allele_annotation_service
- ************* /variantannotations ****************
This section will be re-instated when features are available in the API
Only return variant annotations for any of these features.
Features may include specific transcripts or genes. A search by gene will
return information for all transcripts associated with the gene in the
variant annotation set.
This or a location (referenceName/referenceId plus optional start and end)
must be supplied.
If empty, return all variant annotations in specified window.
repeated string feature_ids;
************* /variantannotationsets ****************
-
SearchVariantAnnotationSets(request)
-
Returns a list of available variant annotation sets.
POST /variantannotationsets/search must accept a JSON version of
SearchVariantAnnotationSetsRequest as the post body and will return a
JSON version of SearchVariantAnnotationSetsResponse.
-
SearchVariantAnnotations(request)
-
Gets a list of VariantAnnotation messages matching the search criteria.
This allows the mining of allele-specific annotations on a VariantSet by
either a region or by a set of genomic features. Where a region is supplied
annotation of all alleles vs all features in the region is returned. Where
a set of features is supplied, only annotations against these features
(matching on featuretype and id) are returned and other overlapping
features are ignored.
variantannotationsets/search returns information on the input to the
annotation. This will be a VariantSet and the reference data and software
versions used in calculating the annotation. It is essential this
information is exhaustive.
POST /variantannotations/search must accept a JSON version of
SearchVariantAnnotationsRequest as the post body and will return a JSON
version of SearchVariantAnnotationsResponse.
-
GetVariantAnnotationSet(request)
-
Gets an VariantAnnotationSet by ID.
GET /variantannotationsets/{variant_annotation_set_id} will return a JSON
version of VariantAnnotationSet.
-
message
SearchVariantAnnotationsRequest
| Fields: |
- variant_annotation_set_id (string) – Required. The ID of the variant annotation set to search over.
- reference_name (string) – Only return variants with reference alleles on the reference with this
name. One of this field or reference_id is required.
- reference_id (string) – Only return variants with reference alleles on the reference with this
ID. One of this field or reference_name is required.
- start (long) – Required if reference_name or reference_id supplied. The beginning of the
window (0-based, inclusive) for which variants with overlapping reference
alleles should be returned. Genomic positions are non-negative integers
less than reference length. Requests spanning the join of circular
genomes are represented as two requests one on each side of the join
(position 0).
- end (long) – Required if reference_name or reference_id supplied. The end of the window
(0-based, exclusive) for which variants with overlapping reference
alleles should be returned.
- effects (list of
OntologyTerm) – This filter allows variant, transcript combinations to be extracted by
effect type(s). Only return variant annotations including any of these
effects and only return transcript effects including any of these
effects. Exact matching across all fields of the Sequence Ontology
OntologyTerm is required. (A transcript effect may have multiple SO
effects which will all be reported.) If empty, return all variant
annotations.
- page_size (integer) – Specifies the maximum number of results to return in a single page. If
unspecified, a system default will be used.
- page_token (string) – 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
next_page_token from the previous response.
|
|---|
This request maps to the body of POST /variantannotations/search as JSON.
-
message
SearchVariantAnnotationsResponse
| Fields: |
- variant_annotations (list of
VariantAnnotation) – The list of matching variant annotations.
- next_page_token (string) – The continuation token, which is used to page through large result sets.
Provide this value in a subsequent request to return the next page of
results. This field will be empty if there aren’t any additional results.
|
|---|
This is the response from POST /variantannotations/search expressed as
JSON.
-
message
SearchVariantAnnotationSetsRequest
| Fields: |
- variant_set_id (string) – Required. The VariantSet to search.
- page_size (integer) – Specifies the maximum number of results to return in a single page. If
unspecified, a system default will be used.
- page_token (string) – 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
next_page_token from the previous response.
|
|---|
This request maps to the body of POST /variantannotationsets/search as
JSON.
-
message
SearchVariantAnnotationSetsResponse
| Fields: |
- variant_annotation_sets (list of
VariantAnnotationSet) – The list of matching variant annotation sets.
- next_page_token (string) – The continuation token, which is used to page through large result sets.
Provide this value in a subsequent request to return the next page of
results. This field will be empty if there aren’t any additional results.
|
|---|
This is the response from POST /variantannotationsets/search expressed as
JSON.
-
message
GetVariantAnnotationSetRequest
| Fields: |
- variant_annotation_set_id (string) – The ID of the VariantAnnotationSet to be retrieved.
|
|---|
This request maps to the URL GET /variantannotationsets/{id}.