Module gapi_grpc::google::genomics::v1 [−][src]
Modules
| annotation | |
| annotation_service_v1_client | Generated client implementations. |
| batch_create_annotations_response | |
| cigar_unit | |
| dataset_service_v1_client | Generated client implementations. |
| export_variant_set_request | |
| import_read_group_sets_request | |
| import_variants_request | |
| read_group | |
| read_service_v1_client | Generated client implementations. |
| reference_service_v1_client | Generated client implementations. |
| search_annotations_request | |
| streaming_read_service_client | Generated client implementations. |
| streaming_variant_service_client | Generated client implementations. |
| transcript | |
| variant_annotation | |
| variant_service_v1_client | Generated client implementations. |
| variant_set_metadata |
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 |
| 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’. |
| BatchCreateAnnotationsRequest | |
| BatchCreateAnnotationsResponse | |
| CallSet | A call set is a collection of variant calls, typically for one sample. It belongs to a variant set. |
| CigarUnit | A single CIGAR operation. |
| CoverageBucket | A bucket over which read coverage has been precomputed. A bucket corresponds to a specific range of the reference sequence. |
| CreateAnnotationRequest | |
| CreateAnnotationSetRequest | |
| CreateCallSetRequest | |
| CreateDatasetRequest | |
| CreateVariantRequest | |
| CreateVariantSetRequest | The CreateVariantSet request |
| Dataset | A Dataset is a collection of genomic data. |
| DeleteAnnotationRequest | |
| DeleteAnnotationSetRequest | |
| DeleteCallSetRequest | |
| DeleteDatasetRequest | |
| DeleteReadGroupSetRequest | |
| DeleteVariantRequest | |
| DeleteVariantSetRequest | The delete variant set request. |
| ExportReadGroupSetRequest | The read group set export request. |
| ExportVariantSetRequest | The variant data export request. |
| ExternalId | |
| GetAnnotationRequest | |
| GetAnnotationSetRequest | |
| GetCallSetRequest | |
| GetDatasetRequest | |
| GetReadGroupSetRequest | |
| GetReferenceRequest | |
| GetReferenceSetRequest | |
| GetVariantRequest | |
| GetVariantSetRequest | The variant set request. |
| ImportReadGroupSetsRequest | The read group set import request. |
| ImportReadGroupSetsResponse | The read group set import response. |
| ImportVariantsRequest | The variant data import request. |
| ImportVariantsResponse | The variant data import response. |
| LinearAlignment | A linear alignment can be represented by one CIGAR string. Describes the mapped position and local alignment of the read to the reference. |
| ListBasesRequest | |
| ListBasesResponse | |
| ListCoverageBucketsRequest | |
| ListCoverageBucketsResponse | |
| ListDatasetsRequest | The dataset list request. |
| ListDatasetsResponse | The dataset list response. |
| MergeVariantsRequest | |
| OperationEvent | An event that occurred during an [Operation][google.longrunning.Operation]. |
| OperationMetadata | Metadata describing an [Operation][google.longrunning.Operation]. |
| 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. |
| 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][google.genomics.v1.Reference], 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][google.genomics.v1.ReadGroupSet]. |
| 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. |
| 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. |
| ReferenceBound | ReferenceBound records an upper bound for the starting coordinate of variants in a particular reference. |
| ReferenceSet | A reference set is a set of references which typically comprise a reference
assembly for a species, such as |
| SearchAnnotationSetsRequest | |
| SearchAnnotationSetsResponse | |
| SearchAnnotationsRequest | |
| SearchAnnotationsResponse | |
| 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 | |
| SearchReferenceSetsResponse | |
| SearchReferencesRequest | |
| SearchReferencesResponse | |
| SearchVariantSetsRequest | The search variant sets request. |
| SearchVariantSetsResponse | The search variant sets response. |
| SearchVariantsRequest | The variant search request. |
| SearchVariantsResponse | The variant search response. |
| StreamReadsRequest | The stream reads request. |
| StreamReadsResponse | |
| StreamVariantsRequest | The stream variants request. |
| StreamVariantsResponse | |
| Transcript | A transcript represents the assertion that a particular region of the reference genome may be transcribed as RNA. |
| UndeleteDatasetRequest | |
| UpdateAnnotationRequest | |
| UpdateAnnotationSetRequest | |
| UpdateCallSetRequest | |
| UpdateDatasetRequest | |
| UpdateReadGroupSetRequest | |
| UpdateVariantRequest | |
| UpdateVariantSetRequest | |
| 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. |
| VariantAnnotation | |
| 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. |
| 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. |
| 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. |
Enums
| AnnotationType | When an [Annotation][google.genomics.v1.Annotation] or
[AnnotationSet][google.genomics.v1.AnnotationSet] is created, if |
| InfoMergeOperation | Operations to be performed during import on Variant info fields. These operations are set for each info field in the info_merge_config map of ImportVariantsRequest, which is plumbed down to the MergeVariantRequests generated by the import job. |