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// Copyright 2019 Google Inc. All rights reserved.
// Use of this source code is governed by a BSD-style
// license that can be found in the LICENSE file.
// Code generated file. DO NOT EDIT.
// Package genomics provides access to the Genomics API.
//
// See https://cloud.google.com/genomics
//
// Usage example:
//
// import "google.golang.org/api/genomics/v1"
// ...
// genomicsService, err := genomics.New(oauthHttpClient)
package genomics // import "google.golang.org/api/genomics/v1"
import (
"bytes"
"context"
"encoding/json"
"errors"
"fmt"
"io"
"net/http"
"net/url"
"strconv"
"strings"
gensupport "google.golang.org/api/gensupport"
googleapi "google.golang.org/api/googleapi"
)
// Always reference these packages, just in case the auto-generated code
// below doesn't.
var _ = bytes.NewBuffer
var _ = strconv.Itoa
var _ = fmt.Sprintf
var _ = json.NewDecoder
var _ = io.Copy
var _ = url.Parse
var _ = gensupport.MarshalJSON
var _ = googleapi.Version
var _ = errors.New
var _ = strings.Replace
var _ = context.Canceled
const apiId = "genomics:v1"
const apiName = "genomics"
const apiVersion = "v1"
const basePath = "https://genomics.googleapis.com/"
// OAuth2 scopes used by this API.
const (
// View and manage your data in Google BigQuery
BigqueryScope = "https://www.googleapis.com/auth/bigquery"
// View and manage your data across Google Cloud Platform services
CloudPlatformScope = "https://www.googleapis.com/auth/cloud-platform"
// Manage your data in Google Cloud Storage
DevstorageReadWriteScope = "https://www.googleapis.com/auth/devstorage.read_write"
// View and manage Genomics data
GenomicsScope = "https://www.googleapis.com/auth/genomics"
// View Genomics data
GenomicsReadonlyScope = "https://www.googleapis.com/auth/genomics.readonly"
)
func New(client *http.Client) (*Service, error) {
if client == nil {
return nil, errors.New("client is nil")
}
s := &Service{client: client, BasePath: basePath}
s.Annotations = NewAnnotationsService(s)
s.Annotationsets = NewAnnotationsetsService(s)
s.Callsets = NewCallsetsService(s)
s.Datasets = NewDatasetsService(s)
s.Operations = NewOperationsService(s)
s.Readgroupsets = NewReadgroupsetsService(s)
s.Reads = NewReadsService(s)
s.References = NewReferencesService(s)
s.Referencesets = NewReferencesetsService(s)
s.Variants = NewVariantsService(s)
s.Variantsets = NewVariantsetsService(s)
return s, nil
}
type Service struct {
client *http.Client
BasePath string // API endpoint base URL
UserAgent string // optional additional User-Agent fragment
Annotations *AnnotationsService
Annotationsets *AnnotationsetsService
Callsets *CallsetsService
Datasets *DatasetsService
Operations *OperationsService
Readgroupsets *ReadgroupsetsService
Reads *ReadsService
References *ReferencesService
Referencesets *ReferencesetsService
Variants *VariantsService
Variantsets *VariantsetsService
}
func (s *Service) userAgent() string {
if s.UserAgent == "" {
return googleapi.UserAgent
}
return googleapi.UserAgent + " " + s.UserAgent
}
func NewAnnotationsService(s *Service) *AnnotationsService {
rs := &AnnotationsService{s: s}
return rs
}
type AnnotationsService struct {
s *Service
}
func NewAnnotationsetsService(s *Service) *AnnotationsetsService {
rs := &AnnotationsetsService{s: s}
return rs
}
type AnnotationsetsService struct {
s *Service
}
func NewCallsetsService(s *Service) *CallsetsService {
rs := &CallsetsService{s: s}
return rs
}
type CallsetsService struct {
s *Service
}
func NewDatasetsService(s *Service) *DatasetsService {
rs := &DatasetsService{s: s}
return rs
}
type DatasetsService struct {
s *Service
}
func NewOperationsService(s *Service) *OperationsService {
rs := &OperationsService{s: s}
return rs
}
type OperationsService struct {
s *Service
}
func NewReadgroupsetsService(s *Service) *ReadgroupsetsService {
rs := &ReadgroupsetsService{s: s}
rs.Coveragebuckets = NewReadgroupsetsCoveragebucketsService(s)
return rs
}
type ReadgroupsetsService struct {
s *Service
Coveragebuckets *ReadgroupsetsCoveragebucketsService
}
func NewReadgroupsetsCoveragebucketsService(s *Service) *ReadgroupsetsCoveragebucketsService {
rs := &ReadgroupsetsCoveragebucketsService{s: s}
return rs
}
type ReadgroupsetsCoveragebucketsService struct {
s *Service
}
func NewReadsService(s *Service) *ReadsService {
rs := &ReadsService{s: s}
return rs
}
type ReadsService struct {
s *Service
}
func NewReferencesService(s *Service) *ReferencesService {
rs := &ReferencesService{s: s}
rs.Bases = NewReferencesBasesService(s)
return rs
}
type ReferencesService struct {
s *Service
Bases *ReferencesBasesService
}
func NewReferencesBasesService(s *Service) *ReferencesBasesService {
rs := &ReferencesBasesService{s: s}
return rs
}
type ReferencesBasesService struct {
s *Service
}
func NewReferencesetsService(s *Service) *ReferencesetsService {
rs := &ReferencesetsService{s: s}
return rs
}
type ReferencesetsService struct {
s *Service
}
func NewVariantsService(s *Service) *VariantsService {
rs := &VariantsService{s: s}
return rs
}
type VariantsService struct {
s *Service
}
func NewVariantsetsService(s *Service) *VariantsetsService {
rs := &VariantsetsService{s: s}
return rs
}
type VariantsetsService struct {
s *Service
}
// 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`.
type Annotation struct {
// AnnotationSetId: The annotation set to which this annotation belongs.
AnnotationSetId string `json:"annotationSetId,omitempty"`
// End: The end position of the range on the reference, 0-based
// exclusive.
End int64 `json:"end,omitempty,string"`
// Id: The server-generated annotation ID, unique across all
// annotations.
Id string `json:"id,omitempty"`
// Info: A map of additional read alignment information. This must be of
// the form
// map<string, string[]> (string key mapping to a list of string
// values).
Info map[string][]interface{} `json:"info,omitempty"`
// Name: The display name of this annotation.
Name string `json:"name,omitempty"`
// ReferenceId: The ID of the Google Genomics reference associated with
// this range.
ReferenceId string `json:"referenceId,omitempty"`
// ReferenceName: The display name corresponding to the reference
// specified by
// `referenceId`, for example `chr1`, `1`, or `chrX`.
ReferenceName string `json:"referenceName,omitempty"`
// ReverseStrand: Whether this range refers to the reverse strand, as
// opposed to the forward
// strand. Note that regardless of this field, the start/end position of
// the
// range always refer to the forward strand.
ReverseStrand bool `json:"reverseStrand,omitempty"`
// Start: The start position of the range on the reference, 0-based
// inclusive.
Start int64 `json:"start,omitempty,string"`
// Transcript: A transcript value represents the assertion that a
// particular region of
// the reference genome may be transcribed as RNA. An alternative
// splicing
// pattern would be represented as a separate transcript object. This
// field
// is only set for annotations of type `TRANSCRIPT`.
Transcript *Transcript `json:"transcript,omitempty"`
// Type: The data type for this annotation. Must match the containing
// annotation
// set's type.
//
// Possible values:
// "ANNOTATION_TYPE_UNSPECIFIED"
// "GENERIC" - A `GENERIC` annotation type should be used when no
// other annotation
// type will suffice. This represents an untyped annotation of the
// reference
// genome.
// "VARIANT" - A `VARIANT` annotation type.
// "GENE" - A `GENE` annotation type represents the existence of a
// gene at the
// associated reference coordinates. The start coordinate is typically
// the
// gene's transcription start site and the end is typically the end of
// the
// gene's last exon.
// "TRANSCRIPT" - A `TRANSCRIPT` annotation type represents the
// assertion that a
// particular region of the reference genome may be transcribed as RNA.
Type string `json:"type,omitempty"`
// Variant: A variant annotation, which describes the effect of a
// variant on the
// genome, the coding sequence, and/or higher level consequences at
// the
// organism level e.g. pathogenicity. This field is only set for
// annotations
// of type `VARIANT`.
Variant *VariantAnnotation `json:"variant,omitempty"`
// ServerResponse contains the HTTP response code and headers from the
// server.
googleapi.ServerResponse `json:"-"`
// ForceSendFields is a list of field names (e.g. "AnnotationSetId") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "AnnotationSetId") to
// include in API requests with the JSON null value. By default, fields
// with empty values are omitted from API requests. However, any field
// with an empty value appearing in NullFields will be sent to the
// server as null. It is an error if a field in this list has a
// non-empty value. This may be used to include null fields in Patch
// requests.
NullFields []string `json:"-"`
}
func (s *Annotation) MarshalJSON() ([]byte, error) {
type NoMethod Annotation
raw := NoMethod(*s)
return gensupport.MarshalJSON(raw, s.ForceSendFields, s.NullFields)
}
// 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'.
type AnnotationSet struct {
// DatasetId: The dataset to which this annotation set belongs.
DatasetId string `json:"datasetId,omitempty"`
// Id: The server-generated annotation set ID, unique across all
// annotation sets.
Id string `json:"id,omitempty"`
// Info: A map of additional read alignment information. This must be of
// the form
// map<string, string[]> (string key mapping to a list of string
// values).
Info map[string][]interface{} `json:"info,omitempty"`
// Name: The display name for this annotation set.
Name string `json:"name,omitempty"`
// ReferenceSetId: The ID of the reference set that defines the
// coordinate space for this
// set's annotations.
ReferenceSetId string `json:"referenceSetId,omitempty"`
// SourceUri: The source URI describing the file from which this
// annotation set was
// generated, if any.
SourceUri string `json:"sourceUri,omitempty"`
// Type: The type of annotations contained within this set.
//
// Possible values:
// "ANNOTATION_TYPE_UNSPECIFIED"
// "GENERIC" - A `GENERIC` annotation type should be used when no
// other annotation
// type will suffice. This represents an untyped annotation of the
// reference
// genome.
// "VARIANT" - A `VARIANT` annotation type.
// "GENE" - A `GENE` annotation type represents the existence of a
// gene at the
// associated reference coordinates. The start coordinate is typically
// the
// gene's transcription start site and the end is typically the end of
// the
// gene's last exon.
// "TRANSCRIPT" - A `TRANSCRIPT` annotation type represents the
// assertion that a
// particular region of the reference genome may be transcribed as RNA.
Type string `json:"type,omitempty"`
// ServerResponse contains the HTTP response code and headers from the
// server.
googleapi.ServerResponse `json:"-"`
// ForceSendFields is a list of field names (e.g. "DatasetId") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "DatasetId") to include in
// API requests with the JSON null value. By default, fields with empty
// values are omitted from API requests. However, any field with an
// empty value appearing in NullFields will be sent to the server as
// null. It is an error if a field in this list has a non-empty value.
// This may be used to include null fields in Patch requests.
NullFields []string `json:"-"`
}
func (s *AnnotationSet) MarshalJSON() ([]byte, error) {
type NoMethod AnnotationSet
raw := NoMethod(*s)
return gensupport.MarshalJSON(raw, s.ForceSendFields, s.NullFields)
}
type BatchCreateAnnotationsRequest struct {
// Annotations: The annotations to be created. At most 4096 can be
// specified in a single
// request.
Annotations []*Annotation `json:"annotations,omitempty"`
// RequestId: A unique request ID which enables the server to detect
// duplicated requests.
// If provided, duplicated requests will result in the same response; if
// not
// provided, duplicated requests may result in duplicated data. For a
// given
// annotation set, callers should not reuse `request_id`s when
// writing
// different batches of annotations - behavior in this case is
// undefined.
// A common approach is to use a UUID. For batch jobs where worker
// crashes are
// a possibility, consider using some unique variant of a worker or run
// ID.
RequestId string `json:"requestId,omitempty"`
// ForceSendFields is a list of field names (e.g. "Annotations") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "Annotations") to include
// in API requests with the JSON null value. By default, fields with
// empty values are omitted from API requests. However, any field with
// an empty value appearing in NullFields will be sent to the server as
// null. It is an error if a field in this list has a non-empty value.
// This may be used to include null fields in Patch requests.
NullFields []string `json:"-"`
}
func (s *BatchCreateAnnotationsRequest) MarshalJSON() ([]byte, error) {
type NoMethod BatchCreateAnnotationsRequest
raw := NoMethod(*s)
return gensupport.MarshalJSON(raw, s.ForceSendFields, s.NullFields)
}
type BatchCreateAnnotationsResponse struct {
// Entries: The resulting per-annotation entries, ordered consistently
// with the
// original request.
Entries []*Entry `json:"entries,omitempty"`
// ServerResponse contains the HTTP response code and headers from the
// server.
googleapi.ServerResponse `json:"-"`
// ForceSendFields is a list of field names (e.g. "Entries") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "Entries") to include in
// API requests with the JSON null value. By default, fields with empty
// values are omitted from API requests. However, any field with an
// empty value appearing in NullFields will be sent to the server as
// null. It is an error if a field in this list has a non-empty value.
// This may be used to include null fields in Patch requests.
NullFields []string `json:"-"`
}
func (s *BatchCreateAnnotationsResponse) MarshalJSON() ([]byte, error) {
type NoMethod BatchCreateAnnotationsResponse
raw := NoMethod(*s)
return gensupport.MarshalJSON(raw, s.ForceSendFields, s.NullFields)
}
// Binding: Associates `members` with a `role`.
type Binding struct {
// Condition: Unimplemented. The condition that is associated with this
// binding.
// NOTE: an unsatisfied condition will not allow user access via
// current
// binding. Different bindings, including their conditions, are
// examined
// independently.
Condition *Expr `json:"condition,omitempty"`
// Members: Specifies the identities requesting access for a Cloud
// Platform resource.
// `members` can have the following values:
//
// * `allUsers`: A special identifier that represents anyone who is
// on the internet; with or without a Google account.
//
// * `allAuthenticatedUsers`: A special identifier that represents
// anyone
// who is authenticated with a Google account or a service
// account.
//
// * `user:{emailid}`: An email address that represents a specific
// Google
// account. For example, `alice@gmail.com` .
//
//
// * `serviceAccount:{emailid}`: An email address that represents a
// service
// account. For example,
// `my-other-app@appspot.gserviceaccount.com`.
//
// * `group:{emailid}`: An email address that represents a Google
// group.
// For example, `admins@example.com`.
//
//
// * `domain:{domain}`: A Google Apps domain name that represents all
// the
// users of that domain. For example, `google.com` or
// `example.com`.
//
//
Members []string `json:"members,omitempty"`
// Role: Role that is assigned to `members`.
// For example, `roles/viewer`, `roles/editor`, or `roles/owner`.
Role string `json:"role,omitempty"`
// ForceSendFields is a list of field names (e.g. "Condition") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "Condition") to include in
// API requests with the JSON null value. By default, fields with empty
// values are omitted from API requests. However, any field with an
// empty value appearing in NullFields will be sent to the server as
// null. It is an error if a field in this list has a non-empty value.
// This may be used to include null fields in Patch requests.
NullFields []string `json:"-"`
}
func (s *Binding) MarshalJSON() ([]byte, error) {
type NoMethod Binding
raw := NoMethod(*s)
return gensupport.MarshalJSON(raw, s.ForceSendFields, s.NullFields)
}
// CallSet: A call set is a collection of variant calls, typically for
// one sample. It
// belongs to a variant set.
type CallSet struct {
// Created: The date this call set was created in milliseconds from the
// epoch.
Created int64 `json:"created,omitempty,string"`
// Id: The server-generated call set ID, unique across all call sets.
Id string `json:"id,omitempty"`
// Info: A map of additional call set information. This must be of the
// form
// map<string, string[]> (string key mapping to a list of string
// values).
Info map[string][]interface{} `json:"info,omitempty"`
// Name: The call set name.
Name string `json:"name,omitempty"`
// SampleId: The sample ID this call set corresponds to.
SampleId string `json:"sampleId,omitempty"`
// VariantSetIds: The IDs of the variant sets this call set belongs to.
// This field must
// have exactly length one, as a call set belongs to a single variant
// set.
// This field is repeated for compatibility with the
// [GA4GH
// 0.5.1
// API](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resou
// rces/avro/variants.avdl#L76).
VariantSetIds []string `json:"variantSetIds,omitempty"`
// ServerResponse contains the HTTP response code and headers from the
// server.
googleapi.ServerResponse `json:"-"`
// ForceSendFields is a list of field names (e.g. "Created") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "Created") to include in
// API requests with the JSON null value. By default, fields with empty
// values are omitted from API requests. However, any field with an
// empty value appearing in NullFields will be sent to the server as
// null. It is an error if a field in this list has a non-empty value.
// This may be used to include null fields in Patch requests.
NullFields []string `json:"-"`
}
func (s *CallSet) MarshalJSON() ([]byte, error) {
type NoMethod CallSet
raw := NoMethod(*s)
return gensupport.MarshalJSON(raw, s.ForceSendFields, s.NullFields)
}
// CancelOperationRequest: The request message for
// Operations.CancelOperation.
type CancelOperationRequest struct {
}
// CigarUnit: A single CIGAR operation.
type CigarUnit struct {
// Possible values:
// "OPERATION_UNSPECIFIED"
// "ALIGNMENT_MATCH" - An alignment match indicates that a sequence
// can be aligned to the
// reference without evidence of an INDEL. Unlike the
// `SEQUENCE_MATCH` and `SEQUENCE_MISMATCH` operators,
// the `ALIGNMENT_MATCH` operator does not indicate whether
// the
// reference and read sequences are an exact match. This operator
// is
// equivalent to SAM's `M`.
// "INSERT" - The insert operator indicates that the read contains
// evidence of bases
// being inserted into the reference. This operator is equivalent to
// SAM's
// `I`.
// "DELETE" - The delete operator indicates that the read contains
// evidence of bases
// being deleted from the reference. This operator is equivalent to
// SAM's
// `D`.
// "SKIP" - The skip operator indicates that this read skips a long
// segment of the
// reference, but the bases have not been deleted. This operator is
// commonly
// used when working with RNA-seq data, where reads may skip long
// segments
// of the reference between exons. This operator is equivalent to
// SAM's
// `N`.
// "CLIP_SOFT" - The soft clip operator indicates that bases at the
// start/end of a read
// have not been considered during alignment. This may occur if the
// majority
// of a read maps, except for low quality bases at the start/end of a
// read.
// This operator is equivalent to SAM's `S`. Bases that are soft
// clipped will still be stored in the read.
// "CLIP_HARD" - The hard clip operator indicates that bases at the
// start/end of a read
// have been omitted from this alignment. This may occur if this
// linear
// alignment is part of a chimeric alignment, or if the read has
// been
// trimmed (for example, during error correction or to trim poly-A tails
// for
// RNA-seq). This operator is equivalent to SAM's `H`.
// "PAD" - The pad operator indicates that there is padding in an
// alignment. This
// operator is equivalent to SAM's `P`.
// "SEQUENCE_MATCH" - This operator indicates that this portion of the
// aligned sequence exactly
// matches the reference. This operator is equivalent to SAM's `=`.
// "SEQUENCE_MISMATCH" - This operator indicates that this portion of
// the aligned sequence is an
// alignment match to the reference, but a sequence mismatch. This
// can
// indicate a SNP or a read error. This operator is equivalent to
// SAM's
// `X`.
Operation string `json:"operation,omitempty"`
// OperationLength: The number of genomic bases that the operation runs
// for. Required.
OperationLength int64 `json:"operationLength,omitempty,string"`
// ReferenceSequence: `referenceSequence` is only used at
// mismatches
// (`SEQUENCE_MISMATCH`) and deletions (`DELETE`).
// Filling this field replaces SAM's MD tag. If the relevant information
// is
// not available, this field is unset.
ReferenceSequence string `json:"referenceSequence,omitempty"`
// ForceSendFields is a list of field names (e.g. "Operation") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "Operation") to include in
// API requests with the JSON null value. By default, fields with empty
// values are omitted from API requests. However, any field with an
// empty value appearing in NullFields will be sent to the server as
// null. It is an error if a field in this list has a non-empty value.
// This may be used to include null fields in Patch requests.
NullFields []string `json:"-"`
}
func (s *CigarUnit) MarshalJSON() ([]byte, error) {
type NoMethod CigarUnit
raw := NoMethod(*s)
return gensupport.MarshalJSON(raw, s.ForceSendFields, s.NullFields)
}
type ClinicalCondition struct {
// ConceptId: The MedGen concept id associated with this gene.
// Search for these IDs at http://www.ncbi.nlm.nih.gov/medgen/
ConceptId string `json:"conceptId,omitempty"`
// ExternalIds: The set of external IDs for this condition.
ExternalIds []*ExternalId `json:"externalIds,omitempty"`
// Names: A set of names for the condition.
Names []string `json:"names,omitempty"`
// OmimId: The OMIM id for this condition.
// Search for these IDs at http://omim.org/
OmimId string `json:"omimId,omitempty"`
// ForceSendFields is a list of field names (e.g. "ConceptId") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "ConceptId") to include in
// API requests with the JSON null value. By default, fields with empty
// values are omitted from API requests. However, any field with an
// empty value appearing in NullFields will be sent to the server as
// null. It is an error if a field in this list has a non-empty value.
// This may be used to include null fields in Patch requests.
NullFields []string `json:"-"`
}
func (s *ClinicalCondition) MarshalJSON() ([]byte, error) {
type NoMethod ClinicalCondition
raw := NoMethod(*s)
return gensupport.MarshalJSON(raw, s.ForceSendFields, s.NullFields)
}
type CodingSequence struct {
// End: The end of the coding sequence on this annotation's reference
// sequence,
// 0-based exclusive. Note that this position is relative to the
// reference
// start, and *not* the containing annotation start.
End int64 `json:"end,omitempty,string"`
// Start: The start of the coding sequence on this annotation's
// reference sequence,
// 0-based inclusive. Note that this position is relative to the
// reference
// start, and *not* the containing annotation start.
Start int64 `json:"start,omitempty,string"`
// ForceSendFields is a list of field names (e.g. "End") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "End") to include in API
// requests with the JSON null value. By default, fields with empty
// values are omitted from API requests. However, any field with an
// empty value appearing in NullFields will be sent to the server as
// null. It is an error if a field in this list has a non-empty value.
// This may be used to include null fields in Patch requests.
NullFields []string `json:"-"`
}
func (s *CodingSequence) MarshalJSON() ([]byte, error) {
type NoMethod CodingSequence
raw := NoMethod(*s)
return gensupport.MarshalJSON(raw, s.ForceSendFields, s.NullFields)
}
// ComputeEngine: Describes a Compute Engine resource that is being
// managed by a running
// pipeline.
type ComputeEngine struct {
// DiskNames: The names of the disks that were created for this
// pipeline.
DiskNames []string `json:"diskNames,omitempty"`
// InstanceName: The instance on which the operation is running.
InstanceName string `json:"instanceName,omitempty"`
// MachineType: The machine type of the instance.
MachineType string `json:"machineType,omitempty"`
// Zone: The availability zone in which the instance resides.
Zone string `json:"zone,omitempty"`
// ForceSendFields is a list of field names (e.g. "DiskNames") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "DiskNames") to include in
// API requests with the JSON null value. By default, fields with empty
// values are omitted from API requests. However, any field with an
// empty value appearing in NullFields will be sent to the server as
// null. It is an error if a field in this list has a non-empty value.
// This may be used to include null fields in Patch requests.
NullFields []string `json:"-"`
}
func (s *ComputeEngine) MarshalJSON() ([]byte, error) {
type NoMethod ComputeEngine
raw := NoMethod(*s)
return gensupport.MarshalJSON(raw, s.ForceSendFields, s.NullFields)
}
// ContainerKilledEvent: An event generated when a container is forcibly
// terminated by the
// worker. Currently, this only occurs when the container outlives
// the
// timeout specified by the user.
type ContainerKilledEvent struct {
// ActionId: The numeric ID of the action that started the container.
ActionId int64 `json:"actionId,omitempty"`
// ForceSendFields is a list of field names (e.g. "ActionId") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "ActionId") to include in
// API requests with the JSON null value. By default, fields with empty
// values are omitted from API requests. However, any field with an
// empty value appearing in NullFields will be sent to the server as
// null. It is an error if a field in this list has a non-empty value.
// This may be used to include null fields in Patch requests.
NullFields []string `json:"-"`
}
func (s *ContainerKilledEvent) MarshalJSON() ([]byte, error) {
type NoMethod ContainerKilledEvent
raw := NoMethod(*s)
return gensupport.MarshalJSON(raw, s.ForceSendFields, s.NullFields)
}
// ContainerStartedEvent: An event generated when a container starts.
type ContainerStartedEvent struct {
// ActionId: The numeric ID of the action that started this container.
ActionId int64 `json:"actionId,omitempty"`
// IpAddress: The public IP address that can be used to connect to the
// container. This
// field is only populated when at least one port mapping is present. If
// the
// instance was created with a private address, this field will be empty
// even
// if port mappings exist.
IpAddress string `json:"ipAddress,omitempty"`
// PortMappings: The container-to-host port mappings installed for this
// container. This
// set will contain any ports exposed using the `PUBLISH_EXPOSED_PORTS`
// flag
// as well as any specified in the `Action` definition.
PortMappings map[string]int64 `json:"portMappings,omitempty"`
// ForceSendFields is a list of field names (e.g. "ActionId") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "ActionId") to include in
// API requests with the JSON null value. By default, fields with empty
// values are omitted from API requests. However, any field with an
// empty value appearing in NullFields will be sent to the server as
// null. It is an error if a field in this list has a non-empty value.
// This may be used to include null fields in Patch requests.
NullFields []string `json:"-"`
}
func (s *ContainerStartedEvent) MarshalJSON() ([]byte, error) {
type NoMethod ContainerStartedEvent
raw := NoMethod(*s)
return gensupport.MarshalJSON(raw, s.ForceSendFields, s.NullFields)
}
// ContainerStoppedEvent: An event generated when a container exits.
type ContainerStoppedEvent struct {
// ActionId: The numeric ID of the action that started this container.
ActionId int64 `json:"actionId,omitempty"`
// ExitStatus: The exit status of the container.
ExitStatus int64 `json:"exitStatus,omitempty"`
// Stderr: The tail end of any content written to standard error by the
// container.
// If the content emits large amounts of debugging noise or
// contains
// sensitive information, you can prevent the content from being printed
// by
// setting the `DISABLE_STANDARD_ERROR_CAPTURE` flag.
//
// Note that only a small amount of the end of the stream is captured
// here.
// The entire stream is stored in the `/google/logs` directory mounted
// into
// each action, and can be copied off the machine as described
// elsewhere.
Stderr string `json:"stderr,omitempty"`
// ForceSendFields is a list of field names (e.g. "ActionId") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "ActionId") to include in
// API requests with the JSON null value. By default, fields with empty
// values are omitted from API requests. However, any field with an
// empty value appearing in NullFields will be sent to the server as
// null. It is an error if a field in this list has a non-empty value.
// This may be used to include null fields in Patch requests.
NullFields []string `json:"-"`
}
func (s *ContainerStoppedEvent) MarshalJSON() ([]byte, error) {
type NoMethod ContainerStoppedEvent
raw := NoMethod(*s)
return gensupport.MarshalJSON(raw, s.ForceSendFields, s.NullFields)
}
// CoverageBucket: A bucket over which read coverage has been
// precomputed. A bucket corresponds
// to a specific range of the reference sequence.
type CoverageBucket struct {
// MeanCoverage: The average number of reads which are aligned to each
// individual
// reference base in this bucket.
MeanCoverage float64 `json:"meanCoverage,omitempty"`
// Range: The genomic coordinate range spanned by this bucket.
Range *Range `json:"range,omitempty"`
// ForceSendFields is a list of field names (e.g. "MeanCoverage") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "MeanCoverage") to include
// in API requests with the JSON null value. By default, fields with
// empty values are omitted from API requests. However, any field with
// an empty value appearing in NullFields will be sent to the server as
// null. It is an error if a field in this list has a non-empty value.
// This may be used to include null fields in Patch requests.
NullFields []string `json:"-"`
}
func (s *CoverageBucket) MarshalJSON() ([]byte, error) {
type NoMethod CoverageBucket
raw := NoMethod(*s)
return gensupport.MarshalJSON(raw, s.ForceSendFields, s.NullFields)
}
func (s *CoverageBucket) UnmarshalJSON(data []byte) error {
type NoMethod CoverageBucket
var s1 struct {
MeanCoverage gensupport.JSONFloat64 `json:"meanCoverage"`
*NoMethod
}
s1.NoMethod = (*NoMethod)(s)
if err := json.Unmarshal(data, &s1); err != nil {
return err
}
s.MeanCoverage = float64(s1.MeanCoverage)
return nil
}
// Dataset: A Dataset is a collection of genomic data.
type Dataset struct {
// CreateTime: The time this dataset was created, in seconds from the
// epoch.
CreateTime string `json:"createTime,omitempty"`
// Id: The server-generated dataset ID, unique across all datasets.
Id string `json:"id,omitempty"`
// Name: The dataset name.
Name string `json:"name,omitempty"`
// ProjectId: The Google Cloud project ID that this dataset belongs to.
ProjectId string `json:"projectId,omitempty"`
// ServerResponse contains the HTTP response code and headers from the
// server.
googleapi.ServerResponse `json:"-"`
// ForceSendFields is a list of field names (e.g. "CreateTime") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "CreateTime") to include in
// API requests with the JSON null value. By default, fields with empty
// values are omitted from API requests. However, any field with an
// empty value appearing in NullFields will be sent to the server as
// null. It is an error if a field in this list has a non-empty value.
// This may be used to include null fields in Patch requests.
NullFields []string `json:"-"`
}
func (s *Dataset) MarshalJSON() ([]byte, error) {
type NoMethod Dataset
raw := NoMethod(*s)
return gensupport.MarshalJSON(raw, s.ForceSendFields, s.NullFields)
}
// DelayedEvent: An event generated whenever a resource limitation or
// transient error
// delays execution of a pipeline that was otherwise ready to run.
type DelayedEvent struct {
// Cause: A textual description of the cause of the delay. The string
// can change
// without notice because it is often generated by another service (such
// as
// Compute Engine).
Cause string `json:"cause,omitempty"`
// Metrics: If the delay was caused by a resource shortage, this field
// lists the
// Compute Engine metrics that are preventing this operation from
// running
// (for example, `CPUS` or `INSTANCES`). If the particular metric is
// not
// known, a single `UNKNOWN` metric will be present.
Metrics []string `json:"metrics,omitempty"`
// ForceSendFields is a list of field names (e.g. "Cause") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "Cause") to include in API
// requests with the JSON null value. By default, fields with empty
// values are omitted from API requests. However, any field with an
// empty value appearing in NullFields will be sent to the server as
// null. It is an error if a field in this list has a non-empty value.
// This may be used to include null fields in Patch requests.
NullFields []string `json:"-"`
}
func (s *DelayedEvent) MarshalJSON() ([]byte, error) {
type NoMethod DelayedEvent
raw := NoMethod(*s)
return gensupport.MarshalJSON(raw, s.ForceSendFields, s.NullFields)
}
// 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 `{}`.
type Empty struct {
// ServerResponse contains the HTTP response code and headers from the
// server.
googleapi.ServerResponse `json:"-"`
}
type Entry struct {
// Annotation: The created annotation, if creation was successful.
Annotation *Annotation `json:"annotation,omitempty"`
// Status: The creation status.
Status *Status `json:"status,omitempty"`
// ForceSendFields is a list of field names (e.g. "Annotation") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "Annotation") to include in
// API requests with the JSON null value. By default, fields with empty
// values are omitted from API requests. However, any field with an
// empty value appearing in NullFields will be sent to the server as
// null. It is an error if a field in this list has a non-empty value.
// This may be used to include null fields in Patch requests.
NullFields []string `json:"-"`
}
func (s *Entry) MarshalJSON() ([]byte, error) {
type NoMethod Entry
raw := NoMethod(*s)
return gensupport.MarshalJSON(raw, s.ForceSendFields, s.NullFields)
}
// Event: Carries information about events that occur during pipeline
// execution.
type Event struct {
// Description: A human-readable description of the event. Note that
// these strings can
// change at any time without notice. Any application logic must use
// the
// information in the `details` field.
Description string `json:"description,omitempty"`
// Details: Machine-readable details about the event.
Details googleapi.RawMessage `json:"details,omitempty"`
// Timestamp: The time at which the event occurred.
Timestamp string `json:"timestamp,omitempty"`
// ForceSendFields is a list of field names (e.g. "Description") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "Description") to include
// in API requests with the JSON null value. By default, fields with
// empty values are omitted from API requests. However, any field with
// an empty value appearing in NullFields will be sent to the server as
// null. It is an error if a field in this list has a non-empty value.
// This may be used to include null fields in Patch requests.
NullFields []string `json:"-"`
}
func (s *Event) MarshalJSON() ([]byte, error) {
type NoMethod Event
raw := NoMethod(*s)
return gensupport.MarshalJSON(raw, s.ForceSendFields, s.NullFields)
}
type Exon struct {
// End: The end position of the exon on this annotation's reference
// sequence,
// 0-based exclusive. Note that this is relative to the reference start,
// and
// *not* the containing annotation start.
End int64 `json:"end,omitempty,string"`
// Frame: The frame of this exon. Contains a value of 0, 1, or 2, which
// indicates
// the offset of the first coding base of the exon within the reading
// frame
// of the coding DNA sequence, if any. This field is dependent on
// the
// strandedness of this annotation (see
// Annotation.reverse_strand).
// For forward stranded annotations, this offset is relative to
// the
// exon.start. For reverse
// strand annotations, this offset is relative to the
// exon.end `- 1`.
//
// Unset if this exon does not intersect the coding sequence. Upon
// creation
// of a transcript, the frame must be populated for all or none of
// the
// coding exons.
Frame int64 `json:"frame,omitempty"`
// Start: The start position of the exon on this annotation's reference
// sequence,
// 0-based inclusive. Note that this is relative to the reference start,
// and
// **not** the containing annotation start.
Start int64 `json:"start,omitempty,string"`
// ForceSendFields is a list of field names (e.g. "End") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "End") to include in API
// requests with the JSON null value. By default, fields with empty
// values are omitted from API requests. However, any field with an
// empty value appearing in NullFields will be sent to the server as
// null. It is an error if a field in this list has a non-empty value.
// This may be used to include null fields in Patch requests.
NullFields []string `json:"-"`
}
func (s *Exon) MarshalJSON() ([]byte, error) {
type NoMethod Exon
raw := NoMethod(*s)
return gensupport.MarshalJSON(raw, s.ForceSendFields, s.NullFields)
}
type Experiment struct {
// InstrumentModel: The instrument model used as part of this
// experiment. This maps to
// sequencing technology in the SAM spec.
InstrumentModel string `json:"instrumentModel,omitempty"`
// LibraryId: A client-supplied library identifier; a library is a
// collection of DNA
// fragments which have been prepared for sequencing from a sample.
// This
// field is important for quality control as error or bias can be
// introduced
// during sample preparation.
LibraryId string `json:"libraryId,omitempty"`
// PlatformUnit: The platform unit used as part of this experiment, for
// example
// flowcell-barcode.lane for Illumina or slide for SOLiD. Corresponds to
// the
// @RG PU field in the SAM spec.
PlatformUnit string `json:"platformUnit,omitempty"`
// SequencingCenter: The sequencing center used as part of this
// experiment.
SequencingCenter string `json:"sequencingCenter,omitempty"`
// ForceSendFields is a list of field names (e.g. "InstrumentModel") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "InstrumentModel") to
// include in API requests with the JSON null value. By default, fields
// with empty values are omitted from API requests. However, any field
// with an empty value appearing in NullFields will be sent to the
// server as null. It is an error if a field in this list has a
// non-empty value. This may be used to include null fields in Patch
// requests.
NullFields []string `json:"-"`
}
func (s *Experiment) MarshalJSON() ([]byte, error) {
type NoMethod Experiment
raw := NoMethod(*s)
return gensupport.MarshalJSON(raw, s.ForceSendFields, s.NullFields)
}
// ExportReadGroupSetRequest: The read group set export request.
type ExportReadGroupSetRequest struct {
// ExportUri: Required. A Google Cloud Storage URI for the exported BAM
// file.
// The currently authenticated user must have write access to the new
// file.
// An error will be returned if the URI already contains data.
ExportUri string `json:"exportUri,omitempty"`
// ProjectId: Required. The Google Cloud project ID that owns
// this
// export. The caller must have WRITE access to this project.
ProjectId string `json:"projectId,omitempty"`
// ReferenceNames: The reference names to export. If this is not
// specified, all reference
// sequences, including unmapped reads, are exported.
// Use `*` to export only unmapped reads.
ReferenceNames []string `json:"referenceNames,omitempty"`
// ForceSendFields is a list of field names (e.g. "ExportUri") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "ExportUri") to include in
// API requests with the JSON null value. By default, fields with empty
// values are omitted from API requests. However, any field with an
// empty value appearing in NullFields will be sent to the server as
// null. It is an error if a field in this list has a non-empty value.
// This may be used to include null fields in Patch requests.
NullFields []string `json:"-"`
}
func (s *ExportReadGroupSetRequest) MarshalJSON() ([]byte, error) {
type NoMethod ExportReadGroupSetRequest
raw := NoMethod(*s)
return gensupport.MarshalJSON(raw, s.ForceSendFields, s.NullFields)
}
// ExportVariantSetRequest: The variant data export request.
type ExportVariantSetRequest struct {
// BigqueryDataset: Required. The BigQuery dataset to export data to.
// This dataset must already
// exist. Note that this is distinct from the Genomics concept of
// "dataset".
BigqueryDataset string `json:"bigqueryDataset,omitempty"`
// BigqueryTable: Required. The BigQuery table to export data to.
// If the table doesn't exist, it will be created. If it already exists,
// it
// will be overwritten.
BigqueryTable string `json:"bigqueryTable,omitempty"`
// CallSetIds: If provided, only variant call information from the
// specified call sets
// will be exported. By default all variant calls are exported.
CallSetIds []string `json:"callSetIds,omitempty"`
// Format: The format for the exported data.
//
// Possible values:
// "FORMAT_UNSPECIFIED"
// "FORMAT_BIGQUERY" - Export the data to Google BigQuery.
Format string `json:"format,omitempty"`
// ProjectId: Required. The Google Cloud project ID that owns the
// destination
// BigQuery dataset. The caller must have WRITE access to this project.
// This
// project will also own the resulting export job.
ProjectId string `json:"projectId,omitempty"`
// ForceSendFields is a list of field names (e.g. "BigqueryDataset") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "BigqueryDataset") to
// include in API requests with the JSON null value. By default, fields
// with empty values are omitted from API requests. However, any field
// with an empty value appearing in NullFields will be sent to the
// server as null. It is an error if a field in this list has a
// non-empty value. This may be used to include null fields in Patch
// requests.
NullFields []string `json:"-"`
}
func (s *ExportVariantSetRequest) MarshalJSON() ([]byte, error) {
type NoMethod ExportVariantSetRequest
raw := NoMethod(*s)
return gensupport.MarshalJSON(raw, s.ForceSendFields, s.NullFields)
}
// Expr: Represents an expression text. Example:
//
// title: "User account presence"
// description: "Determines whether the request has a user account"
// expression: "size(request.user) > 0"
type Expr struct {
// Description: An optional description of the expression. This is a
// longer text which
// describes the expression, e.g. when hovered over it in a UI.
Description string `json:"description,omitempty"`
// Expression: Textual representation of an expression in
// Common Expression Language syntax.
//
// The application context of the containing message determines
// which
// well-known feature set of CEL is supported.
Expression string `json:"expression,omitempty"`
// Location: An optional string indicating the location of the
// expression for error
// reporting, e.g. a file name and a position in the file.
Location string `json:"location,omitempty"`
// Title: An optional title for the expression, i.e. a short string
// describing
// its purpose. This can be used e.g. in UIs which allow to enter
// the
// expression.
Title string `json:"title,omitempty"`
// ForceSendFields is a list of field names (e.g. "Description") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "Description") to include
// in API requests with the JSON null value. By default, fields with
// empty values are omitted from API requests. However, any field with
// an empty value appearing in NullFields will be sent to the server as
// null. It is an error if a field in this list has a non-empty value.
// This may be used to include null fields in Patch requests.
NullFields []string `json:"-"`
}
func (s *Expr) MarshalJSON() ([]byte, error) {
type NoMethod Expr
raw := NoMethod(*s)
return gensupport.MarshalJSON(raw, s.ForceSendFields, s.NullFields)
}
type ExternalId struct {
// Id: The id used by the source of this data.
Id string `json:"id,omitempty"`
// SourceName: The name of the source of this data.
SourceName string `json:"sourceName,omitempty"`
// ForceSendFields is a list of field names (e.g. "Id") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "Id") to include in API
// requests with the JSON null value. By default, fields with empty
// values are omitted from API requests. However, any field with an
// empty value appearing in NullFields will be sent to the server as
// null. It is an error if a field in this list has a non-empty value.
// This may be used to include null fields in Patch requests.
NullFields []string `json:"-"`
}
func (s *ExternalId) MarshalJSON() ([]byte, error) {
type NoMethod ExternalId
raw := NoMethod(*s)
return gensupport.MarshalJSON(raw, s.ForceSendFields, s.NullFields)
}
// FailedEvent: An event generated when the execution of a pipeline has
// failed. Note
// that other events can continue to occur after this event.
type FailedEvent struct {
// Cause: The human-readable description of the cause of the failure.
Cause string `json:"cause,omitempty"`
// Code: The Google standard error code that best describes this
// failure.
//
// Possible values:
// "OK" - Not an error; returned on success
//
// HTTP Mapping: 200 OK
// "CANCELLED" - The operation was cancelled, typically by the
// caller.
//
// HTTP Mapping: 499 Client Closed Request
// "UNKNOWN" - Unknown error. For example, this error may be returned
// when
// a `Status` value received from another address space belongs to
// an error space that is not known in this address space. Also
// errors raised by APIs that do not return enough error information
// may be converted to this error.
//
// HTTP Mapping: 500 Internal Server Error
// "INVALID_ARGUMENT" - The client specified an invalid argument.
// Note that this differs
// from `FAILED_PRECONDITION`. `INVALID_ARGUMENT` indicates
// arguments
// that are problematic regardless of the state of the system
// (e.g., a malformed file name).
//
// HTTP Mapping: 400 Bad Request
// "DEADLINE_EXCEEDED" - The deadline expired before the operation
// could complete. For operations
// that change the state of the system, this error may be returned
// even if the operation has completed successfully. For example,
// a
// successful response from a server could have been delayed long
// enough for the deadline to expire.
//
// HTTP Mapping: 504 Gateway Timeout
// "NOT_FOUND" - Some requested entity (e.g., file or directory) was
// not found.
//
// Note to server developers: if a request is denied for an entire
// class
// of users, such as gradual feature rollout or undocumented
// whitelist,
// `NOT_FOUND` may be used. If a request is denied for some users
// within
// a class of users, such as user-based access control,
// `PERMISSION_DENIED`
// must be used.
//
// HTTP Mapping: 404 Not Found
// "ALREADY_EXISTS" - The entity that a client attempted to create
// (e.g., file or directory)
// already exists.
//
// HTTP Mapping: 409 Conflict
// "PERMISSION_DENIED" - The caller does not have permission to
// execute the specified
// operation. `PERMISSION_DENIED` must not be used for rejections
// caused by exhausting some resource (use `RESOURCE_EXHAUSTED`
// instead for those errors). `PERMISSION_DENIED` must not be
// used if the caller can not be identified (use
// `UNAUTHENTICATED`
// instead for those errors). This error code does not imply the
// request is valid or the requested entity exists or satisfies
// other pre-conditions.
//
// HTTP Mapping: 403 Forbidden
// "UNAUTHENTICATED" - The request does not have valid authentication
// credentials for the
// operation.
//
// HTTP Mapping: 401 Unauthorized
// "RESOURCE_EXHAUSTED" - Some resource has been exhausted, perhaps a
// per-user quota, or
// perhaps the entire file system is out of space.
//
// HTTP Mapping: 429 Too Many Requests
// "FAILED_PRECONDITION" - The operation was rejected because the
// system is not in a state
// required for the operation's execution. For example, the
// directory
// to be deleted is non-empty, an rmdir operation is applied to
// a non-directory, etc.
//
// Service implementors can use the following guidelines to
// decide
// between `FAILED_PRECONDITION`, `ABORTED`, and `UNAVAILABLE`:
// (a) Use `UNAVAILABLE` if the client can retry just the failing
// call.
// (b) Use `ABORTED` if the client should retry at a higher level
// (e.g., when a client-specified test-and-set fails, indicating
// the
// client should restart a read-modify-write sequence).
// (c) Use `FAILED_PRECONDITION` if the client should not retry until
// the system state has been explicitly fixed. E.g., if an
// "rmdir"
// fails because the directory is non-empty, `FAILED_PRECONDITION`
// should be returned since the client should not retry unless
// the files are deleted from the directory.
//
// HTTP Mapping: 400 Bad Request
// "ABORTED" - The operation was aborted, typically due to a
// concurrency issue such as
// a sequencer check failure or transaction abort.
//
// See the guidelines above for deciding between
// `FAILED_PRECONDITION`,
// `ABORTED`, and `UNAVAILABLE`.
//
// HTTP Mapping: 409 Conflict
// "OUT_OF_RANGE" - The operation was attempted past the valid range.
// E.g., seeking or
// reading past end-of-file.
//
// Unlike `INVALID_ARGUMENT`, this error indicates a problem that may
// be fixed if the system state changes. For example, a 32-bit
// file
// system will generate `INVALID_ARGUMENT` if asked to read at an
// offset that is not in the range [0,2^32-1], but it will
// generate
// `OUT_OF_RANGE` if asked to read from an offset past the current
// file size.
//
// There is a fair bit of overlap between `FAILED_PRECONDITION`
// and
// `OUT_OF_RANGE`. We recommend using `OUT_OF_RANGE` (the more
// specific
// error) when it applies so that callers who are iterating through
// a space can easily look for an `OUT_OF_RANGE` error to detect
// when
// they are done.
//
// HTTP Mapping: 400 Bad Request
// "UNIMPLEMENTED" - The operation is not implemented or is not
// supported/enabled in this
// service.
//
// HTTP Mapping: 501 Not Implemented
// "INTERNAL" - Internal errors. This means that some invariants
// expected by the
// underlying system have been broken. This error code is reserved
// for serious errors.
//
// HTTP Mapping: 500 Internal Server Error
// "UNAVAILABLE" - The service is currently unavailable. This is most
// likely a
// transient condition, which can be corrected by retrying with
// a backoff.
//
// See the guidelines above for deciding between
// `FAILED_PRECONDITION`,
// `ABORTED`, and `UNAVAILABLE`.
//
// HTTP Mapping: 503 Service Unavailable
// "DATA_LOSS" - Unrecoverable data loss or corruption.
//
// HTTP Mapping: 500 Internal Server Error
Code string `json:"code,omitempty"`
// ForceSendFields is a list of field names (e.g. "Cause") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "Cause") to include in API
// requests with the JSON null value. By default, fields with empty
// values are omitted from API requests. However, any field with an
// empty value appearing in NullFields will be sent to the server as
// null. It is an error if a field in this list has a non-empty value.
// This may be used to include null fields in Patch requests.
NullFields []string `json:"-"`
}
func (s *FailedEvent) MarshalJSON() ([]byte, error) {
type NoMethod FailedEvent
raw := NoMethod(*s)
return gensupport.MarshalJSON(raw, s.ForceSendFields, s.NullFields)
}
// GetIamPolicyRequest: Request message for `GetIamPolicy` method.
type GetIamPolicyRequest struct {
}
// ImportReadGroupSetsRequest: The read group set import request.
type ImportReadGroupSetsRequest struct {
// DatasetId: Required. The ID of the dataset these read group sets will
// belong to. The
// caller must have WRITE permissions to this dataset.
DatasetId string `json:"datasetId,omitempty"`
// PartitionStrategy: The partition strategy describes how read groups
// are partitioned into read
// group sets.
//
// Possible values:
// "PARTITION_STRATEGY_UNSPECIFIED"
// "PER_FILE_PER_SAMPLE" - In most cases, this strategy yields one
// read group set per file. This is
// the default behavior.
//
// Allocate one read group set per file per sample. For BAM files,
// read
// groups are considered to share a sample if they have identical
// sample
// names. Furthermore, all reads for each file which do not belong to a
// read
// group, if any, will be grouped into a single read group set per-file.
// "MERGE_ALL" - Includes all read groups in all imported files into a
// single read group
// set. Requires that the headers for all imported files are equivalent.
// All
// reads which do not belong to a read group, if any, will be grouped
// into a
// separate read group set.
PartitionStrategy string `json:"partitionStrategy,omitempty"`
// ReferenceSetId: The reference set to which the imported read group
// sets are aligned to, if
// any. The reference names of this reference set must be a superset of
// those
// found in the imported file headers. If no reference set id is
// provided, a
// best effort is made to associate with a matching reference set.
ReferenceSetId string `json:"referenceSetId,omitempty"`
// SourceUris: A list of URIs pointing at
// [BAM
// files](https://samtools.github.io/hts-specs/SAMv1.pdf)
// in Google Cloud Storage.
// Those URIs can include wildcards (*), but do not add or
// remove
// matching files before import has completed.
//
// Note that Google Cloud Storage object listing is only
// eventually
// consistent: files added may be not be immediately visible
// to
// everyone. Thus, if using a wildcard it is preferable not to start
// the import immediately after the files are created.
SourceUris []string `json:"sourceUris,omitempty"`
// ForceSendFields is a list of field names (e.g. "DatasetId") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "DatasetId") to include in
// API requests with the JSON null value. By default, fields with empty
// values are omitted from API requests. However, any field with an
// empty value appearing in NullFields will be sent to the server as
// null. It is an error if a field in this list has a non-empty value.
// This may be used to include null fields in Patch requests.
NullFields []string `json:"-"`
}
func (s *ImportReadGroupSetsRequest) MarshalJSON() ([]byte, error) {
type NoMethod ImportReadGroupSetsRequest
raw := NoMethod(*s)
return gensupport.MarshalJSON(raw, s.ForceSendFields, s.NullFields)
}
// ImportReadGroupSetsResponse: The read group set import response.
type ImportReadGroupSetsResponse struct {
// ReadGroupSetIds: IDs of the read group sets that were created.
ReadGroupSetIds []string `json:"readGroupSetIds,omitempty"`
// ForceSendFields is a list of field names (e.g. "ReadGroupSetIds") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "ReadGroupSetIds") to
// include in API requests with the JSON null value. By default, fields
// with empty values are omitted from API requests. However, any field
// with an empty value appearing in NullFields will be sent to the
// server as null. It is an error if a field in this list has a
// non-empty value. This may be used to include null fields in Patch
// requests.
NullFields []string `json:"-"`
}
func (s *ImportReadGroupSetsResponse) MarshalJSON() ([]byte, error) {
type NoMethod ImportReadGroupSetsResponse
raw := NoMethod(*s)
return gensupport.MarshalJSON(raw, s.ForceSendFields, s.NullFields)
}
// ImportVariantsRequest: The variant data import request.
type ImportVariantsRequest struct {
// Format: The format of the variant data being imported. If
// unspecified, defaults to
// to `VCF`.
//
// Possible values:
// "FORMAT_UNSPECIFIED"
// "FORMAT_VCF" - VCF (Variant Call Format). The VCF files may be gzip
// compressed. gVCF is
// also supported. Disclaimer: gzip VCF imports are currently much
// slower
// than equivalent uncompressed VCF imports. For this reason,
// uncompressed
// VCF is currently recommended for imports with more than 1GB
// combined
// uncompressed size, or for time sensitive imports.
// "FORMAT_COMPLETE_GENOMICS" - Complete Genomics masterVarBeta
// format. The masterVarBeta files may
// be bzip2 compressed.
Format string `json:"format,omitempty"`
// InfoMergeConfig: A mapping between info field keys and the
// InfoMergeOperations to
// be performed on them. This is plumbed down to the
// MergeVariantRequests
// generated by the resulting import job.
InfoMergeConfig map[string]string `json:"infoMergeConfig,omitempty"`
// NormalizeReferenceNames: Convert reference names to the canonical
// representation.
// hg19 haploytypes (those reference names containing "_hap")
// are not modified in any way.
// All other reference names are modified according to the following
// rules:
// The reference name is capitalized.
// The "chr" prefix is dropped for all autosomes and sex chromsomes.
// For example "chr17" becomes "17" and "chrX" becomes "X".
// All mitochondrial chromosomes ("chrM", "chrMT", etc) become "MT".
NormalizeReferenceNames bool `json:"normalizeReferenceNames,omitempty"`
// SourceUris: A list of URIs referencing variant files in Google Cloud
// Storage. URIs can
// include wildcards [as
// described
// here](https://cloud.google.com/storage/docs/gsutil/addlhelp/
// WildcardNames).
// Note that recursive wildcards ('**') are not supported.
SourceUris []string `json:"sourceUris,omitempty"`
// VariantSetId: Required. The variant set to which variant data should
// be imported.
VariantSetId string `json:"variantSetId,omitempty"`
// ForceSendFields is a list of field names (e.g. "Format") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "Format") to include in API
// requests with the JSON null value. By default, fields with empty
// values are omitted from API requests. However, any field with an
// empty value appearing in NullFields will be sent to the server as
// null. It is an error if a field in this list has a non-empty value.
// This may be used to include null fields in Patch requests.
NullFields []string `json:"-"`
}
func (s *ImportVariantsRequest) MarshalJSON() ([]byte, error) {
type NoMethod ImportVariantsRequest
raw := NoMethod(*s)
return gensupport.MarshalJSON(raw, s.ForceSendFields, s.NullFields)
}
// ImportVariantsResponse: The variant data import response.
type ImportVariantsResponse struct {
// CallSetIds: IDs of the call sets created during the import.
CallSetIds []string `json:"callSetIds,omitempty"`
// ForceSendFields is a list of field names (e.g. "CallSetIds") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "CallSetIds") to include in
// API requests with the JSON null value. By default, fields with empty
// values are omitted from API requests. However, any field with an
// empty value appearing in NullFields will be sent to the server as
// null. It is an error if a field in this list has a non-empty value.
// This may be used to include null fields in Patch requests.
NullFields []string `json:"-"`
}
func (s *ImportVariantsResponse) MarshalJSON() ([]byte, error) {
type NoMethod ImportVariantsResponse
raw := NoMethod(*s)
return gensupport.MarshalJSON(raw, s.ForceSendFields, s.NullFields)
}
// LinearAlignment: A linear alignment can be represented by one CIGAR
// string. Describes the
// mapped position and local alignment of the read to the reference.
type LinearAlignment struct {
// Cigar: Represents the local alignment of this sequence (alignment
// matches, indels,
// etc) against the reference.
Cigar []*CigarUnit `json:"cigar,omitempty"`
// MappingQuality: The mapping quality of this alignment. Represents how
// likely
// the read maps to this position as opposed to other
// locations.
//
// Specifically, this is -10 log10 Pr(mapping position is wrong),
// rounded to
// the nearest integer.
MappingQuality int64 `json:"mappingQuality,omitempty"`
// Position: The position of this alignment.
Position *Position `json:"position,omitempty"`
// ForceSendFields is a list of field names (e.g. "Cigar") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "Cigar") to include in API
// requests with the JSON null value. By default, fields with empty
// values are omitted from API requests. However, any field with an
// empty value appearing in NullFields will be sent to the server as
// null. It is an error if a field in this list has a non-empty value.
// This may be used to include null fields in Patch requests.
NullFields []string `json:"-"`
}
func (s *LinearAlignment) MarshalJSON() ([]byte, error) {
type NoMethod LinearAlignment
raw := NoMethod(*s)
return gensupport.MarshalJSON(raw, s.ForceSendFields, s.NullFields)
}
type ListBasesResponse struct {
// NextPageToken: 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.
NextPageToken string `json:"nextPageToken,omitempty"`
// Offset: The offset position (0-based) of the given `sequence` from
// the
// start of this `Reference`. This value will differ for each page
// in a paginated request.
Offset int64 `json:"offset,omitempty,string"`
// Sequence: A substring of the bases that make up this reference.
Sequence string `json:"sequence,omitempty"`
// ServerResponse contains the HTTP response code and headers from the
// server.
googleapi.ServerResponse `json:"-"`
// ForceSendFields is a list of field names (e.g. "NextPageToken") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "NextPageToken") to include
// in API requests with the JSON null value. By default, fields with
// empty values are omitted from API requests. However, any field with
// an empty value appearing in NullFields will be sent to the server as
// null. It is an error if a field in this list has a non-empty value.
// This may be used to include null fields in Patch requests.
NullFields []string `json:"-"`
}
func (s *ListBasesResponse) MarshalJSON() ([]byte, error) {
type NoMethod ListBasesResponse
raw := NoMethod(*s)
return gensupport.MarshalJSON(raw, s.ForceSendFields, s.NullFields)
}
type ListCoverageBucketsResponse struct {
// BucketWidth: The length of each coverage bucket in base pairs. Note
// that buckets at the
// end of a reference sequence may be shorter. This value is omitted if
// the
// bucket width is infinity (the default behaviour, with no range
// or
// `targetBucketWidth`).
BucketWidth int64 `json:"bucketWidth,omitempty,string"`
// CoverageBuckets: The coverage buckets. The list of buckets is sparse;
// a bucket with 0
// overlapping reads is not returned. A bucket never crosses more than
// one
// reference sequence. Each bucket has width `bucketWidth`, unless
// its end is the end of the reference sequence.
CoverageBuckets []*CoverageBucket `json:"coverageBuckets,omitempty"`
// NextPageToken: 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.
NextPageToken string `json:"nextPageToken,omitempty"`
// ServerResponse contains the HTTP response code and headers from the
// server.
googleapi.ServerResponse `json:"-"`
// ForceSendFields is a list of field names (e.g. "BucketWidth") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "BucketWidth") to include
// in API requests with the JSON null value. By default, fields with
// empty values are omitted from API requests. However, any field with
// an empty value appearing in NullFields will be sent to the server as
// null. It is an error if a field in this list has a non-empty value.
// This may be used to include null fields in Patch requests.
NullFields []string `json:"-"`
}
func (s *ListCoverageBucketsResponse) MarshalJSON() ([]byte, error) {
type NoMethod ListCoverageBucketsResponse
raw := NoMethod(*s)
return gensupport.MarshalJSON(raw, s.ForceSendFields, s.NullFields)
}
// ListDatasetsResponse: The dataset list response.
type ListDatasetsResponse struct {
// Datasets: The list of matching Datasets.
Datasets []*Dataset `json:"datasets,omitempty"`
// NextPageToken: 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.
NextPageToken string `json:"nextPageToken,omitempty"`
// ServerResponse contains the HTTP response code and headers from the
// server.
googleapi.ServerResponse `json:"-"`
// ForceSendFields is a list of field names (e.g. "Datasets") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "Datasets") to include in
// API requests with the JSON null value. By default, fields with empty
// values are omitted from API requests. However, any field with an
// empty value appearing in NullFields will be sent to the server as
// null. It is an error if a field in this list has a non-empty value.
// This may be used to include null fields in Patch requests.
NullFields []string `json:"-"`
}
func (s *ListDatasetsResponse) MarshalJSON() ([]byte, error) {
type NoMethod ListDatasetsResponse
raw := NoMethod(*s)
return gensupport.MarshalJSON(raw, s.ForceSendFields, s.NullFields)
}
// ListOperationsResponse: The response message for
// Operations.ListOperations.
type ListOperationsResponse struct {
// NextPageToken: The standard List next-page token.
NextPageToken string `json:"nextPageToken,omitempty"`
// Operations: A list of operations that matches the specified filter in
// the request.
Operations []*Operation `json:"operations,omitempty"`
// ServerResponse contains the HTTP response code and headers from the
// server.
googleapi.ServerResponse `json:"-"`
// ForceSendFields is a list of field names (e.g. "NextPageToken") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "NextPageToken") to include
// in API requests with the JSON null value. By default, fields with
// empty values are omitted from API requests. However, any field with
// an empty value appearing in NullFields will be sent to the server as
// null. It is an error if a field in this list has a non-empty value.
// This may be used to include null fields in Patch requests.
NullFields []string `json:"-"`
}
func (s *ListOperationsResponse) MarshalJSON() ([]byte, error) {
type NoMethod ListOperationsResponse
raw := NoMethod(*s)
return gensupport.MarshalJSON(raw, s.ForceSendFields, s.NullFields)
}
type MergeVariantsRequest struct {
// InfoMergeConfig: A mapping between info field keys and the
// InfoMergeOperations to
// be performed on them.
InfoMergeConfig map[string]string `json:"infoMergeConfig,omitempty"`
// VariantSetId: The destination variant set.
VariantSetId string `json:"variantSetId,omitempty"`
// Variants: The variants to be merged with existing variants.
Variants []*Variant `json:"variants,omitempty"`
// ForceSendFields is a list of field names (e.g. "InfoMergeConfig") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "InfoMergeConfig") to
// include in API requests with the JSON null value. By default, fields
// with empty values are omitted from API requests. However, any field
// with an empty value appearing in NullFields will be sent to the
// server as null. It is an error if a field in this list has a
// non-empty value. This may be used to include null fields in Patch
// requests.
NullFields []string `json:"-"`
}
func (s *MergeVariantsRequest) MarshalJSON() ([]byte, error) {
type NoMethod MergeVariantsRequest
raw := NoMethod(*s)
return gensupport.MarshalJSON(raw, s.ForceSendFields, s.NullFields)
}
// Operation: This resource represents a long-running operation that is
// the result of a
// network API call.
type Operation struct {
// Done: If the value is `false`, it means the operation is still in
// progress.
// If `true`, the operation is completed, and either `error` or
// `response` is
// available.
Done bool `json:"done,omitempty"`
// Error: The error result of the operation in case of failure or
// cancellation.
Error *Status `json:"error,omitempty"`
// Metadata: An OperationMetadata or Metadata object. This will always
// be returned with the Operation.
Metadata googleapi.RawMessage `json:"metadata,omitempty"`
// Name: The server-assigned name, which is only unique within the same
// service that originally returns it. For example&#58;
// `operations/CJHU7Oi_ChDrveSpBRjfuL-qzoWAgEw`
Name string `json:"name,omitempty"`
// Response: If importing ReadGroupSets, an ImportReadGroupSetsResponse
// is returned. If importing Variants, an ImportVariantsResponse is
// returned. For pipelines and exports, an Empty response is returned.
Response googleapi.RawMessage `json:"response,omitempty"`
// ServerResponse contains the HTTP response code and headers from the
// server.
googleapi.ServerResponse `json:"-"`
// ForceSendFields is a list of field names (e.g. "Done") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "Done") to include in API
// requests with the JSON null value. By default, fields with empty
// values are omitted from API requests. However, any field with an
// empty value appearing in NullFields will be sent to the server as
// null. It is an error if a field in this list has a non-empty value.
// This may be used to include null fields in Patch requests.
NullFields []string `json:"-"`
}
func (s *Operation) MarshalJSON() ([]byte, error) {
type NoMethod Operation
raw := NoMethod(*s)
return gensupport.MarshalJSON(raw, s.ForceSendFields, s.NullFields)
}
// OperationEvent: An event that occurred during an Operation.
type OperationEvent struct {
// Description: Required description of event.
Description string `json:"description,omitempty"`
// EndTime: Optional time of when event finished. An event can have a
// start time and no
// finish time. If an event has a finish time, there must be a start
// time.
EndTime string `json:"endTime,omitempty"`
// StartTime: Optional time of when event started.
StartTime string `json:"startTime,omitempty"`
// ForceSendFields is a list of field names (e.g. "Description") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "Description") to include
// in API requests with the JSON null value. By default, fields with
// empty values are omitted from API requests. However, any field with
// an empty value appearing in NullFields will be sent to the server as
// null. It is an error if a field in this list has a non-empty value.
// This may be used to include null fields in Patch requests.
NullFields []string `json:"-"`
}
func (s *OperationEvent) MarshalJSON() ([]byte, error) {
type NoMethod OperationEvent
raw := NoMethod(*s)
return gensupport.MarshalJSON(raw, s.ForceSendFields, s.NullFields)
}
// OperationMetadata: Metadata describing an Operation.
type OperationMetadata struct {
// ClientId: This field is deprecated. Use `labels` instead. Optionally
// provided by the
// caller when submitting the request that creates the operation.
ClientId string `json:"clientId,omitempty"`
// CreateTime: The time at which the job was submitted to the Genomics
// service.
CreateTime string `json:"createTime,omitempty"`
// EndTime: The time at which the job stopped running.
EndTime string `json:"endTime,omitempty"`
// Events: Optional event messages that were generated during the job's
// execution.
// This also contains any warnings that were generated during import
// or export.
Events []*OperationEvent `json:"events,omitempty"`
// Labels: Optionally provided by the caller when submitting the request
// that creates
// the operation.
Labels map[string]string `json:"labels,omitempty"`
// ProjectId: The Google Cloud Project in which the job is scoped.
ProjectId string `json:"projectId,omitempty"`
// Request: The original request that started the operation. Note that
// this will be in
// current version of the API. If the operation was started with v1beta2
// API
// and a GetOperation is performed on v1 API, a v1 request will be
// returned.
Request googleapi.RawMessage `json:"request,omitempty"`
// RuntimeMetadata: Runtime metadata on this Operation.
RuntimeMetadata googleapi.RawMessage `json:"runtimeMetadata,omitempty"`
// StartTime: The time at which the job began to run.
StartTime string `json:"startTime,omitempty"`
// ForceSendFields is a list of field names (e.g. "ClientId") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "ClientId") to include in
// API requests with the JSON null value. By default, fields with empty
// values are omitted from API requests. However, any field with an
// empty value appearing in NullFields will be sent to the server as
// null. It is an error if a field in this list has a non-empty value.
// This may be used to include null fields in Patch requests.
NullFields []string `json:"-"`
}
func (s *OperationMetadata) MarshalJSON() ([]byte, error) {
type NoMethod OperationMetadata
raw := NoMethod(*s)
return gensupport.MarshalJSON(raw, s.ForceSendFields, s.NullFields)
}
// 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.
//
// **JSON 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"]
// }
// ]
// }
//
// **YAML Example**
//
// bindings:
// - members:
// - user:mike@example.com
// - group:admins@example.com
// - domain:google.com
// - serviceAccount:my-other-app@appspot.gserviceaccount.com
// role: roles/owner
// - members:
// - user:sean@example.com
// role: roles/viewer
//
//
// For a description of IAM and its features, see the
// [IAM developer's guide](https://cloud.google.com/iam/docs).
type Policy struct {
// Bindings: Associates a list of `members` to a `role`.
// `bindings` with no members will result in an error.
Bindings []*Binding `json:"bindings,omitempty"`
// Etag: `etag` is used for optimistic concurrency control as a way to
// help
// prevent simultaneous updates of a policy from overwriting each
// other.
// It is strongly suggested that systems make use of the `etag` in
// the
// read-modify-write cycle to perform policy updates in order to avoid
// race
// conditions: An `etag` is returned in the response to `getIamPolicy`,
// and
// systems are expected to put that etag in the request to
// `setIamPolicy` to
// ensure that their change will be applied to the same version of the
// policy.
//
// If no `etag` is provided in the call to `setIamPolicy`, then the
// existing
// policy is overwritten blindly.
Etag string `json:"etag,omitempty"`
// Version: Deprecated.
Version int64 `json:"version,omitempty"`
// ServerResponse contains the HTTP response code and headers from the
// server.
googleapi.ServerResponse `json:"-"`
// ForceSendFields is a list of field names (e.g. "Bindings") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "Bindings") to include in
// API requests with the JSON null value. By default, fields with empty
// values are omitted from API requests. However, any field with an
// empty value appearing in NullFields will be sent to the server as
// null. It is an error if a field in this list has a non-empty value.
// This may be used to include null fields in Patch requests.
NullFields []string `json:"-"`
}
func (s *Policy) MarshalJSON() ([]byte, error) {
type NoMethod Policy
raw := NoMethod(*s)
return gensupport.MarshalJSON(raw, s.ForceSendFields, s.NullFields)
}
// 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.
type Position struct {
// Position: The 0-based offset from the start of the forward strand for
// that reference.
Position int64 `json:"position,omitempty,string"`
// ReferenceName: The name of the reference in whatever reference set is
// being used.
ReferenceName string `json:"referenceName,omitempty"`
// ReverseStrand: Whether this position is on the reverse strand, as
// opposed to the forward
// strand.
ReverseStrand bool `json:"reverseStrand,omitempty"`
// ForceSendFields is a list of field names (e.g. "Position") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "Position") to include in
// API requests with the JSON null value. By default, fields with empty
// values are omitted from API requests. However, any field with an
// empty value appearing in NullFields will be sent to the server as
// null. It is an error if a field in this list has a non-empty value.
// This may be used to include null fields in Patch requests.
NullFields []string `json:"-"`
}
func (s *Position) MarshalJSON() ([]byte, error) {
type NoMethod Position
raw := NoMethod(*s)
return gensupport.MarshalJSON(raw, s.ForceSendFields, s.NullFields)
}
type Program struct {
// CommandLine: The command line used to run this program.
CommandLine string `json:"commandLine,omitempty"`
// Id: The user specified locally unique ID of the program. Used along
// with
// `prevProgramId` to define an ordering between programs.
Id string `json:"id,omitempty"`
// Name: The display name of the program. This is typically the
// colloquial name of
// the tool used, for example 'bwa' or 'picard'.
Name string `json:"name,omitempty"`
// PrevProgramId: The ID of the program run before this one.
PrevProgramId string `json:"prevProgramId,omitempty"`
// Version: The version of the program run.
Version string `json:"version,omitempty"`
// ForceSendFields is a list of field names (e.g. "CommandLine") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "CommandLine") to include
// in API requests with the JSON null value. By default, fields with
// empty values are omitted from API requests. However, any field with
// an empty value appearing in NullFields will be sent to the server as
// null. It is an error if a field in this list has a non-empty value.
// This may be used to include null fields in Patch requests.
NullFields []string `json:"-"`
}
func (s *Program) MarshalJSON() ([]byte, error) {
type NoMethod Program
raw := NoMethod(*s)
return gensupport.MarshalJSON(raw, s.ForceSendFields, s.NullFields)
}
// PullStartedEvent: An event generated when the worker starts pulling
// an image.
type PullStartedEvent struct {
// ImageUri: The URI of the image that was pulled.
ImageUri string `json:"imageUri,omitempty"`
// ForceSendFields is a list of field names (e.g. "ImageUri") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "ImageUri") to include in
// API requests with the JSON null value. By default, fields with empty
// values are omitted from API requests. However, any field with an
// empty value appearing in NullFields will be sent to the server as
// null. It is an error if a field in this list has a non-empty value.
// This may be used to include null fields in Patch requests.
NullFields []string `json:"-"`
}
func (s *PullStartedEvent) MarshalJSON() ([]byte, error) {
type NoMethod PullStartedEvent
raw := NoMethod(*s)
return gensupport.MarshalJSON(raw, s.ForceSendFields, s.NullFields)
}
// PullStoppedEvent: An event generated when the worker stops pulling an
// image.
type PullStoppedEvent struct {
// ImageUri: The URI of the image that was pulled.
ImageUri string `json:"imageUri,omitempty"`
// ForceSendFields is a list of field names (e.g. "ImageUri") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "ImageUri") to include in
// API requests with the JSON null value. By default, fields with empty
// values are omitted from API requests. However, any field with an
// empty value appearing in NullFields will be sent to the server as
// null. It is an error if a field in this list has a non-empty value.
// This may be used to include null fields in Patch requests.
NullFields []string `json:"-"`
}
func (s *PullStoppedEvent) MarshalJSON() ([]byte, error) {
type NoMethod PullStoppedEvent
raw := NoMethod(*s)
return gensupport.MarshalJSON(raw, s.ForceSendFields, s.NullFields)
}
// Range: A 0-based half-open genomic coordinate range for search
// requests.
type Range struct {
// End: The end position of the range on the reference, 0-based
// exclusive.
End int64 `json:"end,omitempty,string"`
// ReferenceName: The reference sequence name, for example `chr1`,
// `1`, or `chrX`.
ReferenceName string `json:"referenceName,omitempty"`
// Start: The start position of the range on the reference, 0-based
// inclusive.
Start int64 `json:"start,omitempty,string"`
// ForceSendFields is a list of field names (e.g. "End") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "End") to include in API
// requests with the JSON null value. By default, fields with empty
// values are omitted from API requests. However, any field with an
// empty value appearing in NullFields will be sent to the server as
// null. It is an error if a field in this list has a non-empty value.
// This may be used to include null fields in Patch requests.
NullFields []string `json:"-"`
}
func (s *Range) MarshalJSON() ([]byte, error) {
type NoMethod Range
raw := NoMethod(*s)
return gensupport.MarshalJSON(raw, s.ForceSendFields, s.NullFields)
}
// 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.
//
// ### 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
type Read struct {
// AlignedQuality: The quality of the read sequence contained in this
// alignment record
// (equivalent to QUAL in SAM).
// `alignedSequence` and `alignedQuality` may be shorter than the full
// read
// sequence and quality. This will occur if the alignment is part of
// a
// chimeric alignment, or if the read was trimmed. When this occurs, the
// CIGAR
// for this read will begin/end with a hard clip operator that will
// indicate
// the length of the excised sequence.
AlignedQuality []int64 `json:"alignedQuality,omitempty"`
// AlignedSequence: The bases of the read sequence contained in this
// alignment record,
// **without CIGAR operations applied** (equivalent to SEQ in
// SAM).
// `alignedSequence` and `alignedQuality` may be
// shorter than the full read sequence and quality. This will occur if
// the
// alignment is part of a chimeric alignment, or if the read was
// trimmed. When
// this occurs, the CIGAR for this read will begin/end with a hard
// clip
// operator that will indicate the length of the excised sequence.
AlignedSequence string `json:"alignedSequence,omitempty"`
// Alignment: The linear alignment for this alignment record. This field
// is null for
// unmapped reads.
Alignment *LinearAlignment `json:"alignment,omitempty"`
// DuplicateFragment: The fragment is a PCR or optical duplicate (SAM
// flag 0x400).
DuplicateFragment bool `json:"duplicateFragment,omitempty"`
// FailedVendorQualityChecks: Whether this read did not pass filters,
// such as platform or vendor quality
// controls (SAM flag 0x200).
FailedVendorQualityChecks bool `json:"failedVendorQualityChecks,omitempty"`
// FragmentLength: The observed length of the fragment, equivalent to
// TLEN in SAM.
FragmentLength int64 `json:"fragmentLength,omitempty"`
// FragmentName: The fragment name. Equivalent to QNAME (query template
// name) in SAM.
FragmentName string `json:"fragmentName,omitempty"`
// Id: The server-generated read ID, unique across all reads. This is
// different
// from the `fragmentName`.
Id string `json:"id,omitempty"`
// Info: A map of additional read alignment information. This must be of
// the form
// map<string, string[]> (string key mapping to a list of string
// values).
Info map[string][]interface{} `json:"info,omitempty"`
// NextMatePosition: The mapping of the primary alignment of
// the
// `(readNumber+1)%numberReads` read in the fragment. It replaces
// mate position and mate strand in SAM.
NextMatePosition *Position `json:"nextMatePosition,omitempty"`
// NumberReads: The number of reads in the fragment (extension to SAM
// flag 0x1).
NumberReads int64 `json:"numberReads,omitempty"`
// ProperPlacement: The orientation and the distance between reads from
// the fragment are
// consistent with the sequencing protocol (SAM flag 0x2).
ProperPlacement bool `json:"properPlacement,omitempty"`
// ReadGroupId: The ID of the read group this read belongs to. A read
// belongs to exactly
// one read group. This is a server-generated ID which is distinct from
// SAM's
// RG tag (for that value, see
// ReadGroup.name).
ReadGroupId string `json:"readGroupId,omitempty"`
// ReadGroupSetId: The ID of the read group set this read belongs to. A
// read belongs to
// exactly one read group set.
ReadGroupSetId string `json:"readGroupSetId,omitempty"`
// ReadNumber: The read number in sequencing. 0-based and less than
// numberReads. This
// field replaces SAM flag 0x40 and 0x80.
ReadNumber int64 `json:"readNumber,omitempty"`
// SecondaryAlignment: Whether this alignment is secondary. Equivalent
// to SAM flag 0x100.
// A secondary alignment represents an alternative to the primary
// alignment
// for this read. Aligners may return secondary alignments if a read can
// map
// ambiguously to multiple coordinates in the genome. By convention,
// each read
// has one and only one alignment where both `secondaryAlignment`
// and `supplementaryAlignment` are false.
SecondaryAlignment bool `json:"secondaryAlignment,omitempty"`
// SupplementaryAlignment: Whether this alignment is supplementary.
// Equivalent to SAM flag 0x800.
// Supplementary alignments are used in the representation of a
// chimeric
// alignment. In a chimeric alignment, a read is split into
// multiple
// linear alignments that map to different reference contigs. The
// first
// linear alignment in the read will be designated as the
// representative
// alignment; the remaining linear alignments will be designated
// as
// supplementary alignments. These alignments may have different
// mapping
// quality scores. In each linear alignment in a chimeric alignment, the
// read
// will be hard clipped. The `alignedSequence` and
// `alignedQuality` fields in the alignment record will only
// represent the bases for its respective linear alignment.
SupplementaryAlignment bool `json:"supplementaryAlignment,omitempty"`
// ForceSendFields is a list of field names (e.g. "AlignedQuality") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "AlignedQuality") to
// include in API requests with the JSON null value. By default, fields
// with empty values are omitted from API requests. However, any field
// with an empty value appearing in NullFields will be sent to the
// server as null. It is an error if a field in this list has a
// non-empty value. This may be used to include null fields in Patch
// requests.
NullFields []string `json:"-"`
}
func (s *Read) MarshalJSON() ([]byte, error) {
type NoMethod Read
raw := NoMethod(*s)
return gensupport.MarshalJSON(raw, s.ForceSendFields, s.NullFields)
}
// ReadGroup: A read group is all the data that's processed the same way
// by the sequencer.
type ReadGroup struct {
// DatasetId: The dataset to which this read group belongs.
DatasetId string `json:"datasetId,omitempty"`
// Description: A free-form text description of this read group.
Description string `json:"description,omitempty"`
// Experiment: The experiment used to generate this read group.
Experiment *Experiment `json:"experiment,omitempty"`
// Id: The server-generated read group ID, unique for all read
// groups.
// Note: This is different than the @RG ID field in the SAM spec. For
// that
// value, see name.
Id string `json:"id,omitempty"`
// Info: A map of additional read group information. This must be of the
// form
// map<string, string[]> (string key mapping to a list of string
// values).
Info map[string][]interface{} `json:"info,omitempty"`
// Name: The read group name. This corresponds to the @RG ID field in
// the SAM spec.
Name string `json:"name,omitempty"`
// PredictedInsertSize: The predicted insert size of this read group.
// The insert size is the length
// the sequenced DNA fragment from end-to-end, not including the
// adapters.
PredictedInsertSize int64 `json:"predictedInsertSize,omitempty"`
// Programs: The programs used to generate this read group. Programs are
// always
// identical for all read groups within a read group set. For this
// reason,
// only the first read group in a returned set will have this
// field
// populated.
Programs []*Program `json:"programs,omitempty"`
// ReferenceSetId: The reference set the reads in this read group are
// aligned to.
ReferenceSetId string `json:"referenceSetId,omitempty"`
// SampleId: A client-supplied sample identifier for the reads in this
// read group.
SampleId string `json:"sampleId,omitempty"`
// ForceSendFields is a list of field names (e.g. "DatasetId") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "DatasetId") to include in
// API requests with the JSON null value. By default, fields with empty
// values are omitted from API requests. However, any field with an
// empty value appearing in NullFields will be sent to the server as
// null. It is an error if a field in this list has a non-empty value.
// This may be used to include null fields in Patch requests.
NullFields []string `json:"-"`
}
func (s *ReadGroup) MarshalJSON() ([]byte, error) {
type NoMethod ReadGroup
raw := NoMethod(*s)
return gensupport.MarshalJSON(raw, s.ForceSendFields, s.NullFields)
}
// 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.
type ReadGroupSet struct {
// DatasetId: The dataset to which this read group set belongs.
DatasetId string `json:"datasetId,omitempty"`
// Filename: The filename of the original source file for this read
// group set, if any.
Filename string `json:"filename,omitempty"`
// Id: The server-generated read group set ID, unique for all read group
// sets.
Id string `json:"id,omitempty"`
// Info: A map of additional read group set information.
Info map[string][]interface{} `json:"info,omitempty"`
// Name: The read group set name. By default this will be initialized to
// the sample
// name of the sequenced data contained in this set.
Name string `json:"name,omitempty"`
// ReadGroups: The read groups in this set. There are typically 1-10
// read groups in a read
// group set.
ReadGroups []*ReadGroup `json:"readGroups,omitempty"`
// ReferenceSetId: The reference set to which the reads in this read
// group set are aligned.
ReferenceSetId string `json:"referenceSetId,omitempty"`
// ServerResponse contains the HTTP response code and headers from the
// server.
googleapi.ServerResponse `json:"-"`
// ForceSendFields is a list of field names (e.g. "DatasetId") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "DatasetId") to include in
// API requests with the JSON null value. By default, fields with empty
// values are omitted from API requests. However, any field with an
// empty value appearing in NullFields will be sent to the server as
// null. It is an error if a field in this list has a non-empty value.
// This may be used to include null fields in Patch requests.
NullFields []string `json:"-"`
}
func (s *ReadGroupSet) MarshalJSON() ([]byte, error) {
type NoMethod ReadGroupSet
raw := NoMethod(*s)
return gensupport.MarshalJSON(raw, s.ForceSendFields, s.NullFields)
}
// 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.
type Reference struct {
// Id: The server-generated reference ID, unique across all references.
Id string `json:"id,omitempty"`
// Length: The length of this reference's sequence.
Length int64 `json:"length,omitempty,string"`
// Md5checksum: MD5 of the upper-case sequence excluding all whitespace
// characters (this
// is equivalent to SQ:M5 in SAM). This value is represented in lower
// case
// hexadecimal format.
Md5checksum string `json:"md5checksum,omitempty"`
// Name: The name of this reference, for example `22`.
Name string `json:"name,omitempty"`
// NcbiTaxonId: ID from http://www.ncbi.nlm.nih.gov/taxonomy. For
// example, 9606 for human.
NcbiTaxonId int64 `json:"ncbiTaxonId,omitempty"`
// SourceAccessions: All known corresponding accession IDs in INSDC
// (GenBank/ENA/DDBJ) ideally
// with a version number, for example `GCF_000001405.26`.
SourceAccessions []string `json:"sourceAccessions,omitempty"`
// SourceUri: The URI from which the sequence was obtained. Typically
// specifies a FASTA
// format file.
SourceUri string `json:"sourceUri,omitempty"`
// ServerResponse contains the HTTP response code and headers from the
// server.
googleapi.ServerResponse `json:"-"`
// ForceSendFields is a list of field names (e.g. "Id") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "Id") to include in API
// requests with the JSON null value. By default, fields with empty
// values are omitted from API requests. However, any field with an
// empty value appearing in NullFields will be sent to the server as
// null. It is an error if a field in this list has a non-empty value.
// This may be used to include null fields in Patch requests.
NullFields []string `json:"-"`
}
func (s *Reference) MarshalJSON() ([]byte, error) {
type NoMethod Reference
raw := NoMethod(*s)
return gensupport.MarshalJSON(raw, s.ForceSendFields, s.NullFields)
}
// ReferenceBound: ReferenceBound records an upper bound for the
// starting coordinate of
// variants in a particular reference.
type ReferenceBound struct {
// ReferenceName: The name of the reference associated with this
// reference bound.
ReferenceName string `json:"referenceName,omitempty"`
// UpperBound: An upper bound (inclusive) on the starting coordinate of
// any
// variant in the reference sequence.
UpperBound int64 `json:"upperBound,omitempty,string"`
// ForceSendFields is a list of field names (e.g. "ReferenceName") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "ReferenceName") to include
// in API requests with the JSON null value. By default, fields with
// empty values are omitted from API requests. However, any field with
// an empty value appearing in NullFields will be sent to the server as
// null. It is an error if a field in this list has a non-empty value.
// This may be used to include null fields in Patch requests.
NullFields []string `json:"-"`
}
func (s *ReferenceBound) MarshalJSON() ([]byte, error) {
type NoMethod ReferenceBound
raw := NoMethod(*s)
return gensupport.MarshalJSON(raw, s.ForceSendFields, s.NullFields)
}
// 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.
type ReferenceSet struct {
// AssemblyId: Public id of this reference set, such as `GRCh37`.
AssemblyId string `json:"assemblyId,omitempty"`
// Description: Free text description of this reference set.
Description string `json:"description,omitempty"`
// Id: The server-generated reference set ID, unique across all
// reference sets.
Id string `json:"id,omitempty"`
// Md5checksum: Order-independent MD5 checksum which identifies this
// reference set. The
// checksum is computed by sorting all lower case hexidecimal
// string
// `reference.md5checksum` (for all reference in this set) in
// ascending lexicographic order, concatenating, and taking the MD5 of
// that
// value. The resulting value is represented in lower case hexadecimal
// format.
Md5checksum string `json:"md5checksum,omitempty"`
// NcbiTaxonId: ID from http://www.ncbi.nlm.nih.gov/taxonomy (for
// example, 9606 for human)
// indicating the species which this reference set is intended to model.
// Note
// that contained references may specify a different `ncbiTaxonId`,
// as
// assemblies may contain reference sequences which do not belong to
// the
// modeled species, for example EBV in a human reference genome.
NcbiTaxonId int64 `json:"ncbiTaxonId,omitempty"`
// ReferenceIds: The IDs of the reference objects that are part of this
// set.
// `Reference.md5checksum` must be unique within this set.
ReferenceIds []string `json:"referenceIds,omitempty"`
// SourceAccessions: All known corresponding accession IDs in INSDC
// (GenBank/ENA/DDBJ) ideally
// with a version number, for example `NC_000001.11`.
SourceAccessions []string `json:"sourceAccessions,omitempty"`
// SourceUri: The URI from which the references were obtained.
SourceUri string `json:"sourceUri,omitempty"`
// ServerResponse contains the HTTP response code and headers from the
// server.
googleapi.ServerResponse `json:"-"`
// ForceSendFields is a list of field names (e.g. "AssemblyId") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "AssemblyId") to include in
// API requests with the JSON null value. By default, fields with empty
// values are omitted from API requests. However, any field with an
// empty value appearing in NullFields will be sent to the server as
// null. It is an error if a field in this list has a non-empty value.
// This may be used to include null fields in Patch requests.
NullFields []string `json:"-"`
}
func (s *ReferenceSet) MarshalJSON() ([]byte, error) {
type NoMethod ReferenceSet
raw := NoMethod(*s)
return gensupport.MarshalJSON(raw, s.ForceSendFields, s.NullFields)
}
// RunPipelineResponse: The response to the RunPipeline method, returned
// in the operation's result
// field on success.
type RunPipelineResponse struct {
}
// RuntimeMetadata: Runtime metadata that will be populated in
// the
// runtimeMetadata
// field of the Operation associated with a RunPipeline execution.
type RuntimeMetadata struct {
// ComputeEngine: Execution information specific to Google Compute
// Engine.
ComputeEngine *ComputeEngine `json:"computeEngine,omitempty"`
// ForceSendFields is a list of field names (e.g. "ComputeEngine") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "ComputeEngine") to include
// in API requests with the JSON null value. By default, fields with
// empty values are omitted from API requests. However, any field with
// an empty value appearing in NullFields will be sent to the server as
// null. It is an error if a field in this list has a non-empty value.
// This may be used to include null fields in Patch requests.
NullFields []string `json:"-"`
}
func (s *RuntimeMetadata) MarshalJSON() ([]byte, error) {
type NoMethod RuntimeMetadata
raw := NoMethod(*s)
return gensupport.MarshalJSON(raw, s.ForceSendFields, s.NullFields)
}
type SearchAnnotationSetsRequest struct {
// DatasetIds: Required. The dataset IDs to search within. Caller must
// have `READ` access
// to these datasets.
DatasetIds []string `json:"datasetIds,omitempty"`
// Name: Only return annotations sets for which a substring of the name
// matches this
// string (case insensitive).
Name string `json:"name,omitempty"`
// PageSize: The maximum number of results to return in a single page.
// If unspecified,
// defaults to 128. The maximum value is 1024.
PageSize int64 `json:"pageSize,omitempty"`
// PageToken: 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
// `nextPageToken` from the previous response.
PageToken string `json:"pageToken,omitempty"`
// ReferenceSetId: If specified, only annotation sets associated with
// the given reference set
// are returned.
ReferenceSetId string `json:"referenceSetId,omitempty"`
// Types: If specified, only annotation sets that have any of these
// types are
// returned.
//
// Possible values:
// "ANNOTATION_TYPE_UNSPECIFIED"
// "GENERIC" - A `GENERIC` annotation type should be used when no
// other annotation
// type will suffice. This represents an untyped annotation of the
// reference
// genome.
// "VARIANT" - A `VARIANT` annotation type.
// "GENE" - A `GENE` annotation type represents the existence of a
// gene at the
// associated reference coordinates. The start coordinate is typically
// the
// gene's transcription start site and the end is typically the end of
// the
// gene's last exon.
// "TRANSCRIPT" - A `TRANSCRIPT` annotation type represents the
// assertion that a
// particular region of the reference genome may be transcribed as RNA.
Types []string `json:"types,omitempty"`
// ForceSendFields is a list of field names (e.g. "DatasetIds") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "DatasetIds") to include in
// API requests with the JSON null value. By default, fields with empty
// values are omitted from API requests. However, any field with an
// empty value appearing in NullFields will be sent to the server as
// null. It is an error if a field in this list has a non-empty value.
// This may be used to include null fields in Patch requests.
NullFields []string `json:"-"`
}
func (s *SearchAnnotationSetsRequest) MarshalJSON() ([]byte, error) {
type NoMethod SearchAnnotationSetsRequest
raw := NoMethod(*s)
return gensupport.MarshalJSON(raw, s.ForceSendFields, s.NullFields)
}
type SearchAnnotationSetsResponse struct {
// AnnotationSets: The matching annotation sets.
AnnotationSets []*AnnotationSet `json:"annotationSets,omitempty"`
// NextPageToken: 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.
NextPageToken string `json:"nextPageToken,omitempty"`
// ServerResponse contains the HTTP response code and headers from the
// server.
googleapi.ServerResponse `json:"-"`
// ForceSendFields is a list of field names (e.g. "AnnotationSets") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "AnnotationSets") to
// include in API requests with the JSON null value. By default, fields
// with empty values are omitted from API requests. However, any field
// with an empty value appearing in NullFields will be sent to the
// server as null. It is an error if a field in this list has a
// non-empty value. This may be used to include null fields in Patch
// requests.
NullFields []string `json:"-"`
}
func (s *SearchAnnotationSetsResponse) MarshalJSON() ([]byte, error) {
type NoMethod SearchAnnotationSetsResponse
raw := NoMethod(*s)
return gensupport.MarshalJSON(raw, s.ForceSendFields, s.NullFields)
}
type SearchAnnotationsRequest struct {
// AnnotationSetIds: Required. The annotation sets to search within. The
// caller must have
// `READ` access to these annotation sets.
// All queried annotation sets must have the same type.
AnnotationSetIds []string `json:"annotationSetIds,omitempty"`
// End: The end position of the range on the reference, 0-based
// exclusive. If
// referenceId or
// referenceName
// must be specified, Defaults to the length of the reference.
End int64 `json:"end,omitempty,string"`
// PageSize: The maximum number of results to return in a single page.
// If unspecified,
// defaults to 256. The maximum value is 2048.
PageSize int64 `json:"pageSize,omitempty"`
// PageToken: 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
// `nextPageToken` from the previous response.
PageToken string `json:"pageToken,omitempty"`
// ReferenceId: The ID of the reference to query.
ReferenceId string `json:"referenceId,omitempty"`
// ReferenceName: The name of the reference to query, within the
// reference set associated
// with this query.
ReferenceName string `json:"referenceName,omitempty"`
// Start: The start position of the range on the reference, 0-based
// inclusive. If
// specified,
// referenceId or
// referenceName
// must be specified. Defaults to 0.
Start int64 `json:"start,omitempty,string"`
// ForceSendFields is a list of field names (e.g. "AnnotationSetIds") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "AnnotationSetIds") to
// include in API requests with the JSON null value. By default, fields
// with empty values are omitted from API requests. However, any field
// with an empty value appearing in NullFields will be sent to the
// server as null. It is an error if a field in this list has a
// non-empty value. This may be used to include null fields in Patch
// requests.
NullFields []string `json:"-"`
}
func (s *SearchAnnotationsRequest) MarshalJSON() ([]byte, error) {
type NoMethod SearchAnnotationsRequest
raw := NoMethod(*s)
return gensupport.MarshalJSON(raw, s.ForceSendFields, s.NullFields)
}
type SearchAnnotationsResponse struct {
// Annotations: The matching annotations.
Annotations []*Annotation `json:"annotations,omitempty"`
// NextPageToken: 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.
NextPageToken string `json:"nextPageToken,omitempty"`
// ServerResponse contains the HTTP response code and headers from the
// server.
googleapi.ServerResponse `json:"-"`
// ForceSendFields is a list of field names (e.g. "Annotations") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "Annotations") to include
// in API requests with the JSON null value. By default, fields with
// empty values are omitted from API requests. However, any field with
// an empty value appearing in NullFields will be sent to the server as
// null. It is an error if a field in this list has a non-empty value.
// This may be used to include null fields in Patch requests.
NullFields []string `json:"-"`
}
func (s *SearchAnnotationsResponse) MarshalJSON() ([]byte, error) {
type NoMethod SearchAnnotationsResponse
raw := NoMethod(*s)
return gensupport.MarshalJSON(raw, s.ForceSendFields, s.NullFields)
}
// SearchCallSetsRequest: The call set search request.
type SearchCallSetsRequest struct {
// Name: Only return call sets for which a substring of the name matches
// this
// string.
Name string `json:"name,omitempty"`
// PageSize: The maximum number of results to return in a single page.