Crate google_genomics1 [−] [src]

This documentation was generated from genomics crate version 0.1.15+20160905, where 20160905 is the exact revision of the genomics:v1 schema built by the mako code generator v0.1.15.

Everything else about the genomics v1 API can be found at the official documentation site. The original source code is on github.

Features

Handle the following Resources with ease from the central hub ...

annotations
- batch create, create, delete, get, search and update
annotationsets
- create, delete, get, search and update
callsets
- create, delete, get, patch and search
datasets
- create, delete, get, get iam policy, list, patch, set iam policy, test iam permissions and undelete
operations
- cancel, get and list
readgroupsets
- coveragebuckets list, delete, export, get, import, patch and search
reads
- search and stream
references
- bases list, get and search
referencesets
- get and search
variants
- create, delete, get, import, merge, patch, search and stream
variantsets
- create, delete, export, get, patch and search

Not what you are looking for ? Find all other Google APIs in their Rust documentation index.

Structure of this Library

The API is structured into the following primary items:

Hub
- a central object to maintain state and allow accessing all Activities
- creates Method Builders which in turn allow access to individual Call Builders
Resources
- primary types that you can apply Activities to
- a collection of properties and Parts
- Parts
  - a collection of properties
  - never directly used in Activities
Activities
- operations to apply to Resources

All structures are marked with applicable traits to further categorize them and ease browsing.

Generally speaking, you can invoke Activities like this:

let r = hub.resource().activity(...).doit()

Or specifically ...

let r = hub.datasets().set_iam_policy(...).doit()
let r = hub.datasets().delete(...).doit()
let r = hub.datasets().get_iam_policy(...).doit()
let r = hub.datasets().test_iam_permissions(...).doit()
let r = hub.datasets().get(...).doit()
let r = hub.datasets().undelete(...).doit()
let r = hub.datasets().create(...).doit()
let r = hub.datasets().patch(...).doit()
let r = hub.datasets().list(...).doit()

The resource() and activity(...) calls create builders. The second one dealing with Activities supports various methods to configure the impending operation (not shown here). It is made such that all required arguments have to be specified right away (i.e. (...)), whereas all optional ones can be build up as desired. The doit() method performs the actual communication with the server and returns the respective result.

Usage

Setting up your Project

To use this library, you would put the following lines into your Cargo.toml file:

[dependencies]
google-genomics1 = "*"

A complete example

extern crate hyper;
extern crate yup_oauth2 as oauth2;
extern crate google_genomics1 as genomics1;
use genomics1::Dataset;
use genomics1::{Result, Error};
use std::default::Default;
use oauth2::{Authenticator, DefaultAuthenticatorDelegate, ApplicationSecret, MemoryStorage};
use genomics1::Genomics;
 
// Get an ApplicationSecret instance by some means. It contains the `client_id` and 
// `client_secret`, among other things.
let secret: ApplicationSecret = Default::default();
// Instantiate the authenticator. It will choose a suitable authentication flow for you, 
// unless you replace  `None` with the desired Flow.
// Provide your own `AuthenticatorDelegate` to adjust the way it operates and get feedback about 
// what's going on. You probably want to bring in your own `TokenStorage` to persist tokens and
// retrieve them from storage.
let auth = Authenticator::new(&secret, DefaultAuthenticatorDelegate,
                              hyper::Client::new(),
                              <MemoryStorage as Default>::default(), None);
let mut hub = Genomics::new(hyper::Client::new(), auth);
// As the method needs a request, you would usually fill it with the desired information
// into the respective structure. Some of the parts shown here might not be applicable !
// Values shown here are possibly random and not representative !
let mut req = Dataset::default();
 
// You can configure optional parameters by calling the respective setters at will, and
// execute the final call using `doit()`.
// Values shown here are possibly random and not representative !
let result = hub.datasets().patch(req, "datasetId")
             .update_mask("dolor")
             .doit();
 
match result {
    Err(e) => match e {
        // The Error enum provides details about what exactly happened.
        // You can also just use its `Debug`, `Display` or `Error` traits
         Error::HttpError(_)
        |Error::MissingAPIKey
        |Error::MissingToken(_)
        |Error::Cancelled
        |Error::UploadSizeLimitExceeded(_, _)
        |Error::Failure(_)
        |Error::BadRequest(_)
        |Error::FieldClash(_)
        |Error::JsonDecodeError(_, _) => println!("{}", e),
    },
    Ok(res) => println!("Success: {:?}", res),
}

Handling Errors

All errors produced by the system are provided either as Result enumeration as return value of the doit() methods, or handed as possibly intermediate results to either the Hub Delegate, or the Authenticator Delegate.

When delegates handle errors or intermediate values, they may have a chance to instruct the system to retry. This makes the system potentially resilient to all kinds of errors.

Uploads and Downloads

If a method supports downloads, the response body, which is part of the Result, should be read by you to obtain the media. If such a method also supports a Response Result, it will return that by default. You can see it as meta-data for the actual media. To trigger a media download, you will have to set up the builder by making this call: .param("alt", "media").

Methods supporting uploads can do so using up to 2 different protocols: simple and resumable. The distinctiveness of each is represented by customized doit(...) methods, which are then named upload(...) and upload_resumable(...) respectively.

Customization and Callbacks

You may alter the way an doit() method is called by providing a delegate to the Method Builder before making the final doit() call. Respective methods will be called to provide progress information, as well as determine whether the system should retry on failure.

The delegate trait is default-implemented, allowing you to customize it with minimal effort.

Optional Parts in Server-Requests

All structures provided by this library are made to be enocodable and decodable via json. Optionals are used to indicate that partial requests are responses are valid. Most optionals are are considered Parts which are identifiable by name, which will be sent to the server to indicate either the set parts of the request or the desired parts in the response.

Builder Arguments

Using method builders, you are able to prepare an action call by repeatedly calling it's methods. These will always take a single argument, for which the following statements are true.

PODs are handed by copy
strings are passed as &str
request values are moved

Arguments will always be copied or cloned into the builder, to make them independent of their original life times.

Structs

Annotation	An annotation describes a region of reference genome. The value of an annotation may be one of several canonical types, supplemented by arbitrary info tags. An annotation is not inherently associated with a specific sample or individual (though a client could choose to use annotations in this way). Example canonical annotation types are `GENE` and `VARIANT`.
AnnotationBatchCreateCall	Creates one or more new annotations atomically. All annotations must belong to the same annotation set. Caller must have WRITE permission for this annotation set. For optimal performance, batch positionally adjacent annotations together. If the request has a systemic issue, such as an attempt to write to an inaccessible annotation set, the entire RPC will fail accordingly. For lesser data issues, when possible an error will be isolated to the corresponding batch entry in the response; the remaining well formed annotations will be created normally. For details on the requirements for each individual annotation resource, see CreateAnnotation.
AnnotationCreateCall	Creates a new annotation. Caller must have WRITE permission for the associated annotation set. The following fields are required: * annotationSetId * referenceName or referenceId ### Transcripts For annotations of type TRANSCRIPT, the following fields of transcript must be provided: * exons.start * exons.end All other fields may be optionally specified, unless documented as being server-generated (for example, the `id` field). The annotated range must be no longer than 100Mbp (mega base pairs). See the Annotation resource for additional restrictions on each field.
AnnotationDeleteCall	Deletes an annotation. Caller must have WRITE permission for the associated annotation set.
AnnotationGetCall	Gets an annotation. Caller must have READ permission for the associated annotation set.
AnnotationMethods	A builder providing access to all methods supported on annotation resources. It is not used directly, but through the `Genomics` hub.
AnnotationSearchCall	Searches for annotations that match the given criteria. Results are ordered by genomic coordinate (by reference sequence, then position). Annotations with equivalent genomic coordinates are returned in an unspecified order. This order is consistent, such that two queries for the same content (regardless of page size) yield annotations in the same order across their respective streams of paginated responses. Caller must have READ permission for the queried annotation sets.
AnnotationSet	An annotation set is a logical grouping of annotations that share consistent type information and provenance. Examples of annotation sets include 'all genes from refseq', and 'all variant annotations from ClinVar'.
AnnotationUpdateCall	Updates an annotation. Caller must have WRITE permission for the associated dataset.
AnnotationsetCreateCall	Creates a new annotation set. Caller must have WRITE permission for the associated dataset. The following fields are required: * datasetId * referenceSetId All other fields may be optionally specified, unless documented as being server-generated (for example, the `id` field).
AnnotationsetDeleteCall	Deletes an annotation set. Caller must have WRITE permission for the associated annotation set.
AnnotationsetGetCall	Gets an annotation set. Caller must have READ permission for the associated dataset.
AnnotationsetMethods	A builder providing access to all methods supported on annotationset resources. It is not used directly, but through the `Genomics` hub.
AnnotationsetSearchCall	Searches for annotation sets that match the given criteria. Annotation sets are returned in an unspecified order. This order is consistent, such that two queries for the same content (regardless of page size) yield annotation sets in the same order across their respective streams of paginated responses. Caller must have READ permission for the queried datasets.
AnnotationsetUpdateCall	Updates an annotation set. The update must respect all mutability restrictions and other invariants described on the annotation set resource. Caller must have WRITE permission for the associated dataset.
BatchCreateAnnotationsRequest	There is no detailed description.
BatchCreateAnnotationsResponse	There is no detailed description.
Binding	Associates `members` with a `role`.
CallSet	A call set is a collection of variant calls, typically for one sample. It belongs to a variant set. For more genomics resource definitions, see Fundamentals of Google Genomics
CallsetCreateCall	Creates a new call set. For the definitions of call sets and other genomics resources, see Fundamentals of Google Genomics
CallsetDeleteCall	Deletes a call set. For the definitions of call sets and other genomics resources, see Fundamentals of Google Genomics
CallsetGetCall	Gets a call set by ID. For the definitions of call sets and other genomics resources, see Fundamentals of Google Genomics
CallsetMethods	A builder providing access to all methods supported on callset resources. It is not used directly, but through the `Genomics` hub.
CallsetPatchCall	Updates a call set. For the definitions of call sets and other genomics resources, see Fundamentals of Google Genomics This method supports patch semantics.
CallsetSearchCall	Gets a list of call sets matching the criteria. For the definitions of call sets and other genomics resources, see Fundamentals of Google Genomics Implements GlobalAllianceApi.searchCallSets.
CancelOperationRequest	The request message for Operations.CancelOperation.
CigarUnit	A single CIGAR operation.
ClinicalCondition	There is no detailed description.
CodingSequence	There is no detailed description.
CoverageBucket	A bucket over which read coverage has been precomputed. A bucket corresponds to a specific range of the reference sequence.
Dataset	A Dataset is a collection of genomic data. For more genomics resource definitions, see Fundamentals of Google Genomics
DatasetCreateCall	Creates a new dataset. For the definitions of datasets and other genomics resources, see Fundamentals of Google Genomics
DatasetDeleteCall	Deletes a dataset and all of its contents (all read group sets, reference sets, variant sets, call sets, annotation sets, etc.) 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
DatasetGetCall	Gets a dataset by ID. For the definitions of datasets and other genomics resources, see Fundamentals of Google Genomics
DatasetGetIamPolicyCall	Gets the access control policy for the dataset. This is empty if the policy or resource does not exist. See Getting a Policy for more information. For the definitions of datasets and other genomics resources, see Fundamentals of Google Genomics
DatasetListCall	Lists datasets within a project. For the definitions of datasets and other genomics resources, see Fundamentals of Google Genomics
DatasetMethods	A builder providing access to all methods supported on dataset resources. It is not used directly, but through the `Genomics` hub.
DatasetPatchCall	Updates a dataset. For the definitions of datasets and other genomics resources, see Fundamentals of Google Genomics This method supports patch semantics.
DatasetSetIamPolicyCall	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 See Setting a Policy for more information.
DatasetTestIamPermissionCall	Returns permissions that a caller has on the specified resource. See Testing Permissions for more information. For the definitions of datasets and other genomics resources, see Fundamentals of Google Genomics
DatasetUndeleteCall	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 This operation is only possible for a week after the deletion occurred.
DefaultDelegate	A delegate with a conservative default implementation, which is used if no other delegate is set.
Empty	A generic empty message that you can re-use to avoid defining duplicated empty messages in your APIs. A typical example is to use it as the request or the response type of an API method. For instance: service Foo { rpc Bar(google.protobuf.Empty) returns (google.protobuf.Empty); } The JSON representation for `Empty` is empty JSON object `{}`.
Entry	There is no detailed description.
ErrorResponse	A utility to represent detailed errors we might see in case there are BadRequests. The latter happen if the sent parameters or request structures are unsound
Exon	There is no detailed description.
Experiment	There is no detailed description.
ExportReadGroupSetRequest	The read group set export request.
ExportVariantSetRequest	The variant data export request.
ExternalId	There is no detailed description.
Genomics	Central instance to access all Genomics related resource activities
GetIamPolicyRequest	Request message for `GetIamPolicy` method.
ImportReadGroupSetsRequest	The read group set import request.
ImportVariantsRequest	The variant data import request.
LinearAlignment	A linear alignment can be represented by one CIGAR string. Describes the mapped position and local alignment of the read to the reference.
ListBasesResponse	There is no detailed description.
ListCoverageBucketsResponse	There is no detailed description.
ListDatasetsResponse	The dataset list response.
ListOperationsResponse	The response message for Operations.ListOperations.
MergeVariantsRequest	There is no detailed description.
MethodInfo	Contains information about an API request.
MultiPartReader	Provides a `Read` interface that converts multiple parts into the protocol identified by RFC2387. Note: This implementation is just as rich as it needs to be to perform uploads to google APIs, and might not be a fully-featured implementation.
Operation	This resource represents a long-running operation that is the result of a network API call.
OperationCancelCall	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.
OperationGetCall	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.
OperationListCall	Lists operations that match the specified filter in the request.
OperationMethods	A builder providing access to all methods supported on operation resources. It is not used directly, but through the `Genomics` hub.
Policy	Defines an Identity and Access Management (IAM) policy. It is used to specify access control policies for Cloud Platform resources. A `Policy` consists of a list of `bindings`. A `Binding` binds a list of `members` to a `role`, where the members can be user accounts, Google groups, Google domains, and service accounts. A `role` is a named list of permissions defined by IAM. Example { "bindings": [ { "role": "roles/owner", "members": [ "user:mike@example.com", "group:admins@example.com", "domain:google.com", "serviceAccount:my-other-app@appspot.gserviceaccount.com", ] }, { "role": "roles/viewer", "members": ["user:sean@example.com"] } ] } For a description of IAM and its features, see the IAM developer's guide.
Position	An abstraction for referring to a genomic position, in relation to some already known reference. For now, represents a genomic position as a reference name, a base number on that reference (0-based), and a determination of forward or reverse strand.
Program	There is no detailed description.
Range	A 0-based half-open genomic coordinate range for search requests.
Read	A read alignment describes a linear alignment of a string of DNA to a reference sequence, in addition to metadata about the fragment (the molecule of DNA sequenced) and the read (the bases which were read by the sequencer). A read is equivalent to a line in a SAM file. A read belongs to exactly one read group and exactly one read group set. For more genomics resource definitions, see Fundamentals of Google Genomics ### Reverse-stranded reads Mapped reads (reads having a non-null `alignment`) can be aligned to either the forward or the reverse strand of their associated reference. Strandedness of a mapped read is encoded by `alignment.position.reverseStrand`. If we consider the reference to be a forward-stranded coordinate space of `[0, reference.length)` with `0` as the left-most position and `reference.length` as the right-most position, reads are always aligned left to right. That is, `alignment.position.position` always refers to the left-most reference coordinate and `alignment.cigar` describes the alignment of this read to the reference from left to right. All per-base fields such as `alignedSequence` and `alignedQuality` share this same left-to-right orientation; this is true of reads which are aligned to either strand. For reverse-stranded reads, this means that `alignedSequence` is the reverse complement of the bases that were originally reported by the sequencing machine. ### Generating a reference-aligned sequence string When interacting with mapped reads, it's often useful to produce a string representing the local alignment of the read to reference. The following pseudocode demonstrates one way of doing this: out = "" offset = 0 for c in read.alignment.cigar { switch c.operation { case "ALIGNMENT_MATCH", "SEQUENCE_MATCH", "SEQUENCE_MISMATCH": out += read.alignedSequence[offset:offset+c.operationLength] offset += c.operationLength break case "CLIP_SOFT", "INSERT": offset += c.operationLength break case "PAD": out += repeat("*", c.operationLength) break case "DELETE": out += repeat("-", c.operationLength) break case "SKIP": out += repeat(" ", c.operationLength) break case "CLIP_HARD": break } } return out ### Converting to SAM's CIGAR string The following pseudocode generates a SAM CIGAR string from the `cigar` field. Note that this is a lossy conversion (`cigar.referenceSequence` is lost). cigarMap = { "ALIGNMENT_MATCH": "M", "INSERT": "I", "DELETE": "D", "SKIP": "N", "CLIP_SOFT": "S", "CLIP_HARD": "H", "PAD": "P", "SEQUENCE_MATCH": "=", "SEQUENCE_MISMATCH": "X", } cigarStr = "" for c in read.alignment.cigar { cigarStr += c.operationLength + cigarMap[c.operation] } return cigarStr
ReadGroup	A read group is all the data that's processed the same way by the sequencer.
ReadGroupSet	A read group set is a logical collection of read groups, which are collections of reads produced by a sequencer. A read group set typically models reads corresponding to one sample, sequenced one way, and aligned one way. * A read group set belongs to one dataset. * A read group belongs to one read group set. * A read belongs to one read group. For more genomics resource definitions, see Fundamentals of Google Genomics
ReadMethods	A builder providing access to all methods supported on read resources. It is not used directly, but through the `Genomics` hub.
ReadSearchCall	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 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. If a target positional range is specified, search returns all reads whose alignment to the reference genome overlap the range. A query which specifies only read group set IDs yields all reads in those read group sets, including unmapped reads. All reads returned (including reads on subsequent pages) are ordered by genomic coordinate (by reference sequence, then position). Reads with equivalent genomic coordinates are returned in an unspecified order. This order is consistent, such that two queries for the same content (regardless of page size) yield reads in the same order across their respective streams of paginated responses. Implements GlobalAllianceApi.searchReads.
ReadStreamCall	Returns a stream of all the reads matching the search request, ordered by reference name, position, and ID.
ReadgroupsetCoveragebucketListCall	Lists fixed width coverage buckets for a read group set, each of which 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 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 levels'. The caller must have READ permissions for the target read group set.
ReadgroupsetDeleteCall	Deletes a read group set. For the definitions of read group sets and other genomics resources, see Fundamentals of Google Genomics
ReadgroupsetExportCall	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 Note that currently there may be some differences between exported BAM files and the original BAM file at the time of import. See ImportReadGroupSets for caveats.
ReadgroupsetGetCall	Gets a read group set by ID. For the definitions of read group sets and other genomics resources, see Fundamentals of Google Genomics
ReadgroupsetImportCall	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 The caller must have WRITE permissions to the dataset. ## Notes on BAM import - Tags will be converted to strings - tag types are not preserved - Comments (`@CO`) in the input file header will not be preserved - Original header order of references (`@SQ`) will not be preserved - Any reverse stranded unmapped reads will be reverse complemented, and their qualities (also the "BQ" and "OQ" tags, if any) will be reversed - Unmapped reads will be stripped of positional information (reference name and position)
ReadgroupsetMethods	A builder providing access to all methods supported on readgroupset resources. It is not used directly, but through the `Genomics` hub.
ReadgroupsetPatchCall	Updates a read group set. For the definitions of read group sets and other genomics resources, see Fundamentals of Google Genomics This method supports patch semantics.
ReadgroupsetSearchCall	Searches for read group sets matching the criteria. For the definitions of read group sets and other genomics resources, see Fundamentals of Google Genomics Implements GlobalAllianceApi.searchReadGroupSets.
Reference	A reference is a canonical assembled DNA sequence, intended to act as a reference coordinate space for other genomic annotations. A single reference might represent the human chromosome 1 or mitochandrial DNA, for instance. A reference belongs to one or more reference sets. For more genomics resource definitions, see Fundamentals of Google Genomics
ReferenceBaseListCall	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 Implements GlobalAllianceApi.getReferenceBases.
ReferenceBound	ReferenceBound records an upper bound for the starting coordinate of variants in a particular reference.
ReferenceGetCall	Gets a reference. For the definitions of references and other genomics resources, see Fundamentals of Google Genomics Implements GlobalAllianceApi.getReference.
ReferenceMethods	A builder providing access to all methods supported on reference resources. It is not used directly, but through the `Genomics` hub.
ReferenceSearchCall	Searches for references which match the given criteria. For the definitions of references and other genomics resources, see Fundamentals of Google Genomics Implements GlobalAllianceApi.searchReferences.
ReferenceSet	A reference set is a set of references which typically comprise a reference assembly for a species, such as `GRCh38` which is representative of the human genome. A reference set defines a common coordinate space for comparing reference-aligned experimental data. A reference set contains 1 or more references. For more genomics resource definitions, see Fundamentals of Google Genomics
ReferencesetGetCall	Gets a reference set. For the definitions of references and other genomics resources, see Fundamentals of Google Genomics Implements GlobalAllianceApi.getReferenceSet.
ReferencesetMethods	A builder providing access to all methods supported on referenceset resources. It is not used directly, but through the `Genomics` hub.
ReferencesetSearchCall	Searches for reference sets which match the given criteria. For the definitions of references and other genomics resources, see Fundamentals of Google Genomics Implements GlobalAllianceApi.searchReferenceSets
SearchAnnotationSetsRequest	There is no detailed description.
SearchAnnotationSetsResponse	There is no detailed description.
SearchAnnotationsRequest	There is no detailed description.
SearchAnnotationsResponse	There is no detailed description.
SearchCallSetsRequest	The call set search request.
SearchCallSetsResponse	The call set search response.
SearchReadGroupSetsRequest	The read group set search request.
SearchReadGroupSetsResponse	The read group set search response.
SearchReadsRequest	The read search request.
SearchReadsResponse	The read search response.
SearchReferenceSetsRequest	There is no detailed description.
SearchReferenceSetsResponse	There is no detailed description.
SearchReferencesRequest	There is no detailed description.
SearchReferencesResponse	There is no detailed description.
SearchVariantSetsRequest	The search variant sets request.
SearchVariantSetsResponse	The search variant sets response.
SearchVariantsRequest	The variant search request.
SearchVariantsResponse	The variant search response.
SetIamPolicyRequest	Request message for `SetIamPolicy` method.
Status	The `Status` type defines a logical error model that is suitable for different programming environments, including REST APIs and RPC APIs. It is used by gRPC. The error model is designed to be: - Simple to use and understand for most users - Flexible enough to meet unexpected needs # Overview The `Status` message contains three pieces of data: error code, error message, and error details. The error code should be an enum value of google.rpc.Code, but it may accept additional error codes if needed. The error message should be a developer-facing English message that helps developers understand and resolve the error. If a localized user-facing error message is needed, put the localized message in the error details or localize it in the client. The optional error details may contain arbitrary information about the error. There is a predefined set of error detail types in the package `google.rpc` which can be used for common error conditions. # Language mapping The `Status` message is the logical representation of the error model, but it is not necessarily the actual wire format. When the `Status` message is exposed in different client libraries and different wire protocols, it can be mapped differently. For example, it will likely be mapped to some exceptions in Java, but more likely mapped to some error codes in C. # Other uses The error model and the `Status` message can be used in a variety of environments, either with or without APIs, to provide a consistent developer experience across different environments. Example uses of this error model include: - Partial errors. If a service needs to return partial errors to the client, it may embed the `Status` in the normal response to indicate the partial errors. - Workflow errors. A typical workflow has multiple steps. Each step may have a `Status` message for error reporting purpose. - Batch operations. If a client uses batch request and batch response, the `Status` message should be used directly inside batch response, one for each error sub-response. - Asynchronous operations. If an API call embeds asynchronous operation results in its response, the status of those operations should be represented directly using the `Status` message. - Logging. If some API errors are stored in logs, the message `Status` could be used directly after any stripping needed for security/privacy reasons.
StreamReadsRequest	The stream reads request.
StreamReadsResponse	There is no detailed description.
StreamVariantsRequest	The stream variants request.
StreamVariantsResponse	There is no detailed description.
TestIamPermissionsRequest	Request message for `TestIamPermissions` method.
TestIamPermissionsResponse	Response message for `TestIamPermissions` method.
Transcript	A transcript represents the assertion that a particular region of the reference genome may be transcribed as RNA.
UndeleteDatasetRequest	There is no detailed description.
Variant	A variant represents a change in DNA sequence relative to a reference sequence. For example, a variant could represent a SNP or an insertion. Variants belong to a variant set. For more genomics resource definitions, see Fundamentals of Google Genomics Each of the calls on a variant represent a determination of genotype with respect to that variant. For example, a call 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 calls typically from one sample.
VariantAnnotation	There is no detailed description.
VariantCall	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 the occurrence of a SNP named rs1234 in a call set with the name NA12345.
VariantCreateCall	Creates a new variant. For the definitions of variants and other genomics resources, see Fundamentals of Google Genomics
VariantDeleteCall	Deletes a variant. For the definitions of variants and other genomics resources, see Fundamentals of Google Genomics
VariantGetCall	Gets a variant by ID. For the definitions of variants and other genomics resources, see Fundamentals of Google Genomics
VariantImportCall	Creates variant data by asynchronously importing the provided information. For the definitions of variant sets and other genomics resources, see 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. When variants are merged, the call information from the new variant is added to the existing variant, and Variant info fields are merged as specified in infoMergeConfig. As a special case, for single-sample VCF files, QUAL and FILTER fields will be moved to the call level; these are sometimes interpreted in a call-specific context. Imported VCF headers are appended to the metadata already in a variant set.
VariantMergeCall	Merges the given variants with existing variants. For the definitions of variants and other genomics resources, see 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 exists, a new one will be created. When variants are merged, the call information from the new variant is added to the existing variant. Variant info fields are merged as specified in the infoMergeConfig field of the MergeVariantsRequest. Please exercise caution when using this method! It is easy to introduce mistakes in existing variants and difficult to back out of them. For example, suppose you were trying to merge a new variant with an existing one and both variants contain calls that belong to callsets with the same callset ID. // Existing variant - irrelevant fields trimmed for clarity { "variantSetId": "10473108253681171589", "referenceName": "1", "start": "10582", "referenceBases": "G", "alternateBases": [ "A" ], "calls": [ { "callSetId": "10473108253681171589-0", "callSetName": "CALLSET0", "genotype": [ 0, 1 ], } ] } // New variant with conflicting call information { "variantSetId": "10473108253681171589", "referenceName": "1", "start": "10582", "referenceBases": "G", "alternateBases": [ "A" ], "calls": [ { "callSetId": "10473108253681171589-0", "callSetName": "CALLSET0", "genotype": [ 1, 1 ], } ] } The resulting merged variant would overwrite the existing calls with those from the new variant: { "variantSetId": "10473108253681171589", "referenceName": "1", "start": "10582", "referenceBases": "G", "alternateBases": [ "A" ], "calls": [ { "callSetId": "10473108253681171589-0", "callSetName": "CALLSET0", "genotype": [ 1, 1 ], } ] } This may be the desired outcome, but it is up to the user to determine if if that is indeed the case.
VariantMethods	A builder providing access to all methods supported on variant resources. It is not used directly, but through the `Genomics` hub.
VariantPatchCall	Updates a variant. For the definitions of variants and other genomics resources, see Fundamentals of Google Genomics This method supports patch semantics. Returns the modified variant without its calls.
VariantSearchCall	Gets a list of variants matching the criteria. For the definitions of variants and other genomics resources, see Fundamentals of Google Genomics Implements GlobalAllianceApi.searchVariants.
VariantSet	A variant set is a collection of call sets and variants. It contains summary statistics of those contents. A variant set belongs to a dataset. For more genomics resource definitions, see Fundamentals of Google Genomics
VariantSetMetadata	Metadata describes a single piece of variant call metadata. These data include a top level key and either a single value string (value) or a list of key-value pairs (info.) Value and info are mutually exclusive.
VariantStreamCall	Returns a stream of all the variants matching the search request, ordered by reference name, position, and ID.
VariantsetCreateCall	Creates a new variant set. For the definitions of variant sets and other genomics resources, see 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.
VariantsetDeleteCall	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
VariantsetExportCall	Exports variant set data to an external destination. For the definitions of variant sets and other genomics resources, see Fundamentals of Google Genomics
VariantsetGetCall	Gets a variant set by ID. For the definitions of variant sets and other genomics resources, see Fundamentals of Google Genomics
VariantsetMethods	A builder providing access to all methods supported on variantset resources. It is not used directly, but through the `Genomics` hub.
VariantsetPatchCall	Updates a variant set using patch semantics. For the definitions of variant sets and other genomics resources, see Fundamentals of Google Genomics
VariantsetSearchCall	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 Implements GlobalAllianceApi.searchVariantSets.

Enums

Error
Scope	Identifies the an OAuth2 authorization scope. A scope is needed when requesting an authorization token.

Traits

CallBuilder	Identifies types which represent builders for a particular resource method
Delegate	A trait specifying functionality to help controlling any request performed by the API. The trait has a conservative default implementation.
Hub	Identifies the Hub. There is only one per library, this trait is supposed to make intended use more explicit. The hub allows to access all resource methods more easily.
MethodsBuilder	Identifies types for building methods of a particular resource type
NestedType	Identifies types which are only used by other types internally. They have no special meaning, this trait just marks them for completeness.
Part	Identifies types which are only used as part of other types, which usually are carrying the `Resource` trait.
ReadSeek	A utility to specify reader types which provide seeking capabilities too
RequestValue	Identifies types which are used in API requests.
Resource	Identifies types which can be inserted and deleted. Types with this trait are most commonly used by clients of this API.
ResponseResult	Identifies types which are used in API responses.
ToParts	A trait for all types that can convert themselves into a parts string

Functions

remove_json_null_values

Type Definitions

Result

A universal result type used as return for all calls.