Storage.",
1348 "items": {
1349 "type": "string"
1350 },
1351 "type": "array"
1352 }
1353 },
1354 "type": "object"
1355 },
1356 "ImportReadsetsResponse": {
1357 "description": "The readset import response.",
1358 "id": "ImportReadsetsResponse",
1359 "properties": {
1360 "jobId": {
1361 "description": "A job ID that can be used to get status info rmation.",
1362 "type": "string"
1363 }
1364 },
1365 "type": "object"
1366 },
1367 "ImportVariantsRequest": {
1368 "description": "The variant data import request.",
1369 "id": "ImportVariantsRequest",
1370 "properties": {
1371 "format": {
1372 "description": "The format of the variant data being importe d.",
1373 "enum": [
1374 "completeGenomics",
1375 "vcf"
1376 ],
1377 "enumDescriptions": [
1378 "",
1379 ""
1380 ],
1381 "type": "string"
1382 },
1383 "sourceUris": {
1384 "description": "A list of URIs pointing at VCF files in Goog le Cloud Storage. See the VCF Specification for more details on the input format .",
1385 "items": {
1386 "type": "string"
1387 },
1388 "type": "array"
1389 },
1390 "variantSetId": {
1391 "description": "Required. The variant set to which variant d ata should be imported.",
1392 "type": "string"
1393 }
1394 },
1395 "type": "object"
1396 },
1397 "ImportVariantsResponse": {
1398 "description": "The variant data import response.",
1399 "id": "ImportVariantsResponse",
1400 "properties": {
1401 "jobId": {
1402 "description": "A job ID that can be used to get status info rmation.",
1403 "type": "string"
1404 }
1405 },
1406 "type": "object"
1407 },
1408 "Job": {
1409 "description": "A Job represents an ongoing process that can be moni tored for status information.",
1410 "id": "Job",
1411 "properties": {
1412 "created": {
1413 "description": "The date this job was created, in millisecon ds from the epoch.",
1414 "format": "int64",
1415 "type": "string"
1416 },
1417 "description": {
1418 "description": "A more detailed description of this job's cu rrent status.",
1419 "type": "string"
1420 },
1421 "errors": {
1422 "description": "Any errors that occurred during processing." ,
1423 "items": {
1424 "type": "string"
1425 },
1426 "type": "array"
1427 },
1428 "id": {
1429 "description": "The job ID.",
1430 "type": "string"
1431 },
1432 "importedIds": {
1433 "description": "If this Job represents an import, this field will contain the IDs of the objects that were successfully imported.",
1434 "items": {
1435 "type": "string"
1436 },
1437 "type": "array"
1438 },
1439 "projectId": {
1440 "description": "The Google Developers Console project number to which this job belongs.",
1441 "format": "int64",
1442 "type": "string"
1443 },
1444 "request": {
1445 "$ref": "JobRequest",
1446 "description": "A summarized representation of the original service request."
1447 },
1448 "status": {
1449 "description": "The status of this job.",
1450 "enum": [
1451 "canceled",
1452 "failure",
1453 "new",
1454 "pending",
1455 "running",
1456 "success",
1457 "unknownStatus"
1458 ],
1459 "enumDescriptions": [
1460 "",
1461 "",
1462 "",
1463 "",
1464 "",
1465 "",
1466 ""
1467 ],
1468 "type": "string"
1469 },
1470 "warnings": {
1471 "description": "Any warnings that occurred during processing .",
1472 "items": {
1473 "type": "string"
1474 },
1475 "type": "array"
1476 }
1477 },
1478 "type": "object"
1479 },
1480 "JobRequest": {
1481 "description": "A summary representation of the service request that spawned the job.",
1482 "id": "JobRequest",
1483 "properties": {
1484 "destination": {
1485 "description": "The data destination of the request, for exa mple, a Google BigQuery Table or Dataset ID.",
1486 "items": {
1487 "type": "string"
1488 },
1489 "type": "array"
1490 },
1491 "source": {
1492 "description": "The data source of the request, for example, a Google Cloud Storage object path or Readset ID.",
1493 "items": {
1494 "type": "string"
1495 },
1496 "type": "array"
1497 },
1498 "type": {
1499 "description": "The original request type.",
1500 "enum": [
1501 "alignReadsets",
1502 "callReadsets",
1503 "experimentalCreateJob",
1504 "exportReadsets",
1505 "exportVariants",
1506 "importReadsets",
1507 "importVariants",
1508 "unknownType"
1509 ],
1510 "enumDescriptions": [
1511 "",
1512 "",
1513 "",
1514 "",
1515 "",
1516 "",
1517 "",
1518 ""
1519 ],
1520 "type": "string"
1521 }
1522 },
1523 "type": "object"
1524 },
1525 "ListCoverageBucketsResponse": {
1526 "id": "ListCoverageBucketsResponse",
1527 "properties": {
1528 "bucketWidth": {
1529 "description": "The length of each coverage bucket in base p airs. Note that buckets at the end of a reference sequence may be shorter. This value is omitted if the bucket width is infinity (the default behaviour, with no range or targetBucketWidth).",
1530 "format": "uint64",
1531 "type": "string"
1532 },
1533 "coverageBuckets": {
1534 "description": "The coverage buckets. The list of buckets is sparse; a bucket with 0 overlapping reads is not returned. A bucket never cross es more than one reference sequence. Each bucket has width bucketWidth, unless i ts end is the end of the reference sequence.",
1535 "items": {
1536 "$ref": "CoverageBucket"
1537 },
1538 "type": "array"
1539 },
1540 "nextPageToken": {
1541 "description": "The continuation token, which is used to pag e through large result sets. Provide this value in a subsequent request to retur n the next page of results. This field will be empty if there aren't any additio nal results.",
1542 "type": "string"
1543 }
1544 },
1545 "type": "object"
1546 },
1547 "ListDatasetsResponse": {
1548 "description": "The dataset list response.",
1549 "id": "ListDatasetsResponse",
1550 "properties": {
1551 "datasets": {
1552 "description": "The list of matching Datasets.",
1553 "items": {
1554 "$ref": "Dataset"
1555 },
1556 "type": "array"
1557 },
1558 "nextPageToken": {
1559 "description": "The continuation token, which is used to pag e through large result sets. Provide this value in a subsequent request to retur n the next page of results. This field will be empty if there aren't any additio nal results.",
1560 "type": "string"
1561 }
1562 },
1563 "type": "object"
1564 },
1565 "MergeVariantsRequest": {
1566 "id": "MergeVariantsRequest",
1567 "properties": {
1568 "variants": {
1569 "description": "The variants to be merged with existing vari ants.",
1570 "items": {
1571 "$ref": "Variant"
1572 },
1573 "type": "array"
1574 }
1575 },
1576 "type": "object"
1577 },
1578 "Metadata": {
1579 "description": "Metadata describes a single piece of variant call me tadata. These data include a top level key and either a single value string (val ue) or a list of key-value pairs (info.) Value and info are mutually exclusive." ,
1580 "id": "Metadata",
1581 "properties": {
1582 "description": {
1583 "description": "A textual description of this metadata.",
1584 "type": "string"
1585 },
1586 "id": {
1587 "description": "User-provided ID field, not enforced by this API. Two or more pieces of structured metadata with identical id and key fields are considered equivalent.",
1588 "type": "string"
1589 },
1590 "info": {
1591 "additionalProperties": {
1592 "description": "A string which maps to an array of value s.",
1593 "items": {
1594 "type": "string"
1595 },
1596 "type": "array"
1597 },
1598 "description": "Remaining structured metadata key-value pair s.",
1599 "type": "object"
1600 },
1601 "key": {
1602 "description": "The top-level key.",
1603 "type": "string"
1604 },
1605 "number": {
1606 "description": "The number of values that can be included in a field described by this metadata.",
1607 "type": "string"
1608 },
1609 "type": {
1610 "description": "The type of data. Possible types include: In teger, Float, Flag, Character, and String.",
1611 "enum": [
1612 "character",
1613 "flag",
1614 "float",
1615 "integer",
1616 "string",
1617 "unknownType"
1618 ],
1619 "enumDescriptions": [
1620 "",
1621 "",
1622 "",
1623 "",
1624 "",
1625 ""
1626 ],
1627 "type": "string"
1628 },
1629 "value": {
1630 "description": "The value field for simple metadata",
1631 "type": "string"
1632 }
1633 },
1634 "type": "object"
1635 },
1636 "Program": {
1637 "id": "Program",
1638 "properties": {
1639 "commandLine": {
1640 "description": "(CL) Command line.",
1641 "type": "string"
1642 },
1643 "id": {
1644 "description": "(ID) Program record identifier.",
1645 "type": "string"
1646 },
1647 "name": {
1648 "description": "(PN) Program name.",
1649 "type": "string"
1650 },
1651 "prevProgramId": {
1652 "description": "(PP) Previous program ID.",
1653 "type": "string"
1654 },
1655 "version": {
1656 "description": "(VN) Program version.",
1657 "type": "string"
1658 }
1659 },
1660 "type": "object"
1661 },
1662 "Read": {
1663 "description": "A Read is a group of bases that may or may not have been aligned to a reference. It contains quality information and other metadata. ",
1664 "id": "Read",
1665 "properties": {
1666 "alignedBases": {
1667 "description": "The originalBases after the cigar field has been applied. Deletions are represented with '-' and insertions are omitted.",
1668 "type": "string"
1669 },
1670 "baseQuality": {
1671 "description": "Represents the quality of each base in this read. Each character represents one base. To get the quality, take the ASCII val ue of the character and subtract 33. (QUAL)",
1672 "type": "string"
1673 },
1674 "cigar": {
1675 "description": "A condensed representation of how this read matches up to the reference. (CIGAR)",
1676 "type": "string"
1677 },
1678 "flags": {
1679 "description": "Each bit of this number has a different mean ing if enabled. See the full BAM spec for more details. (FLAG)",
1680 "format": "int32",
1681 "type": "integer"
1682 },
1683 "id": {
1684 "description": "The Google generated ID of the read, immutab le.",
1685 "type": "string"
1686 },
1687 "mappingQuality": {
1688 "description": "A score up to 255 that represents how likely this read's aligned position is to be correct. A higher value is better. (MAPQ) ",
1689 "format": "int32",
1690 "type": "integer"
1691 },
1692 "matePosition": {
1693 "description": "The 1-based start position of the paired rea d. (PNEXT)",
1694 "format": "int32",
1695 "type": "integer"
1696 },
1697 "mateReferenceSequenceName": {
1698 "description": "The name of the sequence that the paired rea d is aligned to. This is usually the same as referenceSequenceName. (RNEXT)",
1699 "type": "string"
1700 },
1701 "name": {
1702 "description": "The name of the read. When imported from a B AM file, this is the query template name. (QNAME)",
1703 "type": "string"
1704 },
1705 "originalBases": {
1706 "description": "The list of bases that this read represents (such as \"CATCGA\"). (SEQ)",
1707 "type": "string"
1708 },
1709 "position": {
1710 "description": "The 1-based start position of the aligned re ad. If the first base starts at the very beginning of the reference sequence, th en the position would be '1'. (POS)",
1711 "format": "int32",
1712 "type": "integer"
1713 },
1714 "readsetId": {
1715 "description": "The ID of the readset this read belongs to." ,
1716 "type": "string"
1717 },
1718 "referenceSequenceName": {
1719 "description": "The name of the sequence that this read is a ligned to. This would be, for example, 'X' for the X Chromosome or '20' for Chro mosome 20. (RNAME)",
1720 "type": "string"
1721 },
1722 "tags": {
1723 "additionalProperties": {
1724 "description": "A string which maps to an array of value s.",
1725 "items": {
1726 "type": "string"
1727 },
1728 "type": "array"
1729 },
1730 "description": "A map of additional read information. (TAG)" ,
1731 "type": "object"
1732 },
1733 "templateLength": {
1734 "description": "Length of the original piece of DNA that pro duced both this read and the paired read. (TLEN)",
1735 "format": "int32",
1736 "type": "integer"
1737 }
1738 },
1739 "type": "object"
1740 },
1741 "ReadGroup": {
1742 "id": "ReadGroup",
1743 "properties": {
1744 "date": {
1745 "description": "(DT) Date the run was produced (ISO8601 date or date/time).",
1746 "type": "string"
1747 },
1748 "description": {
1749 "description": "(DS) Description.",
1750 "type": "string"
1751 },
1752 "flowOrder": {
1753 "description": "(FO) Flow order. The array of nucleotide bas es that correspond to the nucleotides used for each flow of each read.",
1754 "type": "string"
1755 },
1756 "id": {
1757 "description": "(ID) Read group identifier.",
1758 "type": "string"
1759 },
1760 "keySequence": {
1761 "description": "(KS) The array of nucleotide bases that corr espond to the key sequence of each read.",
1762 "type": "string"
1763 },
1764 "library": {
1765 "description": "(LS) Library.",
1766 "type": "string"
1767 },
1768 "platformUnit": {
1769 "description": "(PU) Platform unit.",
1770 "type": "string"
1771 },
1772 "predictedInsertSize": {
1773 "description": "(PI) Predicted median insert size.",
1774 "format": "int32",
1775 "type": "integer"
1776 },
1777 "processingProgram": {
1778 "description": "(PG) Programs used for processing the read g roup.",
1779 "type": "string"
1780 },
1781 "sample": {
1782 "description": "(SM) Sample.",
1783 "type": "string"
1784 },
1785 "sequencingCenterName": {
1786 "description": "(CN) Name of sequencing center producing the read.",
1787 "type": "string"
1788 },
1789 "sequencingTechnology": {
1790 "description": "(PL) Platform/technology used to produce the reads.",
1791 "type": "string"
1792 }
1793 },
1794 "type": "object"
1795 },
1796 "Readset": {
1797 "description": "A Readset is a collection of Reads.",
1798 "id": "Readset",
1799 "properties": {
1800 "datasetId": {
1801 "description": "The ID of the dataset this readset belongs t o.",
1802 "type": "string"
1803 },
1804 "fileData": {
1805 "description": "File information from the original BAM impor t. See the BAM format specification for additional information on each field.",
1806 "items": {
1807 "$ref": "HeaderSection"
1808 },
1809 "type": "array"
1810 },
1811 "id": {
1812 "description": "The Google generated ID of the readset, immu table.",
1813 "type": "string"
1814 },
1815 "name": {
1816 "description": "The readset name, typically this is the samp le name.",
1817 "type": "string"
1818 }
1819 },
1820 "type": "object"
1821 },
1822 "ReferenceBound": {
1823 "description": "ReferenceBound records an upper bound for the starti ng coordinate of variants in a particular reference.",
1824 "id": "ReferenceBound",
1825 "properties": {
1826 "referenceName": {
1827 "description": "The reference the bound is associate with.",
1828 "type": "string"
1829 },
1830 "upperBound": {
1831 "description": "An upper bound (inclusive) on the starting c oordinate of any variant in the reference sequence.",
1832 "format": "int64",
1833 "type": "string"
1834 }
1835 },
1836 "type": "object"
1837 },
1838 "ReferenceSequence": {
1839 "id": "ReferenceSequence",
1840 "properties": {
1841 "assemblyId": {
1842 "description": "(AS) Genome assembly identifier.",
1843 "type": "string"
1844 },
1845 "length": {
1846 "description": "(LN) Reference sequence length.",
1847 "format": "int32",
1848 "type": "integer"
1849 },
1850 "md5Checksum": {
1851 "description": "(M5) MD5 checksum of the sequence in the upp ercase, excluding spaces but including pads as *.",
1852 "type": "string"
1853 },
1854 "name": {
1855 "description": "(SN) Reference sequence name.",
1856 "type": "string"
1857 },
1858 "species": {
1859 "description": "(SP) Species.",
1860 "type": "string"
1861 },
1862 "uri": {
1863 "description": "(UR) URI of the sequence.",
1864 "type": "string"
1865 }
1866 },
1867 "type": "object"
1868 },
1869 "SearchCallSetsRequest": {
1870 "description": "The call set search request.",
1871 "id": "SearchCallSetsRequest",
1872 "properties": {
1873 "name": {
1874 "description": "Only return call sets for which a substring of the name matches this string.",
1875 "type": "string"
1876 },
1877 "pageSize": {
1878 "description": "The maximum number of call sets to return.",
1879 "format": "int32",
1880 "type": "integer"
1881 },
1882 "pageToken": {
1883 "description": "The continuation token, which is used to pag e through large result sets. To get the next page of results, set this parameter to the value of nextPageToken from the previous response.",
1884 "type": "string"
1885 },
1886 "variantSetIds": {
1887 "description": "Restrict the query to call sets within the g iven variant sets. At least one ID must be provided.",
1888 "items": {
1889 "type": "string"
1890 },
1891 "type": "array"
1892 }
1893 },
1894 "type": "object"
1895 },
1896 "SearchCallSetsResponse": {
1897 "description": "The call set search response.",
1898 "id": "SearchCallSetsResponse",
1899 "properties": {
1900 "callSets": {
1901 "description": "The list of matching call sets.",
1902 "items": {
1903 "$ref": "CallSet"
1904 },
1905 "type": "array"
1906 },
1907 "nextPageToken": {
1908 "description": "The continuation token, which is used to pag e through large result sets. Provide this value in a subsequent request to retur n the next page of results. This field will be empty if there aren't any additio nal results.",
1909 "type": "string"
1910 }
1911 },
1912 "type": "object"
1913 },
1914 "SearchJobsRequest": {
1915 "description": "The jobs search request.",
1916 "id": "SearchJobsRequest",
1917 "properties": {
1918 "createdAfter": {
1919 "description": "If specified, only jobs created on or after this date, given in milliseconds since Unix epoch, will be returned.",
1920 "format": "int64",
1921 "type": "string"
1922 },
1923 "createdBefore": {
1924 "description": "If specified, only jobs created prior to thi s date, given in milliseconds since Unix epoch, will be returned.",
1925 "format": "int64",
1926 "type": "string"
1927 },
1928 "maxResults": {
1929 "description": "Specifies the number of results to return in a single page. Defaults to 128. The maximum value is 256.",
1930 "format": "uint64",
1931 "type": "string"
1932 },
1933 "pageToken": {
1934 "description": "The continuation token which is used to page through large result sets. To get the next page of results, set this parameter to the value of the nextPageToken from the previous response.",
1935 "type": "string"
1936 },
1937 "projectId": {
1938 "description": "Required. Only return jobs which belong to t his Google Developers Console project.",
1939 "format": "int64",
1940 "type": "string"
1941 },
1942 "status": {
1943 "description": "Only return jobs which have a matching statu s.",
1944 "items": {
1945 "enum": [
1946 "canceled",
1947 "failure",
1948 "new",
1949 "pending",
1950 "running",
1951 "success",
1952 "unknownStatus"
1953 ],
1954 "enumDescriptions": [
1955 "",
1956 "",
1957 "",
1958 "",
1959 "",
1960 "",
1961 ""
1962 ],
1963 "type": "string"
1964 },
1965 "type": "array"
1966 }
1967 },
1968 "type": "object"
1969 },
1970 "SearchJobsResponse": {
1971 "description": "The job search response.",
1972 "id": "SearchJobsResponse",
1973 "properties": {
1974 "jobs": {
1975 "description": "The list of jobs results, ordered newest to oldest.",
1976 "items": {
1977 "$ref": "Job"
1978 },
1979 "type": "array"
1980 },
1981 "nextPageToken": {
1982 "description": "The continuation token which is used to page through large result sets. Provide this value is a subsequent request to return the next page of results. This field will be empty if there are no more results .",
1983 "type": "string"
1984 }
1985 },
1986 "type": "object"
1987 },
1988 "SearchReadsRequest": {
1989 "description": "The read search request.",
1990 "id": "SearchReadsRequest",
1991 "properties": {
1992 "maxResults": {
1993 "description": "Specifies number of results to return in a s ingle page. If unspecified, it will default to 256. The maximum value is 2048.",
1994 "format": "uint64",
1995 "type": "string"
1996 },
1997 "pageToken": {
1998 "description": "The continuation token, which is used to pag e through large result sets. To get the next page of results, set this parameter to the value of nextPageToken from the previous response.",
1999 "type": "string"
2000 },
2001 "readsetIds": {
2002 "description": "The readsets within which to search for read s. At least one readset ID must be provided. All specified readsets must be alig ned against a common set of reference sequences; this defines the genomic coordi nates for the query.",
2003 "items": {
2004 "type": "string"
2005 },
2006 "type": "array"
2007 },
2008 "sequenceEnd": {
2009 "description": "The end position (1-based, inclusive) of the target range. If specified, sequenceName must also be specified. Defaults to th e end of the target reference sequence, if any.",
2010 "format": "uint64",
2011 "type": "string"
2012 },
2013 "sequenceName": {
2014 "description": "Restricts the results to a particular refere nce sequence such as 1, chr1, or X. The set of valid references sequences depend s on the readsets specified. If set to *, only unmapped Reads are returned.",
2015 "type": "string"
2016 },
2017 "sequenceStart": {
2018 "description": "The start position (1-based, inclusive) of t he target range. If specified, sequenceName must also be specified. Defaults to the start of the target reference sequence, if any.",
2019 "format": "uint64",
2020 "type": "string"
2021 }
2022 },
2023 "type": "object"
2024 },
2025 "SearchReadsResponse": {
2026 "description": "The read search response.",
2027 "id": "SearchReadsResponse",
2028 "properties": {
2029 "nextPageToken": {
2030 "description": "The continuation token, which is used to pag e through large result sets. Provide this value in a subsequent request to retur n the next page of results. This field will be empty if there aren't any additio nal results.",
2031 "type": "string"
2032 },
2033 "reads": {
2034 "description": "The list of matching Reads. The resulting Re ads are sorted by position; the smallest positions are returned first. Unmapped reads, which have no position, are returned last and are further sorted alphabet ically by name.",
2035 "items": {
2036 "$ref": "Read"
2037 },
2038 "type": "array"
2039 }
2040 },
2041 "type": "object"
2042 },
2043 "SearchReadsetsRequest": {
2044 "description": "The readset search request.",
2045 "id": "SearchReadsetsRequest",
2046 "properties": {
2047 "datasetIds": {
2048 "description": "Restricts this query to readsets within the given datasets. At least one ID must be provided.",
2049 "items": {
2050 "type": "string"
2051 },
2052 "type": "array"
2053 },
2054 "maxResults": {
2055 "description": "Specifies number of results to return in a s ingle page. If unspecified, it will default to 128. The maximum value is 1024.",
2056 "format": "uint64",
2057 "type": "string"
2058 },
2059 "name": {
2060 "description": "Only return readsets for which a substring o f the name matches this string.",
2061 "type": "string"
2062 },
2063 "pageToken": {
2064 "description": "The continuation token, which is used to pag e through large result sets. To get the next page of results, set this parameter to the value of nextPageToken from the previous response.",
2065 "type": "string"
2066 }
2067 },
2068 "type": "object"
2069 },
2070 "SearchReadsetsResponse": {
2071 "description": "The readset search response.",
2072 "id": "SearchReadsetsResponse",
2073 "properties": {
2074 "nextPageToken": {
2075 "description": "The continuation token, which is used to pag e through large result sets. Provide this value in a subsequent request to retur n the next page of results. This field will be empty if there aren't any additio nal results.",
2076 "type": "string"
2077 },
2078 "readsets": {
2079 "description": "The list of matching Readsets.",
2080 "items": {
2081 "$ref": "Readset"
2082 },
2083 "type": "array"
2084 }
2085 },
2086 "type": "object"
2087 },
2088 "SearchVariantSetsRequest": {
2089 "description": "The search variant sets request.",
2090 "id": "SearchVariantSetsRequest",
2091 "properties": {
2092 "datasetIds": {
2093 "description": "Exactly one dataset ID must be provided here . Only variant sets which belong to this dataset will be returned.",
2094 "items": {
2095 "type": "string"
2096 },
2097 "type": "array"
2098 },
2099 "pageSize": {
2100 "description": "The maximum number of variant sets to return in a request.",
2101 "format": "int32",
2102 "type": "integer"
2103 },
2104 "pageToken": {
2105 "description": "The continuation token, which is used to pag e through large result sets. To get the next page of results, set this parameter to the value of nextPageToken from the previous response.",
2106 "type": "string"
2107 }
2108 },
2109 "type": "object"
2110 },
2111 "SearchVariantSetsResponse": {
2112 "description": "The search variant sets response.",
2113 "id": "SearchVariantSetsResponse",
2114 "properties": {
2115 "nextPageToken": {
2116 "description": "The continuation token, which is used to pag e through large result sets. Provide this value in a subsequent request to retur n the next page of results. This field will be empty if there aren't any additio nal results.",
2117 "type": "string"
2118 },
2119 "variantSets": {
2120 "description": "The variant sets belonging to the requested dataset.",
2121 "items": {
2122 "$ref": "VariantSet"
2123 },
2124 "type": "array"
2125 }
2126 },
2127 "type": "object"
2128 },
2129 "SearchVariantsRequest": {
2130 "description": "The variant search request.",
2131 "id": "SearchVariantsRequest",
2132 "properties": {
2133 "callSetIds": {
2134 "description": "Only return variant calls which belong to ca ll sets with these ids. Leaving this blank returns all variant calls. If a varia nt has no calls belonging to any of these call sets, it won't be returned at all . Currently, variants with no calls from any call set will never be returned.",
2135 "items": {
2136 "type": "string"
2137 },
2138 "type": "array"
2139 },
2140 "end": {
2141 "description": "Required. The end of the window (0-based, ex clusive) for which overlapping variants should be returned.",
2142 "format": "int64",
2143 "type": "string"
2144 },
2145 "maxCalls": {
2146 "description": "The maximum number of calls to return. Howev er, at least one variant will always be returned, even if it has more calls than this limit.",
2147 "format": "int32",
2148 "type": "integer"
2149 },
2150 "pageSize": {
2151 "description": "The maximum number of variants to return.",
2152 "format": "int32",
2153 "type": "integer"
2154 },
2155 "pageToken": {
2156 "description": "The continuation token, which is used to pag e through large result sets. To get the next page of results, set this parameter to the value of nextPageToken from the previous response.",
2157 "type": "string"
2158 },
2159 "referenceName": {
2160 "description": "Required. Only return variants in this refer ence sequence.",
2161 "type": "string"
2162 },
2163 "start": {
2164 "description": "Required. The beginning of the window (0-bas ed, inclusive) for which overlapping variants should be returned.",
2165 "format": "int64",
2166 "type": "string"
2167 },
2168 "variantName": {
2169 "description": "Only return variants which have exactly this name.",
2170 "type": "string"
2171 },
2172 "variantSetIds": {
2173 "description": "Exactly one variant set ID must be provided. Only variants from this variant set will be returned.",
2174 "items": {
2175 "type": "string"
2176 },
2177 "type": "array"
2178 }
2179 },
2180 "type": "object"
2181 },
2182 "SearchVariantsResponse": {
2183 "description": "The variant search response.",
2184 "id": "SearchVariantsResponse",
2185 "properties": {
2186 "nextPageToken": {
2187 "description": "The continuation token, which is used to pag e through large result sets. Provide this value in a subsequent request to retur n the next page of results. This field will be empty if there aren't any additio nal results.",
2188 "type": "string"
2189 },
2190 "variants": {
2191 "description": "The list of matching Variants.",
2192 "items": {
2193 "$ref": "Variant"
2194 },
2195 "type": "array"
2196 }
2197 },
2198 "type": "object"
2199 },
2200 "Variant": {
2201 "description": "A variant represents a change in DNA sequence relati ve to a reference sequence. For example, a variant could represent a SNP or an i nsertion. Variants belong to a variant set. Each of the calls on a variant repre sent a determination of genotype with respect to that variant. For example, a ca ll might assign probability of 0.32 to the occurrence of a SNP named rs1234 in a sample named NA12345. A call belongs to a call set, which contains related call s typically from one sample.",
2202 "id": "Variant",
2203 "properties": {
2204 "alternateBases": {
2205 "description": "The bases that appear instead of the referen ce bases.",
2206 "items": {
2207 "type": "string"
2208 },
2209 "type": "array"
2210 },
2211 "calls": {
2212 "description": "The variant calls for this particular varian t. Each one represents the determination of genotype with respect to this varian t.",
2213 "items": {
2214 "$ref": "Call"
2215 },
2216 "type": "array"
2217 },
2218 "created": {
2219 "description": "The date this variant was created, in millis econds from the epoch.",
2220 "format": "int64",
2221 "type": "string"
2222 },
2223 "end": {
2224 "description": "The end position (0-based) of this variant. This corresponds to the first base after the last base in the reference allele. So, the length of the reference allele is (end - start). This is useful for vari ants that don't explicitly give alternate bases, for example large deletions.",
2225 "format": "int64",
2226 "type": "string"
2227 },
2228 "filter": {
2229 "description": "A list of filters (normally quality filters) this variant has failed. PASS indicates this variant has passed all filters.",
2230 "items": {
2231 "type": "string"
2232 },
2233 "type": "array"
2234 },
2235 "id": {
2236 "description": "The Google generated ID of the variant, immu table.",
2237 "type": "string"
2238 },
2239 "info": {
2240 "additionalProperties": {
2241 "description": "A string which maps to an array of value s.",
2242 "items": {
2243 "type": "string"
2244 },
2245 "type": "array"
2246 },
2247 "description": "A map of additional variant information.",
2248 "type": "object"
2249 },
2250 "names": {
2251 "description": "Names for the variant, for example a RefSNP ID.",
2252 "items": {
2253 "type": "string"
2254 },
2255 "type": "array"
2256 },
2257 "quality": {
2258 "description": "A measure of how likely this variant is to b e real. A higher value is better.",
2259 "format": "double",
2260 "type": "number"
2261 },
2262 "referenceBases": {
2263 "description": "The reference bases for this variant. They s tart at the given position.",
2264 "type": "string"
2265 },
2266 "referenceName": {
2267 "description": "The reference on which this variant occurs. (such as chr20 or X)",
2268 "type": "string"
2269 },
2270 "start": {
2271 "description": "The position at which this variant occurs (0 -based). This corresponds to the first base of the string of reference bases.",
2272 "format": "int64",
2273 "type": "string"
2274 },
2275 "variantSetId": {
2276 "description": "The ID of the variant set this variant belon gs to.",
2277 "type": "string"
2278 }
2279 },
2280 "type": "object"
2281 },
2282 "VariantSet": {
2283 "description": "A variant set is a collection of call sets and varia nts. It contains summary statistics of those contents. A variant set belongs to a dataset.",
2284 "id": "VariantSet",
2285 "properties": {
2286 "datasetId": {
2287 "description": "The dataset to which this variant set belong s. Immutable.",
2288 "type": "string"
2289 },
2290 "id": {
2291 "description": "The Google-generated ID of the variant set. Immutable.",
2292 "type": "string"
2293 },
2294 "metadata": {
2295 "description": "The metadata associated with this variant se t.",
2296 "items": {
2297 "$ref": "Metadata"
2298 },
2299 "type": "array"
2300 },
2301 "referenceBounds": {
2302 "description": "A list of all references used by the variant s in a variant set with associated coordinate upper bounds for each one.",
2303 "items": {
2304 "$ref": "ReferenceBound"
2305 },
2306 "type": "array"
2307 }
2308 },
2309 "type": "object"
2310 }
2311 },
2312 "servicePath": "genomics/v1beta/",
2313 "title": "Genomics API",
2314 "version": "v1beta"
2315 }
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