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Update to latest versions of API declarations

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This commit is contained in:
Sebastian Thiel
2018-10-13 13:49:14 +02:00
parent 5a67475b54
commit 255c7f5ad5
1508 changed files with 819225 additions and 838421 deletions
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251
gen/genomics1-cli/src/main.rs
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@@ -157,9 +157,7 @@ impl<'n> Engine<'n> {
"reference-id" => Some(("referenceId", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
"end" => Some(("end", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
"name" => Some(("name", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
"transcript.coding-sequence.start" => Some(("transcript.codingSequence.start", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
"transcript.coding-sequence.end" => Some(("transcript.codingSequence.end", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
"transcript.gene-id" => Some(("transcript.geneId", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
"type" => Some(("type", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
"variant.effect" => Some(("variant.effect", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
"variant.transcript-ids" => Some(("variant.transcriptIds", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Vec })),
"variant.alternate-bases" => Some(("variant.alternateBases", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
@@ -170,7 +168,9 @@ impl<'n> Engine<'n> {
"annotation-set-id" => Some(("annotationSetId", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
"reference-name" => Some(("referenceName", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
"reverse-strand" => Some(("reverseStrand", JsonTypeInfo { jtype: JsonType::Boolean, ctype: ComplexType::Pod })),
"type" => Some(("type", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
"transcript.coding-sequence.start" => Some(("transcript.codingSequence.start", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
"transcript.coding-sequence.end" => Some(("transcript.codingSequence.end", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
"transcript.gene-id" => Some(("transcript.geneId", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
"id" => Some(("id", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
_ => {
let suggestion = FieldCursor::did_you_mean(key, &vec!["alternate-bases", "annotation-set-id", "clinical-significance", "coding-sequence", "effect", "end", "gene-id", "id", "name", "reference-id", "reference-name", "reverse-strand", "start", "transcript", "transcript-ids", "type", "variant"]);
@@ -454,9 +454,7 @@ impl<'n> Engine<'n> {
"reference-id" => Some(("referenceId", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
"end" => Some(("end", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
"name" => Some(("name", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
"transcript.coding-sequence.start" => Some(("transcript.codingSequence.start", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
"transcript.coding-sequence.end" => Some(("transcript.codingSequence.end", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
"transcript.gene-id" => Some(("transcript.geneId", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
"type" => Some(("type", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
"variant.effect" => Some(("variant.effect", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
"variant.transcript-ids" => Some(("variant.transcriptIds", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Vec })),
"variant.alternate-bases" => Some(("variant.alternateBases", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
@@ -467,7 +465,9 @@ impl<'n> Engine<'n> {
"annotation-set-id" => Some(("annotationSetId", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
"reference-name" => Some(("referenceName", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
"reverse-strand" => Some(("reverseStrand", JsonTypeInfo { jtype: JsonType::Boolean, ctype: ComplexType::Pod })),
"type" => Some(("type", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
"transcript.coding-sequence.start" => Some(("transcript.codingSequence.start", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
"transcript.coding-sequence.end" => Some(("transcript.codingSequence.end", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
"transcript.gene-id" => Some(("transcript.geneId", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
"id" => Some(("id", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
_ => {
let suggestion = FieldCursor::did_you_mean(key, &vec!["alternate-bases", "annotation-set-id", "clinical-significance", "coding-sequence", "effect", "end", "gene-id", "id", "name", "reference-id", "reference-name", "reverse-strand", "start", "transcript", "transcript-ids", "type", "variant"]);
@@ -753,9 +753,9 @@ impl<'n> Engine<'n> {
match &temp_cursor.to_string()[..] {
"name" => Some(("name", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
"page-size" => Some(("pageSize", JsonTypeInfo { jtype: JsonType::Int, ctype: ComplexType::Pod })),
"reference-set-id" => Some(("referenceSetId", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
"page-token" => Some(("pageToken", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
"dataset-ids" => Some(("datasetIds", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Vec })),
"page-token" => Some(("pageToken", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
"reference-set-id" => Some(("referenceSetId", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
"types" => Some(("types", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Vec })),
_ => {
let suggestion = FieldCursor::did_you_mean(key, &vec!["dataset-ids", "name", "page-size", "page-token", "reference-set-id", "types"]);
@@ -2454,8 +2454,8 @@ impl<'n> Engine<'n> {
let type_info: Option<(&'static str, JsonTypeInfo)> =
match &temp_cursor.to_string()[..] {
"source-uris" => Some(("sourceUris", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Vec })),
"reference-set-id" => Some(("referenceSetId", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
"source-uris" => Some(("sourceUris", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Vec })),
"partition-strategy" => Some(("partitionStrategy", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
"dataset-id" => Some(("datasetId", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
_ => {
@@ -3639,10 +3639,10 @@ impl<'n> Engine<'n> {
"start" => Some(("start", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
"max-calls" => Some(("maxCalls", JsonTypeInfo { jtype: JsonType::Int, ctype: ComplexType::Pod })),
"page-token" => Some(("pageToken", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
"call-set-ids" => Some(("callSetIds", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Vec })),
"variant-set-ids" => Some(("variantSetIds", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Vec })),
"variant-name" => Some(("variantName", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
"reference-name" => Some(("referenceName", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
"variant-set-ids" => Some(("variantSetIds", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Vec })),
"call-set-ids" => Some(("callSetIds", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Vec })),
_ => {
let suggestion = FieldCursor::did_you_mean(key, &vec!["call-set-ids", "end", "max-calls", "page-size", "page-token", "reference-name", "start", "variant-name", "variant-set-ids"]);
err.issues.push(CLIError::Field(FieldError::Unknown(temp_cursor.to_string(), suggestion, value.map(|v| v.to_string()))));
@@ -4476,11 +4476,10 @@ impl<'n> Engine<'n> {
let engine = Engine {
opt: opt,
hub: api::Genomics::new(client, auth),
gp: vec!["$-xgafv", "access-token", "alt", "bearer-token", "callback", "fields", "key", "oauth-token", "pp", "pretty-print", "quota-user", "upload-type", "upload-protocol"],
gp: vec!["$-xgafv", "access-token", "alt", "callback", "fields", "key", "oauth-token", "pretty-print", "quota-user", "upload-type", "upload-protocol"],
gpm: vec![
("$-xgafv", "$.xgafv"),
("access-token", "access_token"),
("bearer-token", "bearer_token"),
("oauth-token", "oauth_token"),
("pretty-print", "prettyPrint"),
("quota-user", "quotaUser"),
@@ -4829,11 +4828,7 @@ fn main() {
("callsets", "methods: 'create', 'delete', 'get', 'patch' and 'search'", vec![
("create",
Some(r##"Creates a new call set.
For the definitions of call sets and other genomics resources, see
[Fundamentals of Google
Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)"##),
Some(r##"Creates a new call set."##),
"Details at http://byron.github.io/google-apis-rs/google_genomics1_cli/callsets_create",
vec![
(Some(r##"kv"##),
@@ -4855,11 +4850,7 @@ fn main() {
Some(false)),
]),
("delete",
Some(r##"Deletes a call set.
For the definitions of call sets and other genomics resources, see
[Fundamentals of Google
Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)"##),
Some(r##"Deletes a call set."##),
"Details at http://byron.github.io/google-apis-rs/google_genomics1_cli/callsets_delete",
vec![
(Some(r##"call-set-id"##),
@@ -4881,11 +4872,7 @@ fn main() {
Some(false)),
]),
("get",
Some(r##"Gets a call set by ID.
For the definitions of call sets and other genomics resources, see
[Fundamentals of Google
Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)"##),
Some(r##"Gets a call set by ID."##),
"Details at http://byron.github.io/google-apis-rs/google_genomics1_cli/callsets_get",
vec![
(Some(r##"call-set-id"##),
@@ -4909,10 +4896,6 @@ fn main() {
("patch",
Some(r##"Updates a call set.
For the definitions of call sets and other genomics resources, see
[Fundamentals of Google
Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
This method supports patch semantics."##),
"Details at http://byron.github.io/google-apis-rs/google_genomics1_cli/callsets_patch",
vec![
@@ -4943,10 +4926,6 @@ fn main() {
("search",
Some(r##"Gets a list of call sets matching the criteria.
For the definitions of call sets and other genomics resources, see
[Fundamentals of Google
Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
Implements
[GlobalAllianceApi.searchCallSets](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/variantmethods.avdl#L178)."##),
"Details at http://byron.github.io/google-apis-rs/google_genomics1_cli/callsets_search",
@@ -4973,11 +4952,7 @@ fn main() {
("datasets", "methods: 'create', 'delete', 'get', 'get-iam-policy', 'list', 'patch', 'set-iam-policy', 'test-iam-permissions' and 'undelete'", vec![
("create",
Some(r##"Creates a new dataset.
For the definitions of datasets and other genomics resources, see
[Fundamentals of Google
Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)"##),
Some(r##"Creates a new dataset."##),
"Details at http://byron.github.io/google-apis-rs/google_genomics1_cli/datasets_create",
vec![
(Some(r##"kv"##),
@@ -5004,11 +4979,7 @@ fn main() {
This is reversible (up to one week after the deletion) via
the
datasets.undelete
operation.
For the definitions of datasets and other genomics resources, see
[Fundamentals of Google
Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)"##),
operation."##),
"Details at http://byron.github.io/google-apis-rs/google_genomics1_cli/datasets_delete",
vec![
(Some(r##"dataset-id"##),
@@ -5030,11 +5001,7 @@ fn main() {
Some(false)),
]),
("get",
Some(r##"Gets a dataset by ID.
For the definitions of datasets and other genomics resources, see
[Fundamentals of Google
Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)"##),
Some(r##"Gets a dataset by ID."##),
"Details at http://byron.github.io/google-apis-rs/google_genomics1_cli/datasets_get",
vec![
(Some(r##"dataset-id"##),
@@ -5060,11 +5027,7 @@ fn main() {
policy or resource does not exist.
See <a href="/iam/docs/managing-policies#getting_a_policy">Getting a
Policy</a> for more information.
For the definitions of datasets and other genomics resources, see
[Fundamentals of Google
Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)"##),
Policy</a> for more information."##),
"Details at http://byron.github.io/google-apis-rs/google_genomics1_cli/datasets_get-iam-policy",
vec![
(Some(r##"resource"##),
@@ -5093,11 +5056,7 @@ fn main() {
Some(false)),
]),
("list",
Some(r##"Lists datasets within a project.
For the definitions of datasets and other genomics resources, see
[Fundamentals of Google
Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)"##),
Some(r##"Lists datasets within a project."##),
"Details at http://byron.github.io/google-apis-rs/google_genomics1_cli/datasets_list",
vec![
(Some(r##"v"##),
@@ -5115,10 +5074,6 @@ fn main() {
("patch",
Some(r##"Updates a dataset.
For the definitions of datasets and other genomics resources, see
[Fundamentals of Google
Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
This method supports patch semantics."##),
"Details at http://byron.github.io/google-apis-rs/google_genomics1_cli/datasets_patch",
vec![
@@ -5150,10 +5105,6 @@ fn main() {
Some(r##"Sets the access control policy on the specified dataset. Replaces any
existing policy.
For the definitions of datasets and other genomics resources, see
[Fundamentals of Google
Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
See <a href="/iam/docs/managing-policies#setting_a_policy">Setting a
Policy</a> for more information."##),
"Details at http://byron.github.io/google-apis-rs/google_genomics1_cli/datasets_set-iam-policy",
@@ -5186,11 +5137,7 @@ fn main() {
("test-iam-permissions",
Some(r##"Returns permissions that a caller has on the specified resource.
See <a href="/iam/docs/managing-policies#testing_permissions">Testing
Permissions</a> for more information.
For the definitions of datasets and other genomics resources, see
[Fundamentals of Google
Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)"##),
Permissions</a> for more information."##),
"Details at http://byron.github.io/google-apis-rs/google_genomics1_cli/datasets_test-iam-permissions",
vec![
(Some(r##"resource"##),
@@ -5221,10 +5168,6 @@ fn main() {
("undelete",
Some(r##"Undeletes a dataset by restoring a dataset which was deleted via this API.
For the definitions of datasets and other genomics resources, see
[Fundamentals of Google
Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
This operation is only possible for a week after the deletion occurred."##),
"Details at http://byron.github.io/google-apis-rs/google_genomics1_cli/datasets_undelete",
vec![
@@ -5256,7 +5199,15 @@ fn main() {
("operations", "methods: 'cancel', 'get' and 'list'", vec![
("cancel",
Some(r##"Starts asynchronous cancellation on a long-running operation. The server makes a best effort to cancel the operation, but success is not guaranteed. Clients may use Operations.GetOperation or Operations.ListOperations to check whether the cancellation succeeded or the operation completed despite cancellation."##),
Some(r##"Starts asynchronous cancellation on a long-running operation.
The server makes a best effort to cancel the operation, but success is not
guaranteed. Clients may use Operations.GetOperation
or Operations.ListOperations
to check whether the cancellation succeeded or the operation completed
despite cancellation.
Authorization requires the following [Google IAM](https://cloud.google.com/iam) permission&#58;
* `genomics.operations.cancel`"##),
"Details at http://byron.github.io/google-apis-rs/google_genomics1_cli/operations_cancel",
vec![
(Some(r##"name"##),
@@ -5284,9 +5235,12 @@ fn main() {
Some(false)),
]),
("get",
Some(r##"Gets the latest state of a long-running operation. Clients can use this
method to poll the operation result at intervals as recommended by the API
service."##),
Some(r##"Gets the latest state of a long-running operation.
Clients can use this method to poll the operation result at intervals as
recommended by the API service.
Authorization requires the following [Google IAM](https://cloud.google.com/iam) permission&#58;
* `genomics.operations.get`"##),
"Details at http://byron.github.io/google-apis-rs/google_genomics1_cli/operations_get",
vec![
(Some(r##"name"##),
@@ -5308,7 +5262,10 @@ fn main() {
Some(false)),
]),
("list",
Some(r##"Lists operations that match the specified filter in the request."##),
Some(r##"Lists operations that match the specified filter in the request.
Authorization requires the following [Google IAM](https://cloud.google.com/iam) permission&#58;
* `genomics.operations.list`"##),
"Details at http://byron.github.io/google-apis-rs/google_genomics1_cli/operations_list",
vec![
(Some(r##"name"##),
@@ -5337,10 +5294,6 @@ fn main() {
correspond to a range of a reference sequence. Each bucket summarizes
coverage information across its corresponding genomic range.
For the definitions of read group sets and other genomics resources, see
[Fundamentals of Google
Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
Coverage is defined as the number of reads which are aligned to a given
base in the reference sequence. Coverage buckets are available at several
precomputed bucket widths, enabling retrieval of various coverage 'zoom
@@ -5367,11 +5320,7 @@ fn main() {
Some(false)),
]),
("delete",
Some(r##"Deletes a read group set.
For the definitions of read group sets and other genomics resources, see
[Fundamentals of Google
Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)"##),
Some(r##"Deletes a read group set."##),
"Details at http://byron.github.io/google-apis-rs/google_genomics1_cli/readgroupsets_delete",
vec![
(Some(r##"read-group-set-id"##),
@@ -5396,10 +5345,6 @@ fn main() {
("export",
Some(r##"Exports a read group set to a BAM file in Google Cloud Storage.
For the definitions of read group sets and other genomics resources, see
[Fundamentals of Google
Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
Note that currently there may be some differences between exported BAM
files and the original BAM file at the time of import. See
ImportReadGroupSets
@@ -5432,11 +5377,7 @@ fn main() {
Some(false)),
]),
("get",
Some(r##"Gets a read group set by ID.
For the definitions of read group sets and other genomics resources, see
[Fundamentals of Google
Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)"##),
Some(r##"Gets a read group set by ID."##),
"Details at http://byron.github.io/google-apis-rs/google_genomics1_cli/readgroupsets_get",
vec![
(Some(r##"read-group-set-id"##),
@@ -5461,10 +5402,6 @@ fn main() {
Some(r##"Creates read group sets by asynchronously importing the provided
information.
For the definitions of read group sets and other genomics resources, see
[Fundamentals of Google
Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
The caller must have WRITE permissions to the dataset.
## Notes on [BAM](https://samtools.github.io/hts-specs/SAMv1.pdf) import
@@ -5499,10 +5436,6 @@ fn main() {
("patch",
Some(r##"Updates a read group set.
For the definitions of read group sets and other genomics resources, see
[Fundamentals of Google
Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
This method supports patch semantics."##),
"Details at http://byron.github.io/google-apis-rs/google_genomics1_cli/readgroupsets_patch",
vec![
@@ -5534,10 +5467,6 @@ fn main() {
("search",
Some(r##"Searches for read group sets matching the criteria.
For the definitions of read group sets and other genomics resources, see
[Fundamentals of Google
Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
Implements
[GlobalAllianceApi.searchReadGroupSets](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/readmethods.avdl#L135)."##),
"Details at http://byron.github.io/google-apis-rs/google_genomics1_cli/readgroupsets_search",
@@ -5566,10 +5495,6 @@ fn main() {
("search",
Some(r##"Gets a list of reads for one or more read group sets.
For the definitions of read group sets and other genomics resources, see
[Fundamentals of Google
Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
Reads search operates over a genomic coordinate space of reference sequence
& position defined over the reference sequences to which the requested
read group sets are aligned.
@@ -5614,10 +5539,6 @@ fn main() {
("bases-list",
Some(r##"Lists the bases in a reference, optionally restricted to a range.
For the definitions of references and other genomics resources, see
[Fundamentals of Google
Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
Implements
[GlobalAllianceApi.getReferenceBases](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/referencemethods.avdl#L221)."##),
"Details at http://byron.github.io/google-apis-rs/google_genomics1_cli/references_bases-list",
@@ -5643,10 +5564,6 @@ fn main() {
("get",
Some(r##"Gets a reference.
For the definitions of references and other genomics resources, see
[Fundamentals of Google
Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
Implements
[GlobalAllianceApi.getReference](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/referencemethods.avdl#L158)."##),
"Details at http://byron.github.io/google-apis-rs/google_genomics1_cli/references_get",
@@ -5672,10 +5589,6 @@ fn main() {
("search",
Some(r##"Searches for references which match the given criteria.
For the definitions of references and other genomics resources, see
[Fundamentals of Google
Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
Implements
[GlobalAllianceApi.searchReferences](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/referencemethods.avdl#L146)."##),
"Details at http://byron.github.io/google-apis-rs/google_genomics1_cli/references_search",
@@ -5704,10 +5617,6 @@ fn main() {
("get",
Some(r##"Gets a reference set.
For the definitions of references and other genomics resources, see
[Fundamentals of Google
Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
Implements
[GlobalAllianceApi.getReferenceSet](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/referencemethods.avdl#L83)."##),
"Details at http://byron.github.io/google-apis-rs/google_genomics1_cli/referencesets_get",
@@ -5733,10 +5642,6 @@ fn main() {
("search",
Some(r##"Searches for reference sets which match the given criteria.
For the definitions of references and other genomics resources, see
[Fundamentals of Google
Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
Implements
[GlobalAllianceApi.searchReferenceSets](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/referencemethods.avdl#L71)"##),
"Details at http://byron.github.io/google-apis-rs/google_genomics1_cli/referencesets_search",
@@ -5763,11 +5668,7 @@ fn main() {
("variants", "methods: 'create', 'delete', 'get', 'import', 'merge', 'patch' and 'search'", vec![
("create",
Some(r##"Creates a new variant.
For the definitions of variants and other genomics resources, see
[Fundamentals of Google
Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)"##),
Some(r##"Creates a new variant."##),
"Details at http://byron.github.io/google-apis-rs/google_genomics1_cli/variants_create",
vec![
(Some(r##"kv"##),
@@ -5789,11 +5690,7 @@ fn main() {
Some(false)),
]),
("delete",
Some(r##"Deletes a variant.
For the definitions of variants and other genomics resources, see
[Fundamentals of Google
Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)"##),
Some(r##"Deletes a variant."##),
"Details at http://byron.github.io/google-apis-rs/google_genomics1_cli/variants_delete",
vec![
(Some(r##"variant-id"##),
@@ -5815,11 +5712,7 @@ fn main() {
Some(false)),
]),
("get",
Some(r##"Gets a variant by ID.
For the definitions of variants and other genomics resources, see
[Fundamentals of Google
Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)"##),
Some(r##"Gets a variant by ID."##),
"Details at http://byron.github.io/google-apis-rs/google_genomics1_cli/variants_get",
vec![
(Some(r##"variant-id"##),
@@ -5843,10 +5736,6 @@ fn main() {
("import",
Some(r##"Creates variant data by asynchronously importing the provided information.
For the definitions of variant sets and other genomics resources, see
[Fundamentals of Google
Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
The variants for import will be merged with any existing variant that
matches its reference sequence, start, end, reference bases, and
alternative bases. If no such variant exists, a new one will be created.
@@ -5882,10 +5771,6 @@ fn main() {
("merge",
Some(r##"Merges the given variants with existing variants.
For the definitions of variants and other genomics resources, see
[Fundamentals of Google
Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
Each variant will be
merged with an existing variant that matches its reference sequence,
start, end, reference bases, and alternative bases. If no such variant
@@ -5994,10 +5879,6 @@ fn main() {
("patch",
Some(r##"Updates a variant.
For the definitions of variants and other genomics resources, see
[Fundamentals of Google
Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
This method supports patch semantics. Returns the modified variant without
its calls."##),
"Details at http://byron.github.io/google-apis-rs/google_genomics1_cli/variants_patch",
@@ -6029,10 +5910,6 @@ fn main() {
("search",
Some(r##"Gets a list of variants matching the criteria.
For the definitions of variants and other genomics resources, see
[Fundamentals of Google
Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
Implements
[GlobalAllianceApi.searchVariants](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/variantmethods.avdl#L126)."##),
"Details at http://byron.github.io/google-apis-rs/google_genomics1_cli/variants_search",
@@ -6061,10 +5938,6 @@ fn main() {
("create",
Some(r##"Creates a new variant set.
For the definitions of variant sets and other genomics resources, see
[Fundamentals of Google
Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
The provided variant set must have a valid `datasetId` set - all other
fields are optional. Note that the `id` field will be ignored, as this is
assigned by the server."##),
@@ -6090,11 +5963,7 @@ fn main() {
]),
("delete",
Some(r##"Deletes a variant set including all variants, call sets, and calls within.
This is not reversible.
For the definitions of variant sets and other genomics resources, see
[Fundamentals of Google
Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)"##),
This is not reversible."##),
"Details at http://byron.github.io/google-apis-rs/google_genomics1_cli/variantsets_delete",
vec![
(Some(r##"variant-set-id"##),
@@ -6116,11 +5985,7 @@ fn main() {
Some(false)),
]),
("export",
Some(r##"Exports variant set data to an external destination.
For the definitions of variant sets and other genomics resources, see
[Fundamentals of Google
Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)"##),
Some(r##"Exports variant set data to an external destination."##),
"Details at http://byron.github.io/google-apis-rs/google_genomics1_cli/variantsets_export",
vec![
(Some(r##"variant-set-id"##),
@@ -6149,11 +6014,7 @@ fn main() {
Some(false)),
]),
("get",
Some(r##"Gets a variant set by ID.
For the definitions of variant sets and other genomics resources, see
[Fundamentals of Google
Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)"##),
Some(r##"Gets a variant set by ID."##),
"Details at http://byron.github.io/google-apis-rs/google_genomics1_cli/variantsets_get",
vec![
(Some(r##"variant-set-id"##),
@@ -6175,11 +6036,7 @@ fn main() {
Some(false)),
]),
("patch",
Some(r##"Updates a variant set using patch semantics.
For the definitions of variant sets and other genomics resources, see
[Fundamentals of Google
Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)"##),
Some(r##"Updates a variant set using patch semantics."##),
"Details at http://byron.github.io/google-apis-rs/google_genomics1_cli/variantsets_patch",
vec![
(Some(r##"variant-set-id"##),
@@ -6209,10 +6066,6 @@ fn main() {
("search",
Some(r##"Returns a list of all variant sets matching search criteria.
For the definitions of variant sets and other genomics resources, see
[Fundamentals of Google
Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
Implements
[GlobalAllianceApi.searchVariantSets](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/variantmethods.avdl#L49)."##),
"Details at http://byron.github.io/google-apis-rs/google_genomics1_cli/variantsets_search",
@@ -6241,7 +6094,7 @@ fn main() {
let mut app = App::new("genomics1")
.author("Sebastian Thiel <byronimo@gmail.com>")
.version("1.0.7+20171207")
.version("1.0.7+20181010")
.about("Upload, process, query, and search Genomics data in the cloud.")
.after_help("All documentation details can be found at http://byron.github.io/google-apis-rs/google_genomics1_cli")
.arg(Arg::with_name("url")