Struct gapi_grpc::google::genomics::v1::variant_service_v1_client::VariantServiceV1Client

pub struct VariantServiceV1Client<T> { /* fields omitted */ }

Implementations

impl VariantServiceV1Client<Channel>

pub async fn connect<D>(dst: D) -> Result<Self, Error> where
    D: TryInto<Endpoint>,
    D::Error: Into<StdError>, 

Attempt to create a new client by connecting to a given endpoint.

impl<T> VariantServiceV1Client<T> where
    T: GrpcService<BoxBody>,
    T::ResponseBody: Body + HttpBody + Send + 'static,
    T::Error: Into<StdError>,
    <T::ResponseBody as HttpBody>::Error: Into<StdError> + Send, 

pub fn new(inner: T) -> Self

pub fn with_interceptor(inner: T, interceptor: impl Into<Interceptor>) -> Self

pub async fn import_variants(
    &mut self,
    request: impl IntoRequest<ImportVariantsRequest>
) -> Result<Response<Operation>, Status>

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][google.genomics.v1.ImportVariantsRequest.info_merge_config]. 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.

pub async fn create_variant_set(
    &mut self,
    request: impl IntoRequest<CreateVariantSetRequest>
) -> Result<Response<VariantSet>, Status>

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.

pub async fn export_variant_set(
    &mut self,
    request: impl IntoRequest<ExportVariantSetRequest>
) -> Result<Response<Operation>, Status>

Exports variant set data to an external destination.

For the definitions of variant sets and other genomics resources, see Fundamentals of Google Genomics

pub async fn get_variant_set(
    &mut self,
    request: impl IntoRequest<GetVariantSetRequest>
) -> Result<Response<VariantSet>, Status>

Gets a variant set by ID.

For the definitions of variant sets and other genomics resources, see Fundamentals of Google Genomics

pub async fn search_variant_sets(
    &mut self,
    request: impl IntoRequest<SearchVariantSetsRequest>
) -> Result<Response<SearchVariantSetsResponse>, Status>

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.

pub async fn delete_variant_set(
    &mut self,
    request: impl IntoRequest<DeleteVariantSetRequest>
) -> Result<Response<()>, Status>

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

pub async fn update_variant_set(
    &mut self,
    request: impl IntoRequest<UpdateVariantSetRequest>
) -> Result<Response<VariantSet>, Status>

Updates a variant set using patch semantics.

For the definitions of variant sets and other genomics resources, see Fundamentals of Google Genomics

pub async fn search_variants(
    &mut self,
    request: impl IntoRequest<SearchVariantsRequest>
) -> Result<Response<SearchVariantsResponse>, Status>

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.

pub async fn create_variant(
    &mut self,
    request: impl IntoRequest<CreateVariantRequest>
) -> Result<Response<Variant>, Status>

Creates a new variant.

For the definitions of variants and other genomics resources, see Fundamentals of Google Genomics

pub async fn update_variant(
    &mut self,
    request: impl IntoRequest<UpdateVariantRequest>
) -> Result<Response<Variant>, Status>

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.

pub async fn delete_variant(
    &mut self,
    request: impl IntoRequest<DeleteVariantRequest>
) -> Result<Response<()>, Status>

Deletes a variant.

For the definitions of variants and other genomics resources, see Fundamentals of Google Genomics

pub async fn get_variant(
    &mut self,
    request: impl IntoRequest<GetVariantRequest>
) -> Result<Response<Variant>, Status>

Gets a variant by ID.

For the definitions of variants and other genomics resources, see Fundamentals of Google Genomics

pub async fn merge_variants(
    &mut self,
    request: impl IntoRequest<MergeVariantsRequest>
) -> Result<Response<()>, Status>

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][google.genomics.v1.MergeVariantsRequest.info_merge_config] 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.

pub async fn search_call_sets(
    &mut self,
    request: impl IntoRequest<SearchCallSetsRequest>
) -> Result<Response<SearchCallSetsResponse>, Status>

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.

pub async fn create_call_set(
    &mut self,
    request: impl IntoRequest<CreateCallSetRequest>
) -> Result<Response<CallSet>, Status>

Creates a new call set.

For the definitions of call sets and other genomics resources, see Fundamentals of Google Genomics

pub async fn update_call_set(
    &mut self,
    request: impl IntoRequest<UpdateCallSetRequest>
) -> Result<Response<CallSet>, Status>

Updates a call set.

For the definitions of call sets and other genomics resources, see Fundamentals of Google Genomics

This method supports patch semantics.

pub async fn delete_call_set(
    &mut self,
    request: impl IntoRequest<DeleteCallSetRequest>
) -> Result<Response<()>, Status>

Deletes a call set.

For the definitions of call sets and other genomics resources, see Fundamentals of Google Genomics

pub async fn get_call_set(
    &mut self,
    request: impl IntoRequest<GetCallSetRequest>
) -> Result<Response<CallSet>, Status>

Gets a call set by ID.

For the definitions of call sets and other genomics resources, see Fundamentals of Google Genomics

Trait Implementations

impl<T: Clone> Clone for VariantServiceV1Client<T>

fn clone(&self) -> Self

Returns a copy of the value.

pub fn clone_from(&mut self, source: &Self)

Performs copy-assignment from source.

impl<T> Debug for VariantServiceV1Client<T>

fn fmt(&self, f: &mut Formatter<'_>) -> Result

Formats the value using the given formatter.