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Serguei Bezverkhi
2018-01-09 13:57:14 -05:00
parent 558bc6c02a
commit 7b24313bd6
16547 changed files with 4527373 additions and 0 deletions
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vendor/google.golang.org/genproto/googleapis/genomics/v1/annotations.pb.go generated vendored Normal file
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vendor/google.golang.org/genproto/googleapis/genomics/v1/cigar.pb.go generated vendored Normal file
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// Code generated by protoc-gen-go. DO NOT EDIT.
// source: google/genomics/v1/cigar.proto
package genomics
import proto "github.com/golang/protobuf/proto"
import fmt "fmt"
import math "math"
import _ "google.golang.org/genproto/googleapis/api/annotations"
// Reference imports to suppress errors if they are not otherwise used.
var _ = proto.Marshal
var _ = fmt.Errorf
var _ = math.Inf
// Describes the different types of CIGAR alignment operations that exist.
// Used wherever CIGAR alignments are used.
type CigarUnit_Operation int32
const (
CigarUnit_OPERATION_UNSPECIFIED CigarUnit_Operation = 0
// 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`.
CigarUnit_ALIGNMENT_MATCH CigarUnit_Operation = 1
// The insert operator indicates that the read contains evidence of bases
// being inserted into the reference. This operator is equivalent to SAM's
// `I`.
CigarUnit_INSERT CigarUnit_Operation = 2
// The delete operator indicates that the read contains evidence of bases
// being deleted from the reference. This operator is equivalent to SAM's
// `D`.
CigarUnit_DELETE CigarUnit_Operation = 3
// 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`.
CigarUnit_SKIP CigarUnit_Operation = 4
// 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.
CigarUnit_CLIP_SOFT CigarUnit_Operation = 5
// 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`.
CigarUnit_CLIP_HARD CigarUnit_Operation = 6
// The pad operator indicates that there is padding in an alignment. This
// operator is equivalent to SAM's `P`.
CigarUnit_PAD CigarUnit_Operation = 7
// This operator indicates that this portion of the aligned sequence exactly
// matches the reference. This operator is equivalent to SAM's `=`.
CigarUnit_SEQUENCE_MATCH CigarUnit_Operation = 8
// 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`.
CigarUnit_SEQUENCE_MISMATCH CigarUnit_Operation = 9
)
var CigarUnit_Operation_name = map[int32]string{
0: "OPERATION_UNSPECIFIED",
1: "ALIGNMENT_MATCH",
2: "INSERT",
3: "DELETE",
4: "SKIP",
5: "CLIP_SOFT",
6: "CLIP_HARD",
7: "PAD",
8: "SEQUENCE_MATCH",
9: "SEQUENCE_MISMATCH",
}
var CigarUnit_Operation_value = map[string]int32{
"OPERATION_UNSPECIFIED": 0,
"ALIGNMENT_MATCH": 1,
"INSERT": 2,
"DELETE": 3,
"SKIP": 4,
"CLIP_SOFT": 5,
"CLIP_HARD": 6,
"PAD": 7,
"SEQUENCE_MATCH": 8,
"SEQUENCE_MISMATCH": 9,
}
func (x CigarUnit_Operation) String() string {
return proto.EnumName(CigarUnit_Operation_name, int32(x))
}
func (CigarUnit_Operation) EnumDescriptor() ([]byte, []int) { return fileDescriptor1, []int{0, 0} }
// A single CIGAR operation.
type CigarUnit struct {
Operation CigarUnit_Operation `protobuf:"varint,1,opt,name=operation,enum=google.genomics.v1.CigarUnit_Operation" json:"operation,omitempty"`
// The number of genomic bases that the operation runs for. Required.
OperationLength int64 `protobuf:"varint,2,opt,name=operation_length,json=operationLength" json:"operation_length,omitempty"`
// `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 `protobuf:"bytes,3,opt,name=reference_sequence,json=referenceSequence" json:"reference_sequence,omitempty"`
}
func (m *CigarUnit) Reset() { *m = CigarUnit{} }
func (m *CigarUnit) String() string { return proto.CompactTextString(m) }
func (*CigarUnit) ProtoMessage() {}
func (*CigarUnit) Descriptor() ([]byte, []int) { return fileDescriptor1, []int{0} }
func (m *CigarUnit) GetOperation() CigarUnit_Operation {
if m != nil {
return m.Operation
}
return CigarUnit_OPERATION_UNSPECIFIED
}
func (m *CigarUnit) GetOperationLength() int64 {
if m != nil {
return m.OperationLength
}
return 0
}
func (m *CigarUnit) GetReferenceSequence() string {
if m != nil {
return m.ReferenceSequence
}
return ""
}
func init() {
proto.RegisterType((*CigarUnit)(nil), "google.genomics.v1.CigarUnit")
proto.RegisterEnum("google.genomics.v1.CigarUnit_Operation", CigarUnit_Operation_name, CigarUnit_Operation_value)
}
func init() { proto.RegisterFile("google/genomics/v1/cigar.proto", fileDescriptor1) }
var fileDescriptor1 = []byte{
// 367 bytes of a gzipped FileDescriptorProto
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}

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vendor/google.golang.org/genproto/googleapis/genomics/v1/datasets.pb.go generated vendored Normal file
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// Code generated by protoc-gen-go. DO NOT EDIT.
// source: google/genomics/v1/datasets.proto
package genomics
import proto "github.com/golang/protobuf/proto"
import fmt "fmt"
import math "math"
import _ "google.golang.org/genproto/googleapis/api/annotations"
import google_iam_v11 "google.golang.org/genproto/googleapis/iam/v1"
import google_iam_v1 "google.golang.org/genproto/googleapis/iam/v1"
import google_protobuf1 "github.com/golang/protobuf/ptypes/empty"
import google_protobuf2 "google.golang.org/genproto/protobuf/field_mask"
import google_protobuf6 "github.com/golang/protobuf/ptypes/timestamp"
import (
context "golang.org/x/net/context"
grpc "google.golang.org/grpc"
)
// Reference imports to suppress errors if they are not otherwise used.
var _ = proto.Marshal
var _ = fmt.Errorf
var _ = math.Inf
// A Dataset is a collection of genomic data.
//
// For more genomics resource definitions, see [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
type Dataset struct {
// The server-generated dataset ID, unique across all datasets.
Id string `protobuf:"bytes,1,opt,name=id" json:"id,omitempty"`
// The Google Cloud project ID that this dataset belongs to.
ProjectId string `protobuf:"bytes,2,opt,name=project_id,json=projectId" json:"project_id,omitempty"`
// The dataset name.
Name string `protobuf:"bytes,3,opt,name=name" json:"name,omitempty"`
// The time this dataset was created, in seconds from the epoch.
CreateTime *google_protobuf6.Timestamp `protobuf:"bytes,4,opt,name=create_time,json=createTime" json:"create_time,omitempty"`
}
func (m *Dataset) Reset() { *m = Dataset{} }
func (m *Dataset) String() string { return proto.CompactTextString(m) }
func (*Dataset) ProtoMessage() {}
func (*Dataset) Descriptor() ([]byte, []int) { return fileDescriptor2, []int{0} }
func (m *Dataset) GetId() string {
if m != nil {
return m.Id
}
return ""
}
func (m *Dataset) GetProjectId() string {
if m != nil {
return m.ProjectId
}
return ""
}
func (m *Dataset) GetName() string {
if m != nil {
return m.Name
}
return ""
}
func (m *Dataset) GetCreateTime() *google_protobuf6.Timestamp {
if m != nil {
return m.CreateTime
}
return nil
}
// The dataset list request.
type ListDatasetsRequest struct {
// Required. The Google Cloud project ID to list datasets for.
ProjectId string `protobuf:"bytes,1,opt,name=project_id,json=projectId" json:"project_id,omitempty"`
// The maximum number of results to return in a single page. If unspecified,
// defaults to 50. The maximum value is 1024.
PageSize int32 `protobuf:"varint,2,opt,name=page_size,json=pageSize" json:"page_size,omitempty"`
// 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 `protobuf:"bytes,3,opt,name=page_token,json=pageToken" json:"page_token,omitempty"`
}
func (m *ListDatasetsRequest) Reset() { *m = ListDatasetsRequest{} }
func (m *ListDatasetsRequest) String() string { return proto.CompactTextString(m) }
func (*ListDatasetsRequest) ProtoMessage() {}
func (*ListDatasetsRequest) Descriptor() ([]byte, []int) { return fileDescriptor2, []int{1} }
func (m *ListDatasetsRequest) GetProjectId() string {
if m != nil {
return m.ProjectId
}
return ""
}
func (m *ListDatasetsRequest) GetPageSize() int32 {
if m != nil {
return m.PageSize
}
return 0
}
func (m *ListDatasetsRequest) GetPageToken() string {
if m != nil {
return m.PageToken
}
return ""
}
// The dataset list response.
type ListDatasetsResponse struct {
// The list of matching Datasets.
Datasets []*Dataset `protobuf:"bytes,1,rep,name=datasets" json:"datasets,omitempty"`
// 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 `protobuf:"bytes,2,opt,name=next_page_token,json=nextPageToken" json:"next_page_token,omitempty"`
}
func (m *ListDatasetsResponse) Reset() { *m = ListDatasetsResponse{} }
func (m *ListDatasetsResponse) String() string { return proto.CompactTextString(m) }
func (*ListDatasetsResponse) ProtoMessage() {}
func (*ListDatasetsResponse) Descriptor() ([]byte, []int) { return fileDescriptor2, []int{2} }
func (m *ListDatasetsResponse) GetDatasets() []*Dataset {
if m != nil {
return m.Datasets
}
return nil
}
func (m *ListDatasetsResponse) GetNextPageToken() string {
if m != nil {
return m.NextPageToken
}
return ""
}
type CreateDatasetRequest struct {
// The dataset to be created. Must contain projectId and name.
Dataset *Dataset `protobuf:"bytes,1,opt,name=dataset" json:"dataset,omitempty"`
}
func (m *CreateDatasetRequest) Reset() { *m = CreateDatasetRequest{} }
func (m *CreateDatasetRequest) String() string { return proto.CompactTextString(m) }
func (*CreateDatasetRequest) ProtoMessage() {}
func (*CreateDatasetRequest) Descriptor() ([]byte, []int) { return fileDescriptor2, []int{3} }
func (m *CreateDatasetRequest) GetDataset() *Dataset {
if m != nil {
return m.Dataset
}
return nil
}
type UpdateDatasetRequest struct {
// The ID of the dataset to be updated.
DatasetId string `protobuf:"bytes,1,opt,name=dataset_id,json=datasetId" json:"dataset_id,omitempty"`
// The new dataset data.
Dataset *Dataset `protobuf:"bytes,2,opt,name=dataset" json:"dataset,omitempty"`
// An optional mask specifying which fields to update. At this time, the only
// mutable field is [name][google.genomics.v1.Dataset.name]. The only
// acceptable value is "name". If unspecified, all mutable fields will be
// updated.
UpdateMask *google_protobuf2.FieldMask `protobuf:"bytes,3,opt,name=update_mask,json=updateMask" json:"update_mask,omitempty"`
}
func (m *UpdateDatasetRequest) Reset() { *m = UpdateDatasetRequest{} }
func (m *UpdateDatasetRequest) String() string { return proto.CompactTextString(m) }
func (*UpdateDatasetRequest) ProtoMessage() {}
func (*UpdateDatasetRequest) Descriptor() ([]byte, []int) { return fileDescriptor2, []int{4} }
func (m *UpdateDatasetRequest) GetDatasetId() string {
if m != nil {
return m.DatasetId
}
return ""
}
func (m *UpdateDatasetRequest) GetDataset() *Dataset {
if m != nil {
return m.Dataset
}
return nil
}
func (m *UpdateDatasetRequest) GetUpdateMask() *google_protobuf2.FieldMask {
if m != nil {
return m.UpdateMask
}
return nil
}
type DeleteDatasetRequest struct {
// The ID of the dataset to be deleted.
DatasetId string `protobuf:"bytes,1,opt,name=dataset_id,json=datasetId" json:"dataset_id,omitempty"`
}
func (m *DeleteDatasetRequest) Reset() { *m = DeleteDatasetRequest{} }
func (m *DeleteDatasetRequest) String() string { return proto.CompactTextString(m) }
func (*DeleteDatasetRequest) ProtoMessage() {}
func (*DeleteDatasetRequest) Descriptor() ([]byte, []int) { return fileDescriptor2, []int{5} }
func (m *DeleteDatasetRequest) GetDatasetId() string {
if m != nil {
return m.DatasetId
}
return ""
}
type UndeleteDatasetRequest struct {
// The ID of the dataset to be undeleted.
DatasetId string `protobuf:"bytes,1,opt,name=dataset_id,json=datasetId" json:"dataset_id,omitempty"`
}
func (m *UndeleteDatasetRequest) Reset() { *m = UndeleteDatasetRequest{} }
func (m *UndeleteDatasetRequest) String() string { return proto.CompactTextString(m) }
func (*UndeleteDatasetRequest) ProtoMessage() {}
func (*UndeleteDatasetRequest) Descriptor() ([]byte, []int) { return fileDescriptor2, []int{6} }
func (m *UndeleteDatasetRequest) GetDatasetId() string {
if m != nil {
return m.DatasetId
}
return ""
}
type GetDatasetRequest struct {
// The ID of the dataset.
DatasetId string `protobuf:"bytes,1,opt,name=dataset_id,json=datasetId" json:"dataset_id,omitempty"`
}
func (m *GetDatasetRequest) Reset() { *m = GetDatasetRequest{} }
func (m *GetDatasetRequest) String() string { return proto.CompactTextString(m) }
func (*GetDatasetRequest) ProtoMessage() {}
func (*GetDatasetRequest) Descriptor() ([]byte, []int) { return fileDescriptor2, []int{7} }
func (m *GetDatasetRequest) GetDatasetId() string {
if m != nil {
return m.DatasetId
}
return ""
}
func init() {
proto.RegisterType((*Dataset)(nil), "google.genomics.v1.Dataset")
proto.RegisterType((*ListDatasetsRequest)(nil), "google.genomics.v1.ListDatasetsRequest")
proto.RegisterType((*ListDatasetsResponse)(nil), "google.genomics.v1.ListDatasetsResponse")
proto.RegisterType((*CreateDatasetRequest)(nil), "google.genomics.v1.CreateDatasetRequest")
proto.RegisterType((*UpdateDatasetRequest)(nil), "google.genomics.v1.UpdateDatasetRequest")
proto.RegisterType((*DeleteDatasetRequest)(nil), "google.genomics.v1.DeleteDatasetRequest")
proto.RegisterType((*UndeleteDatasetRequest)(nil), "google.genomics.v1.UndeleteDatasetRequest")
proto.RegisterType((*GetDatasetRequest)(nil), "google.genomics.v1.GetDatasetRequest")
}
// Reference imports to suppress errors if they are not otherwise used.
var _ context.Context
var _ grpc.ClientConn
// This is a compile-time assertion to ensure that this generated file
// is compatible with the grpc package it is being compiled against.
const _ = grpc.SupportPackageIsVersion4
// Client API for DatasetServiceV1 service
type DatasetServiceV1Client interface {
// Lists datasets within a project.
//
// For the definitions of datasets and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
ListDatasets(ctx context.Context, in *ListDatasetsRequest, opts ...grpc.CallOption) (*ListDatasetsResponse, error)
// Creates a new dataset.
//
// For the definitions of datasets and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
CreateDataset(ctx context.Context, in *CreateDatasetRequest, opts ...grpc.CallOption) (*Dataset, error)
// Gets a dataset by ID.
//
// For the definitions of datasets and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
GetDataset(ctx context.Context, in *GetDatasetRequest, opts ...grpc.CallOption) (*Dataset, error)
// Updates a dataset.
//
// For the definitions of datasets and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
//
// This method supports patch semantics.
UpdateDataset(ctx context.Context, in *UpdateDatasetRequest, opts ...grpc.CallOption) (*Dataset, error)
// Deletes a dataset and all of its contents (all read group sets,
// reference sets, variant sets, call sets, annotation sets, etc.)
// This is reversible (up to one week after the deletion) via
// the
// [datasets.undelete][google.genomics.v1.DatasetServiceV1.UndeleteDataset]
// operation.
//
// For the definitions of datasets and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
DeleteDataset(ctx context.Context, in *DeleteDatasetRequest, opts ...grpc.CallOption) (*google_protobuf1.Empty, error)
// Undeletes a dataset by restoring a dataset which was deleted via this API.
//
// For the definitions of datasets and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
//
// This operation is only possible for a week after the deletion occurred.
UndeleteDataset(ctx context.Context, in *UndeleteDatasetRequest, opts ...grpc.CallOption) (*Dataset, error)
// Sets the access control policy on the specified dataset. Replaces any
// existing policy.
//
// For the definitions of datasets and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
//
// See <a href="/iam/docs/managing-policies#setting_a_policy">Setting a
// Policy</a> for more information.
SetIamPolicy(ctx context.Context, in *google_iam_v11.SetIamPolicyRequest, opts ...grpc.CallOption) (*google_iam_v1.Policy, error)
// Gets the access control policy for the dataset. This is empty if the
// policy or resource does not exist.
//
// See <a href="/iam/docs/managing-policies#getting_a_policy">Getting a
// Policy</a> for more information.
//
// For the definitions of datasets and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
GetIamPolicy(ctx context.Context, in *google_iam_v11.GetIamPolicyRequest, opts ...grpc.CallOption) (*google_iam_v1.Policy, error)
// Returns permissions that a caller has on the specified resource.
// See <a href="/iam/docs/managing-policies#testing_permissions">Testing
// Permissions</a> for more information.
//
// For the definitions of datasets and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
TestIamPermissions(ctx context.Context, in *google_iam_v11.TestIamPermissionsRequest, opts ...grpc.CallOption) (*google_iam_v11.TestIamPermissionsResponse, error)
}
type datasetServiceV1Client struct {
cc *grpc.ClientConn
}
func NewDatasetServiceV1Client(cc *grpc.ClientConn) DatasetServiceV1Client {
return &datasetServiceV1Client{cc}
}
func (c *datasetServiceV1Client) ListDatasets(ctx context.Context, in *ListDatasetsRequest, opts ...grpc.CallOption) (*ListDatasetsResponse, error) {
out := new(ListDatasetsResponse)
err := grpc.Invoke(ctx, "/google.genomics.v1.DatasetServiceV1/ListDatasets", in, out, c.cc, opts...)
if err != nil {
return nil, err
}
return out, nil
}
func (c *datasetServiceV1Client) CreateDataset(ctx context.Context, in *CreateDatasetRequest, opts ...grpc.CallOption) (*Dataset, error) {
out := new(Dataset)
err := grpc.Invoke(ctx, "/google.genomics.v1.DatasetServiceV1/CreateDataset", in, out, c.cc, opts...)
if err != nil {
return nil, err
}
return out, nil
}
func (c *datasetServiceV1Client) GetDataset(ctx context.Context, in *GetDatasetRequest, opts ...grpc.CallOption) (*Dataset, error) {
out := new(Dataset)
err := grpc.Invoke(ctx, "/google.genomics.v1.DatasetServiceV1/GetDataset", in, out, c.cc, opts...)
if err != nil {
return nil, err
}
return out, nil
}
func (c *datasetServiceV1Client) UpdateDataset(ctx context.Context, in *UpdateDatasetRequest, opts ...grpc.CallOption) (*Dataset, error) {
out := new(Dataset)
err := grpc.Invoke(ctx, "/google.genomics.v1.DatasetServiceV1/UpdateDataset", in, out, c.cc, opts...)
if err != nil {
return nil, err
}
return out, nil
}
func (c *datasetServiceV1Client) DeleteDataset(ctx context.Context, in *DeleteDatasetRequest, opts ...grpc.CallOption) (*google_protobuf1.Empty, error) {
out := new(google_protobuf1.Empty)
err := grpc.Invoke(ctx, "/google.genomics.v1.DatasetServiceV1/DeleteDataset", in, out, c.cc, opts...)
if err != nil {
return nil, err
}
return out, nil
}
func (c *datasetServiceV1Client) UndeleteDataset(ctx context.Context, in *UndeleteDatasetRequest, opts ...grpc.CallOption) (*Dataset, error) {
out := new(Dataset)
err := grpc.Invoke(ctx, "/google.genomics.v1.DatasetServiceV1/UndeleteDataset", in, out, c.cc, opts...)
if err != nil {
return nil, err
}
return out, nil
}
func (c *datasetServiceV1Client) SetIamPolicy(ctx context.Context, in *google_iam_v11.SetIamPolicyRequest, opts ...grpc.CallOption) (*google_iam_v1.Policy, error) {
out := new(google_iam_v1.Policy)
err := grpc.Invoke(ctx, "/google.genomics.v1.DatasetServiceV1/SetIamPolicy", in, out, c.cc, opts...)
if err != nil {
return nil, err
}
return out, nil
}
func (c *datasetServiceV1Client) GetIamPolicy(ctx context.Context, in *google_iam_v11.GetIamPolicyRequest, opts ...grpc.CallOption) (*google_iam_v1.Policy, error) {
out := new(google_iam_v1.Policy)
err := grpc.Invoke(ctx, "/google.genomics.v1.DatasetServiceV1/GetIamPolicy", in, out, c.cc, opts...)
if err != nil {
return nil, err
}
return out, nil
}
func (c *datasetServiceV1Client) TestIamPermissions(ctx context.Context, in *google_iam_v11.TestIamPermissionsRequest, opts ...grpc.CallOption) (*google_iam_v11.TestIamPermissionsResponse, error) {
out := new(google_iam_v11.TestIamPermissionsResponse)
err := grpc.Invoke(ctx, "/google.genomics.v1.DatasetServiceV1/TestIamPermissions", in, out, c.cc, opts...)
if err != nil {
return nil, err
}
return out, nil
}
// Server API for DatasetServiceV1 service
type DatasetServiceV1Server interface {
// Lists datasets within a project.
//
// For the definitions of datasets and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
ListDatasets(context.Context, *ListDatasetsRequest) (*ListDatasetsResponse, error)
// Creates a new dataset.
//
// For the definitions of datasets and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
CreateDataset(context.Context, *CreateDatasetRequest) (*Dataset, error)
// Gets a dataset by ID.
//
// For the definitions of datasets and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
GetDataset(context.Context, *GetDatasetRequest) (*Dataset, error)
// Updates a dataset.
//
// For the definitions of datasets and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
//
// This method supports patch semantics.
UpdateDataset(context.Context, *UpdateDatasetRequest) (*Dataset, error)
// Deletes a dataset and all of its contents (all read group sets,
// reference sets, variant sets, call sets, annotation sets, etc.)
// This is reversible (up to one week after the deletion) via
// the
// [datasets.undelete][google.genomics.v1.DatasetServiceV1.UndeleteDataset]
// operation.
//
// For the definitions of datasets and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
DeleteDataset(context.Context, *DeleteDatasetRequest) (*google_protobuf1.Empty, error)
// Undeletes a dataset by restoring a dataset which was deleted via this API.
//
// For the definitions of datasets and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
//
// This operation is only possible for a week after the deletion occurred.
UndeleteDataset(context.Context, *UndeleteDatasetRequest) (*Dataset, error)
// Sets the access control policy on the specified dataset. Replaces any
// existing policy.
//
// For the definitions of datasets and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
//
// See <a href="/iam/docs/managing-policies#setting_a_policy">Setting a
// Policy</a> for more information.
SetIamPolicy(context.Context, *google_iam_v11.SetIamPolicyRequest) (*google_iam_v1.Policy, error)
// Gets the access control policy for the dataset. This is empty if the
// policy or resource does not exist.
//
// See <a href="/iam/docs/managing-policies#getting_a_policy">Getting a
// Policy</a> for more information.
//
// For the definitions of datasets and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
GetIamPolicy(context.Context, *google_iam_v11.GetIamPolicyRequest) (*google_iam_v1.Policy, error)
// Returns permissions that a caller has on the specified resource.
// See <a href="/iam/docs/managing-policies#testing_permissions">Testing
// Permissions</a> for more information.
//
// For the definitions of datasets and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
TestIamPermissions(context.Context, *google_iam_v11.TestIamPermissionsRequest) (*google_iam_v11.TestIamPermissionsResponse, error)
}
func RegisterDatasetServiceV1Server(s *grpc.Server, srv DatasetServiceV1Server) {
s.RegisterService(&_DatasetServiceV1_serviceDesc, srv)
}
func _DatasetServiceV1_ListDatasets_Handler(srv interface{}, ctx context.Context, dec func(interface{}) error, interceptor grpc.UnaryServerInterceptor) (interface{}, error) {
in := new(ListDatasetsRequest)
if err := dec(in); err != nil {
return nil, err
}
if interceptor == nil {
return srv.(DatasetServiceV1Server).ListDatasets(ctx, in)
}
info := &grpc.UnaryServerInfo{
Server: srv,
FullMethod: "/google.genomics.v1.DatasetServiceV1/ListDatasets",
}
handler := func(ctx context.Context, req interface{}) (interface{}, error) {
return srv.(DatasetServiceV1Server).ListDatasets(ctx, req.(*ListDatasetsRequest))
}
return interceptor(ctx, in, info, handler)
}
func _DatasetServiceV1_CreateDataset_Handler(srv interface{}, ctx context.Context, dec func(interface{}) error, interceptor grpc.UnaryServerInterceptor) (interface{}, error) {
in := new(CreateDatasetRequest)
if err := dec(in); err != nil {
return nil, err
}
if interceptor == nil {
return srv.(DatasetServiceV1Server).CreateDataset(ctx, in)
}
info := &grpc.UnaryServerInfo{
Server: srv,
FullMethod: "/google.genomics.v1.DatasetServiceV1/CreateDataset",
}
handler := func(ctx context.Context, req interface{}) (interface{}, error) {
return srv.(DatasetServiceV1Server).CreateDataset(ctx, req.(*CreateDatasetRequest))
}
return interceptor(ctx, in, info, handler)
}
func _DatasetServiceV1_GetDataset_Handler(srv interface{}, ctx context.Context, dec func(interface{}) error, interceptor grpc.UnaryServerInterceptor) (interface{}, error) {
in := new(GetDatasetRequest)
if err := dec(in); err != nil {
return nil, err
}
if interceptor == nil {
return srv.(DatasetServiceV1Server).GetDataset(ctx, in)
}
info := &grpc.UnaryServerInfo{
Server: srv,
FullMethod: "/google.genomics.v1.DatasetServiceV1/GetDataset",
}
handler := func(ctx context.Context, req interface{}) (interface{}, error) {
return srv.(DatasetServiceV1Server).GetDataset(ctx, req.(*GetDatasetRequest))
}
return interceptor(ctx, in, info, handler)
}
func _DatasetServiceV1_UpdateDataset_Handler(srv interface{}, ctx context.Context, dec func(interface{}) error, interceptor grpc.UnaryServerInterceptor) (interface{}, error) {
in := new(UpdateDatasetRequest)
if err := dec(in); err != nil {
return nil, err
}
if interceptor == nil {
return srv.(DatasetServiceV1Server).UpdateDataset(ctx, in)
}
info := &grpc.UnaryServerInfo{
Server: srv,
FullMethod: "/google.genomics.v1.DatasetServiceV1/UpdateDataset",
}
handler := func(ctx context.Context, req interface{}) (interface{}, error) {
return srv.(DatasetServiceV1Server).UpdateDataset(ctx, req.(*UpdateDatasetRequest))
}
return interceptor(ctx, in, info, handler)
}
func _DatasetServiceV1_DeleteDataset_Handler(srv interface{}, ctx context.Context, dec func(interface{}) error, interceptor grpc.UnaryServerInterceptor) (interface{}, error) {
in := new(DeleteDatasetRequest)
if err := dec(in); err != nil {
return nil, err
}
if interceptor == nil {
return srv.(DatasetServiceV1Server).DeleteDataset(ctx, in)
}
info := &grpc.UnaryServerInfo{
Server: srv,
FullMethod: "/google.genomics.v1.DatasetServiceV1/DeleteDataset",
}
handler := func(ctx context.Context, req interface{}) (interface{}, error) {
return srv.(DatasetServiceV1Server).DeleteDataset(ctx, req.(*DeleteDatasetRequest))
}
return interceptor(ctx, in, info, handler)
}
func _DatasetServiceV1_UndeleteDataset_Handler(srv interface{}, ctx context.Context, dec func(interface{}) error, interceptor grpc.UnaryServerInterceptor) (interface{}, error) {
in := new(UndeleteDatasetRequest)
if err := dec(in); err != nil {
return nil, err
}
if interceptor == nil {
return srv.(DatasetServiceV1Server).UndeleteDataset(ctx, in)
}
info := &grpc.UnaryServerInfo{
Server: srv,
FullMethod: "/google.genomics.v1.DatasetServiceV1/UndeleteDataset",
}
handler := func(ctx context.Context, req interface{}) (interface{}, error) {
return srv.(DatasetServiceV1Server).UndeleteDataset(ctx, req.(*UndeleteDatasetRequest))
}
return interceptor(ctx, in, info, handler)
}
func _DatasetServiceV1_SetIamPolicy_Handler(srv interface{}, ctx context.Context, dec func(interface{}) error, interceptor grpc.UnaryServerInterceptor) (interface{}, error) {
in := new(google_iam_v11.SetIamPolicyRequest)
if err := dec(in); err != nil {
return nil, err
}
if interceptor == nil {
return srv.(DatasetServiceV1Server).SetIamPolicy(ctx, in)
}
info := &grpc.UnaryServerInfo{
Server: srv,
FullMethod: "/google.genomics.v1.DatasetServiceV1/SetIamPolicy",
}
handler := func(ctx context.Context, req interface{}) (interface{}, error) {
return srv.(DatasetServiceV1Server).SetIamPolicy(ctx, req.(*google_iam_v11.SetIamPolicyRequest))
}
return interceptor(ctx, in, info, handler)
}
func _DatasetServiceV1_GetIamPolicy_Handler(srv interface{}, ctx context.Context, dec func(interface{}) error, interceptor grpc.UnaryServerInterceptor) (interface{}, error) {
in := new(google_iam_v11.GetIamPolicyRequest)
if err := dec(in); err != nil {
return nil, err
}
if interceptor == nil {
return srv.(DatasetServiceV1Server).GetIamPolicy(ctx, in)
}
info := &grpc.UnaryServerInfo{
Server: srv,
FullMethod: "/google.genomics.v1.DatasetServiceV1/GetIamPolicy",
}
handler := func(ctx context.Context, req interface{}) (interface{}, error) {
return srv.(DatasetServiceV1Server).GetIamPolicy(ctx, req.(*google_iam_v11.GetIamPolicyRequest))
}
return interceptor(ctx, in, info, handler)
}
func _DatasetServiceV1_TestIamPermissions_Handler(srv interface{}, ctx context.Context, dec func(interface{}) error, interceptor grpc.UnaryServerInterceptor) (interface{}, error) {
in := new(google_iam_v11.TestIamPermissionsRequest)
if err := dec(in); err != nil {
return nil, err
}
if interceptor == nil {
return srv.(DatasetServiceV1Server).TestIamPermissions(ctx, in)
}
info := &grpc.UnaryServerInfo{
Server: srv,
FullMethod: "/google.genomics.v1.DatasetServiceV1/TestIamPermissions",
}
handler := func(ctx context.Context, req interface{}) (interface{}, error) {
return srv.(DatasetServiceV1Server).TestIamPermissions(ctx, req.(*google_iam_v11.TestIamPermissionsRequest))
}
return interceptor(ctx, in, info, handler)
}
var _DatasetServiceV1_serviceDesc = grpc.ServiceDesc{
ServiceName: "google.genomics.v1.DatasetServiceV1",
HandlerType: (*DatasetServiceV1Server)(nil),
Methods: []grpc.MethodDesc{
{
MethodName: "ListDatasets",
Handler: _DatasetServiceV1_ListDatasets_Handler,
},
{
MethodName: "CreateDataset",
Handler: _DatasetServiceV1_CreateDataset_Handler,
},
{
MethodName: "GetDataset",
Handler: _DatasetServiceV1_GetDataset_Handler,
},
{
MethodName: "UpdateDataset",
Handler: _DatasetServiceV1_UpdateDataset_Handler,
},
{
MethodName: "DeleteDataset",
Handler: _DatasetServiceV1_DeleteDataset_Handler,
},
{
MethodName: "UndeleteDataset",
Handler: _DatasetServiceV1_UndeleteDataset_Handler,
},
{
MethodName: "SetIamPolicy",
Handler: _DatasetServiceV1_SetIamPolicy_Handler,
},
{
MethodName: "GetIamPolicy",
Handler: _DatasetServiceV1_GetIamPolicy_Handler,
},
{
MethodName: "TestIamPermissions",
Handler: _DatasetServiceV1_TestIamPermissions_Handler,
},
},
Streams: []grpc.StreamDesc{},
Metadata: "google/genomics/v1/datasets.proto",
}
func init() { proto.RegisterFile("google/genomics/v1/datasets.proto", fileDescriptor2) }
var fileDescriptor2 = []byte{
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0x00, 0x00,
}

189
vendor/google.golang.org/genproto/googleapis/genomics/v1/operations.pb.go generated vendored Normal file
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@ -0,0 +1,189 @@
// Code generated by protoc-gen-go. DO NOT EDIT.
// source: google/genomics/v1/operations.proto
package genomics
import proto "github.com/golang/protobuf/proto"
import fmt "fmt"
import math "math"
import _ "google.golang.org/genproto/googleapis/api/annotations"
import google_protobuf5 "github.com/golang/protobuf/ptypes/any"
import google_protobuf6 "github.com/golang/protobuf/ptypes/timestamp"
// Reference imports to suppress errors if they are not otherwise used.
var _ = proto.Marshal
var _ = fmt.Errorf
var _ = math.Inf
// Metadata describing an [Operation][google.longrunning.Operation].
type OperationMetadata struct {
// The Google Cloud Project in which the job is scoped.
ProjectId string `protobuf:"bytes,1,opt,name=project_id,json=projectId" json:"project_id,omitempty"`
// The time at which the job was submitted to the Genomics service.
CreateTime *google_protobuf6.Timestamp `protobuf:"bytes,2,opt,name=create_time,json=createTime" json:"create_time,omitempty"`
// The time at which the job began to run.
StartTime *google_protobuf6.Timestamp `protobuf:"bytes,3,opt,name=start_time,json=startTime" json:"start_time,omitempty"`
// The time at which the job stopped running.
EndTime *google_protobuf6.Timestamp `protobuf:"bytes,4,opt,name=end_time,json=endTime" json:"end_time,omitempty"`
// 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 *google_protobuf5.Any `protobuf:"bytes,5,opt,name=request" json:"request,omitempty"`
// 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 `protobuf:"bytes,6,rep,name=events" json:"events,omitempty"`
// This field is deprecated. Use `labels` instead. Optionally provided by the
// caller when submitting the request that creates the operation.
ClientId string `protobuf:"bytes,7,opt,name=client_id,json=clientId" json:"client_id,omitempty"`
// Runtime metadata on this Operation.
RuntimeMetadata *google_protobuf5.Any `protobuf:"bytes,8,opt,name=runtime_metadata,json=runtimeMetadata" json:"runtime_metadata,omitempty"`
// Optionally provided by the caller when submitting the request that creates
// the operation.
Labels map[string]string `protobuf:"bytes,9,rep,name=labels" json:"labels,omitempty" protobuf_key:"bytes,1,opt,name=key" protobuf_val:"bytes,2,opt,name=value"`
}
func (m *OperationMetadata) Reset() { *m = OperationMetadata{} }
func (m *OperationMetadata) String() string { return proto.CompactTextString(m) }
func (*OperationMetadata) ProtoMessage() {}
func (*OperationMetadata) Descriptor() ([]byte, []int) { return fileDescriptor3, []int{0} }
func (m *OperationMetadata) GetProjectId() string {
if m != nil {
return m.ProjectId
}
return ""
}
func (m *OperationMetadata) GetCreateTime() *google_protobuf6.Timestamp {
if m != nil {
return m.CreateTime
}
return nil
}
func (m *OperationMetadata) GetStartTime() *google_protobuf6.Timestamp {
if m != nil {
return m.StartTime
}
return nil
}
func (m *OperationMetadata) GetEndTime() *google_protobuf6.Timestamp {
if m != nil {
return m.EndTime
}
return nil
}
func (m *OperationMetadata) GetRequest() *google_protobuf5.Any {
if m != nil {
return m.Request
}
return nil
}
func (m *OperationMetadata) GetEvents() []*OperationEvent {
if m != nil {
return m.Events
}
return nil
}
func (m *OperationMetadata) GetClientId() string {
if m != nil {
return m.ClientId
}
return ""
}
func (m *OperationMetadata) GetRuntimeMetadata() *google_protobuf5.Any {
if m != nil {
return m.RuntimeMetadata
}
return nil
}
func (m *OperationMetadata) GetLabels() map[string]string {
if m != nil {
return m.Labels
}
return nil
}
// An event that occurred during an [Operation][google.longrunning.Operation].
type OperationEvent struct {
// Optional time of when event started.
StartTime *google_protobuf6.Timestamp `protobuf:"bytes,1,opt,name=start_time,json=startTime" json:"start_time,omitempty"`
// 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 *google_protobuf6.Timestamp `protobuf:"bytes,2,opt,name=end_time,json=endTime" json:"end_time,omitempty"`
// Required description of event.
Description string `protobuf:"bytes,3,opt,name=description" json:"description,omitempty"`
}
func (m *OperationEvent) Reset() { *m = OperationEvent{} }
func (m *OperationEvent) String() string { return proto.CompactTextString(m) }
func (*OperationEvent) ProtoMessage() {}
func (*OperationEvent) Descriptor() ([]byte, []int) { return fileDescriptor3, []int{1} }
func (m *OperationEvent) GetStartTime() *google_protobuf6.Timestamp {
if m != nil {
return m.StartTime
}
return nil
}
func (m *OperationEvent) GetEndTime() *google_protobuf6.Timestamp {
if m != nil {
return m.EndTime
}
return nil
}
func (m *OperationEvent) GetDescription() string {
if m != nil {
return m.Description
}
return ""
}
func init() {
proto.RegisterType((*OperationMetadata)(nil), "google.genomics.v1.OperationMetadata")
proto.RegisterType((*OperationEvent)(nil), "google.genomics.v1.OperationEvent")
}
func init() { proto.RegisterFile("google/genomics/v1/operations.proto", fileDescriptor3) }
var fileDescriptor3 = []byte{
// 456 bytes of a gzipped FileDescriptorProto
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}

78
vendor/google.golang.org/genproto/googleapis/genomics/v1/position.pb.go generated vendored Normal file
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@ -0,0 +1,78 @@
// Code generated by protoc-gen-go. DO NOT EDIT.
// source: google/genomics/v1/position.proto
package genomics
import proto "github.com/golang/protobuf/proto"
import fmt "fmt"
import math "math"
import _ "google.golang.org/genproto/googleapis/api/annotations"
// Reference imports to suppress errors if they are not otherwise used.
var _ = proto.Marshal
var _ = fmt.Errorf
var _ = math.Inf
// 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 {
// The name of the reference in whatever reference set is being used.
ReferenceName string `protobuf:"bytes,1,opt,name=reference_name,json=referenceName" json:"reference_name,omitempty"`
// The 0-based offset from the start of the forward strand for that reference.
Position int64 `protobuf:"varint,2,opt,name=position" json:"position,omitempty"`
// Whether this position is on the reverse strand, as opposed to the forward
// strand.
ReverseStrand bool `protobuf:"varint,3,opt,name=reverse_strand,json=reverseStrand" json:"reverse_strand,omitempty"`
}
func (m *Position) Reset() { *m = Position{} }
func (m *Position) String() string { return proto.CompactTextString(m) }
func (*Position) ProtoMessage() {}
func (*Position) Descriptor() ([]byte, []int) { return fileDescriptor4, []int{0} }
func (m *Position) GetReferenceName() string {
if m != nil {
return m.ReferenceName
}
return ""
}
func (m *Position) GetPosition() int64 {
if m != nil {
return m.Position
}
return 0
}
func (m *Position) GetReverseStrand() bool {
if m != nil {
return m.ReverseStrand
}
return false
}
func init() {
proto.RegisterType((*Position)(nil), "google.genomics.v1.Position")
}
func init() { proto.RegisterFile("google/genomics/v1/position.proto", fileDescriptor4) }
var fileDescriptor4 = []byte{
// 223 bytes of a gzipped FileDescriptorProto
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}

75
vendor/google.golang.org/genproto/googleapis/genomics/v1/range.pb.go generated vendored Normal file
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@ -0,0 +1,75 @@
// Code generated by protoc-gen-go. DO NOT EDIT.
// source: google/genomics/v1/range.proto
package genomics
import proto "github.com/golang/protobuf/proto"
import fmt "fmt"
import math "math"
import _ "google.golang.org/genproto/googleapis/api/annotations"
// Reference imports to suppress errors if they are not otherwise used.
var _ = proto.Marshal
var _ = fmt.Errorf
var _ = math.Inf
// A 0-based half-open genomic coordinate range for search requests.
type Range struct {
// The reference sequence name, for example `chr1`,
// `1`, or `chrX`.
ReferenceName string `protobuf:"bytes,1,opt,name=reference_name,json=referenceName" json:"reference_name,omitempty"`
// The start position of the range on the reference, 0-based inclusive.
Start int64 `protobuf:"varint,2,opt,name=start" json:"start,omitempty"`
// The end position of the range on the reference, 0-based exclusive.
End int64 `protobuf:"varint,3,opt,name=end" json:"end,omitempty"`
}
func (m *Range) Reset() { *m = Range{} }
func (m *Range) String() string { return proto.CompactTextString(m) }
func (*Range) ProtoMessage() {}
func (*Range) Descriptor() ([]byte, []int) { return fileDescriptor5, []int{0} }
func (m *Range) GetReferenceName() string {
if m != nil {
return m.ReferenceName
}
return ""
}
func (m *Range) GetStart() int64 {
if m != nil {
return m.Start
}
return 0
}
func (m *Range) GetEnd() int64 {
if m != nil {
return m.End
}
return 0
}
func init() {
proto.RegisterType((*Range)(nil), "google.genomics.v1.Range")
}
func init() { proto.RegisterFile("google/genomics/v1/range.proto", fileDescriptor5) }
var fileDescriptor5 = []byte{
// 209 bytes of a gzipped FileDescriptorProto
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0x00,
}

393
vendor/google.golang.org/genproto/googleapis/genomics/v1/readalignment.pb.go generated vendored Normal file
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@ -0,0 +1,393 @@
// Code generated by protoc-gen-go. DO NOT EDIT.
// source: google/genomics/v1/readalignment.proto
package genomics
import proto "github.com/golang/protobuf/proto"
import fmt "fmt"
import math "math"
import _ "google.golang.org/genproto/googleapis/api/annotations"
import google_protobuf3 "github.com/golang/protobuf/ptypes/struct"
// Reference imports to suppress errors if they are not otherwise used.
var _ = proto.Marshal
var _ = fmt.Errorf
var _ = math.Inf
// 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 {
// The position of this alignment.
Position *Position `protobuf:"bytes,1,opt,name=position" json:"position,omitempty"`
// 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 int32 `protobuf:"varint,2,opt,name=mapping_quality,json=mappingQuality" json:"mapping_quality,omitempty"`
// Represents the local alignment of this sequence (alignment matches, indels,
// etc) against the reference.
Cigar []*CigarUnit `protobuf:"bytes,3,rep,name=cigar" json:"cigar,omitempty"`
}
func (m *LinearAlignment) Reset() { *m = LinearAlignment{} }
func (m *LinearAlignment) String() string { return proto.CompactTextString(m) }
func (*LinearAlignment) ProtoMessage() {}
func (*LinearAlignment) Descriptor() ([]byte, []int) { return fileDescriptor6, []int{0} }
func (m *LinearAlignment) GetPosition() *Position {
if m != nil {
return m.Position
}
return nil
}
func (m *LinearAlignment) GetMappingQuality() int32 {
if m != nil {
return m.MappingQuality
}
return 0
}
func (m *LinearAlignment) GetCigar() []*CigarUnit {
if m != nil {
return m.Cigar
}
return nil
}
// A read alignment describes a linear alignment of a string of DNA to a
// [reference sequence][google.genomics.v1.Reference], in addition to metadata
// about the fragment (the molecule of DNA sequenced) and the read (the bases
// which were read by the sequencer). A read is equivalent to a line in a SAM
// file. A read belongs to exactly one read group and exactly one
// [read group set][google.genomics.v1.ReadGroupSet].
//
// For more genomics resource definitions, see [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
//
// ### Reverse-stranded reads
//
// Mapped reads (reads having a non-null `alignment`) can be aligned to either
// the forward or the reverse strand of their associated reference. Strandedness
// of a mapped read is encoded by `alignment.position.reverseStrand`.
//
// If we consider the reference to be a forward-stranded coordinate space of
// `[0, reference.length)` with `0` as the left-most position and
// `reference.length` as the right-most position, reads are always aligned left
// to right. That is, `alignment.position.position` always refers to the
// left-most reference coordinate and `alignment.cigar` describes the alignment
// of this read to the reference from left to right. All per-base fields such as
// `alignedSequence` and `alignedQuality` share this same left-to-right
// orientation; this is true of reads which are aligned to either strand. For
// reverse-stranded reads, this means that `alignedSequence` is the reverse
// complement of the bases that were originally reported by the sequencing
// machine.
//
// ### Generating a reference-aligned sequence string
//
// When interacting with mapped reads, it's often useful to produce a string
// representing the local alignment of the read to reference. The following
// pseudocode demonstrates one way of doing this:
//
// out = ""
// offset = 0
// for c in read.alignment.cigar {
// switch c.operation {
// case "ALIGNMENT_MATCH", "SEQUENCE_MATCH", "SEQUENCE_MISMATCH":
// out += read.alignedSequence[offset:offset+c.operationLength]
// offset += c.operationLength
// break
// case "CLIP_SOFT", "INSERT":
// offset += c.operationLength
// break
// case "PAD":
// out += repeat("*", c.operationLength)
// break
// case "DELETE":
// out += repeat("-", c.operationLength)
// break
// case "SKIP":
// out += repeat(" ", c.operationLength)
// break
// case "CLIP_HARD":
// break
// }
// }
// return out
//
// ### Converting to SAM's CIGAR string
//
// The following pseudocode generates a SAM CIGAR string from the
// `cigar` field. Note that this is a lossy conversion
// (`cigar.referenceSequence` is lost).
//
// cigarMap = {
// "ALIGNMENT_MATCH": "M",
// "INSERT": "I",
// "DELETE": "D",
// "SKIP": "N",
// "CLIP_SOFT": "S",
// "CLIP_HARD": "H",
// "PAD": "P",
// "SEQUENCE_MATCH": "=",
// "SEQUENCE_MISMATCH": "X",
// }
// cigarStr = ""
// for c in read.alignment.cigar {
// cigarStr += c.operationLength + cigarMap[c.operation]
// }
// return cigarStr
type Read struct {
// The server-generated read ID, unique across all reads. This is different
// from the `fragmentName`.
Id string `protobuf:"bytes,1,opt,name=id" json:"id,omitempty"`
// 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][google.genomics.v1.ReadGroup.name]).
ReadGroupId string `protobuf:"bytes,2,opt,name=read_group_id,json=readGroupId" json:"read_group_id,omitempty"`
// The ID of the read group set this read belongs to. A read belongs to
// exactly one read group set.
ReadGroupSetId string `protobuf:"bytes,3,opt,name=read_group_set_id,json=readGroupSetId" json:"read_group_set_id,omitempty"`
// The fragment name. Equivalent to QNAME (query template name) in SAM.
FragmentName string `protobuf:"bytes,4,opt,name=fragment_name,json=fragmentName" json:"fragment_name,omitempty"`
// The orientation and the distance between reads from the fragment are
// consistent with the sequencing protocol (SAM flag 0x2).
ProperPlacement bool `protobuf:"varint,5,opt,name=proper_placement,json=properPlacement" json:"proper_placement,omitempty"`
// The fragment is a PCR or optical duplicate (SAM flag 0x400).
DuplicateFragment bool `protobuf:"varint,6,opt,name=duplicate_fragment,json=duplicateFragment" json:"duplicate_fragment,omitempty"`
// The observed length of the fragment, equivalent to TLEN in SAM.
FragmentLength int32 `protobuf:"varint,7,opt,name=fragment_length,json=fragmentLength" json:"fragment_length,omitempty"`
// The read number in sequencing. 0-based and less than numberReads. This
// field replaces SAM flag 0x40 and 0x80.
ReadNumber int32 `protobuf:"varint,8,opt,name=read_number,json=readNumber" json:"read_number,omitempty"`
// The number of reads in the fragment (extension to SAM flag 0x1).
NumberReads int32 `protobuf:"varint,9,opt,name=number_reads,json=numberReads" json:"number_reads,omitempty"`
// Whether this read did not pass filters, such as platform or vendor quality
// controls (SAM flag 0x200).
FailedVendorQualityChecks bool `protobuf:"varint,10,opt,name=failed_vendor_quality_checks,json=failedVendorQualityChecks" json:"failed_vendor_quality_checks,omitempty"`
// The linear alignment for this alignment record. This field is null for
// unmapped reads.
Alignment *LinearAlignment `protobuf:"bytes,11,opt,name=alignment" json:"alignment,omitempty"`
// 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 `protobuf:"varint,12,opt,name=secondary_alignment,json=secondaryAlignment" json:"secondary_alignment,omitempty"`
// 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 `protobuf:"varint,13,opt,name=supplementary_alignment,json=supplementaryAlignment" json:"supplementary_alignment,omitempty"`
// 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 `protobuf:"bytes,14,opt,name=aligned_sequence,json=alignedSequence" json:"aligned_sequence,omitempty"`
// 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 []int32 `protobuf:"varint,15,rep,packed,name=aligned_quality,json=alignedQuality" json:"aligned_quality,omitempty"`
// 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 `protobuf:"bytes,16,opt,name=next_mate_position,json=nextMatePosition" json:"next_mate_position,omitempty"`
// 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]*google_protobuf3.ListValue `protobuf:"bytes,17,rep,name=info" json:"info,omitempty" protobuf_key:"bytes,1,opt,name=key" protobuf_val:"bytes,2,opt,name=value"`
}
func (m *Read) Reset() { *m = Read{} }
func (m *Read) String() string { return proto.CompactTextString(m) }
func (*Read) ProtoMessage() {}
func (*Read) Descriptor() ([]byte, []int) { return fileDescriptor6, []int{1} }
func (m *Read) GetId() string {
if m != nil {
return m.Id
}
return ""
}
func (m *Read) GetReadGroupId() string {
if m != nil {
return m.ReadGroupId
}
return ""
}
func (m *Read) GetReadGroupSetId() string {
if m != nil {
return m.ReadGroupSetId
}
return ""
}
func (m *Read) GetFragmentName() string {
if m != nil {
return m.FragmentName
}
return ""
}
func (m *Read) GetProperPlacement() bool {
if m != nil {
return m.ProperPlacement
}
return false
}
func (m *Read) GetDuplicateFragment() bool {
if m != nil {
return m.DuplicateFragment
}
return false
}
func (m *Read) GetFragmentLength() int32 {
if m != nil {
return m.FragmentLength
}
return 0
}
func (m *Read) GetReadNumber() int32 {
if m != nil {
return m.ReadNumber
}
return 0
}
func (m *Read) GetNumberReads() int32 {
if m != nil {
return m.NumberReads
}
return 0
}
func (m *Read) GetFailedVendorQualityChecks() bool {
if m != nil {
return m.FailedVendorQualityChecks
}
return false
}
func (m *Read) GetAlignment() *LinearAlignment {
if m != nil {
return m.Alignment
}
return nil
}
func (m *Read) GetSecondaryAlignment() bool {
if m != nil {
return m.SecondaryAlignment
}
return false
}
func (m *Read) GetSupplementaryAlignment() bool {
if m != nil {
return m.SupplementaryAlignment
}
return false
}
func (m *Read) GetAlignedSequence() string {
if m != nil {
return m.AlignedSequence
}
return ""
}
func (m *Read) GetAlignedQuality() []int32 {
if m != nil {
return m.AlignedQuality
}
return nil
}
func (m *Read) GetNextMatePosition() *Position {
if m != nil {
return m.NextMatePosition
}
return nil
}
func (m *Read) GetInfo() map[string]*google_protobuf3.ListValue {
if m != nil {
return m.Info
}
return nil
}
func init() {
proto.RegisterType((*LinearAlignment)(nil), "google.genomics.v1.LinearAlignment")
proto.RegisterType((*Read)(nil), "google.genomics.v1.Read")
}
func init() { proto.RegisterFile("google/genomics/v1/readalignment.proto", fileDescriptor6) }
var fileDescriptor6 = []byte{
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}

275
vendor/google.golang.org/genproto/googleapis/genomics/v1/readgroup.pb.go generated vendored Normal file
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@ -0,0 +1,275 @@
// Code generated by protoc-gen-go. DO NOT EDIT.
// source: google/genomics/v1/readgroup.proto
package genomics
import proto "github.com/golang/protobuf/proto"
import fmt "fmt"
import math "math"
import _ "google.golang.org/genproto/googleapis/api/annotations"
import google_protobuf3 "github.com/golang/protobuf/ptypes/struct"
// Reference imports to suppress errors if they are not otherwise used.
var _ = proto.Marshal
var _ = fmt.Errorf
var _ = math.Inf
// A read group is all the data that's processed the same way by the sequencer.
type ReadGroup struct {
// 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][google.genomics.v1.ReadGroup.name].
Id string `protobuf:"bytes,1,opt,name=id" json:"id,omitempty"`
// The dataset to which this read group belongs.
DatasetId string `protobuf:"bytes,2,opt,name=dataset_id,json=datasetId" json:"dataset_id,omitempty"`
// The read group name. This corresponds to the @RG ID field in the SAM spec.
Name string `protobuf:"bytes,3,opt,name=name" json:"name,omitempty"`
// A free-form text description of this read group.
Description string `protobuf:"bytes,4,opt,name=description" json:"description,omitempty"`
// A client-supplied sample identifier for the reads in this read group.
SampleId string `protobuf:"bytes,5,opt,name=sample_id,json=sampleId" json:"sample_id,omitempty"`
// The experiment used to generate this read group.
Experiment *ReadGroup_Experiment `protobuf:"bytes,6,opt,name=experiment" json:"experiment,omitempty"`
// 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 int32 `protobuf:"varint,7,opt,name=predicted_insert_size,json=predictedInsertSize" json:"predicted_insert_size,omitempty"`
// 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 []*ReadGroup_Program `protobuf:"bytes,10,rep,name=programs" json:"programs,omitempty"`
// The reference set the reads in this read group are aligned to.
ReferenceSetId string `protobuf:"bytes,11,opt,name=reference_set_id,json=referenceSetId" json:"reference_set_id,omitempty"`
// 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]*google_protobuf3.ListValue `protobuf:"bytes,12,rep,name=info" json:"info,omitempty" protobuf_key:"bytes,1,opt,name=key" protobuf_val:"bytes,2,opt,name=value"`
}
func (m *ReadGroup) Reset() { *m = ReadGroup{} }
func (m *ReadGroup) String() string { return proto.CompactTextString(m) }
func (*ReadGroup) ProtoMessage() {}
func (*ReadGroup) Descriptor() ([]byte, []int) { return fileDescriptor7, []int{0} }
func (m *ReadGroup) GetId() string {
if m != nil {
return m.Id
}
return ""
}
func (m *ReadGroup) GetDatasetId() string {
if m != nil {
return m.DatasetId
}
return ""
}
func (m *ReadGroup) GetName() string {
if m != nil {
return m.Name
}
return ""
}
func (m *ReadGroup) GetDescription() string {
if m != nil {
return m.Description
}
return ""
}
func (m *ReadGroup) GetSampleId() string {
if m != nil {
return m.SampleId
}
return ""
}
func (m *ReadGroup) GetExperiment() *ReadGroup_Experiment {
if m != nil {
return m.Experiment
}
return nil
}
func (m *ReadGroup) GetPredictedInsertSize() int32 {
if m != nil {
return m.PredictedInsertSize
}
return 0
}
func (m *ReadGroup) GetPrograms() []*ReadGroup_Program {
if m != nil {
return m.Programs
}
return nil
}
func (m *ReadGroup) GetReferenceSetId() string {
if m != nil {
return m.ReferenceSetId
}
return ""
}
func (m *ReadGroup) GetInfo() map[string]*google_protobuf3.ListValue {
if m != nil {
return m.Info
}
return nil
}
type ReadGroup_Experiment struct {
// 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 `protobuf:"bytes,1,opt,name=library_id,json=libraryId" json:"library_id,omitempty"`
// 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 `protobuf:"bytes,2,opt,name=platform_unit,json=platformUnit" json:"platform_unit,omitempty"`
// The sequencing center used as part of this experiment.
SequencingCenter string `protobuf:"bytes,3,opt,name=sequencing_center,json=sequencingCenter" json:"sequencing_center,omitempty"`
// The instrument model used as part of this experiment. This maps to
// sequencing technology in the SAM spec.
InstrumentModel string `protobuf:"bytes,4,opt,name=instrument_model,json=instrumentModel" json:"instrument_model,omitempty"`
}
func (m *ReadGroup_Experiment) Reset() { *m = ReadGroup_Experiment{} }
func (m *ReadGroup_Experiment) String() string { return proto.CompactTextString(m) }
func (*ReadGroup_Experiment) ProtoMessage() {}
func (*ReadGroup_Experiment) Descriptor() ([]byte, []int) { return fileDescriptor7, []int{0, 0} }
func (m *ReadGroup_Experiment) GetLibraryId() string {
if m != nil {
return m.LibraryId
}
return ""
}
func (m *ReadGroup_Experiment) GetPlatformUnit() string {
if m != nil {
return m.PlatformUnit
}
return ""
}
func (m *ReadGroup_Experiment) GetSequencingCenter() string {
if m != nil {
return m.SequencingCenter
}
return ""
}
func (m *ReadGroup_Experiment) GetInstrumentModel() string {
if m != nil {
return m.InstrumentModel
}
return ""
}
type ReadGroup_Program struct {
// The command line used to run this program.
CommandLine string `protobuf:"bytes,1,opt,name=command_line,json=commandLine" json:"command_line,omitempty"`
// The user specified locally unique ID of the program. Used along with
// `prevProgramId` to define an ordering between programs.
Id string `protobuf:"bytes,2,opt,name=id" json:"id,omitempty"`
// The display name of the program. This is typically the colloquial name of
// the tool used, for example 'bwa' or 'picard'.
Name string `protobuf:"bytes,3,opt,name=name" json:"name,omitempty"`
// The ID of the program run before this one.
PrevProgramId string `protobuf:"bytes,4,opt,name=prev_program_id,json=prevProgramId" json:"prev_program_id,omitempty"`
// The version of the program run.
Version string `protobuf:"bytes,5,opt,name=version" json:"version,omitempty"`
}
func (m *ReadGroup_Program) Reset() { *m = ReadGroup_Program{} }
func (m *ReadGroup_Program) String() string { return proto.CompactTextString(m) }
func (*ReadGroup_Program) ProtoMessage() {}
func (*ReadGroup_Program) Descriptor() ([]byte, []int) { return fileDescriptor7, []int{0, 1} }
func (m *ReadGroup_Program) GetCommandLine() string {
if m != nil {
return m.CommandLine
}
return ""
}
func (m *ReadGroup_Program) GetId() string {
if m != nil {
return m.Id
}
return ""
}
func (m *ReadGroup_Program) GetName() string {
if m != nil {
return m.Name
}
return ""
}
func (m *ReadGroup_Program) GetPrevProgramId() string {
if m != nil {
return m.PrevProgramId
}
return ""
}
func (m *ReadGroup_Program) GetVersion() string {
if m != nil {
return m.Version
}
return ""
}
func init() {
proto.RegisterType((*ReadGroup)(nil), "google.genomics.v1.ReadGroup")
proto.RegisterType((*ReadGroup_Experiment)(nil), "google.genomics.v1.ReadGroup.Experiment")
proto.RegisterType((*ReadGroup_Program)(nil), "google.genomics.v1.ReadGroup.Program")
}
func init() { proto.RegisterFile("google/genomics/v1/readgroup.proto", fileDescriptor7) }
var fileDescriptor7 = []byte{
// 585 bytes of a gzipped FileDescriptorProto
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}

132
vendor/google.golang.org/genproto/googleapis/genomics/v1/readgroupset.pb.go generated vendored Normal file
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@ -0,0 +1,132 @@
// Code generated by protoc-gen-go. DO NOT EDIT.
// source: google/genomics/v1/readgroupset.proto
package genomics
import proto "github.com/golang/protobuf/proto"
import fmt "fmt"
import math "math"
import _ "google.golang.org/genproto/googleapis/api/annotations"
import google_protobuf3 "github.com/golang/protobuf/ptypes/struct"
// Reference imports to suppress errors if they are not otherwise used.
var _ = proto.Marshal
var _ = fmt.Errorf
var _ = math.Inf
// A read group set is a logical collection of read groups, which are
// collections of reads produced by a sequencer. A read group set typically
// models reads corresponding to one sample, sequenced one way, and aligned one
// way.
//
// * A read group set belongs to one dataset.
// * A read group belongs to one read group set.
// * A read belongs to one read group.
//
// For more genomics resource definitions, see [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
type ReadGroupSet struct {
// The server-generated read group set ID, unique for all read group sets.
Id string `protobuf:"bytes,1,opt,name=id" json:"id,omitempty"`
// The dataset to which this read group set belongs.
DatasetId string `protobuf:"bytes,2,opt,name=dataset_id,json=datasetId" json:"dataset_id,omitempty"`
// The reference set to which the reads in this read group set are aligned.
ReferenceSetId string `protobuf:"bytes,3,opt,name=reference_set_id,json=referenceSetId" json:"reference_set_id,omitempty"`
// 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 `protobuf:"bytes,4,opt,name=name" json:"name,omitempty"`
// The filename of the original source file for this read group set, if any.
Filename string `protobuf:"bytes,5,opt,name=filename" json:"filename,omitempty"`
// The read groups in this set. There are typically 1-10 read groups in a read
// group set.
ReadGroups []*ReadGroup `protobuf:"bytes,6,rep,name=read_groups,json=readGroups" json:"read_groups,omitempty"`
// A map of additional read group set information.
Info map[string]*google_protobuf3.ListValue `protobuf:"bytes,7,rep,name=info" json:"info,omitempty" protobuf_key:"bytes,1,opt,name=key" protobuf_val:"bytes,2,opt,name=value"`
}
func (m *ReadGroupSet) Reset() { *m = ReadGroupSet{} }
func (m *ReadGroupSet) String() string { return proto.CompactTextString(m) }
func (*ReadGroupSet) ProtoMessage() {}
func (*ReadGroupSet) Descriptor() ([]byte, []int) { return fileDescriptor8, []int{0} }
func (m *ReadGroupSet) GetId() string {
if m != nil {
return m.Id
}
return ""
}
func (m *ReadGroupSet) GetDatasetId() string {
if m != nil {
return m.DatasetId
}
return ""
}
func (m *ReadGroupSet) GetReferenceSetId() string {
if m != nil {
return m.ReferenceSetId
}
return ""
}
func (m *ReadGroupSet) GetName() string {
if m != nil {
return m.Name
}
return ""
}
func (m *ReadGroupSet) GetFilename() string {
if m != nil {
return m.Filename
}
return ""
}
func (m *ReadGroupSet) GetReadGroups() []*ReadGroup {
if m != nil {
return m.ReadGroups
}
return nil
}
func (m *ReadGroupSet) GetInfo() map[string]*google_protobuf3.ListValue {
if m != nil {
return m.Info
}
return nil
}
func init() {
proto.RegisterType((*ReadGroupSet)(nil), "google.genomics.v1.ReadGroupSet")
}
func init() { proto.RegisterFile("google/genomics/v1/readgroupset.proto", fileDescriptor8) }
var fileDescriptor8 = []byte{
// 367 bytes of a gzipped FileDescriptorProto
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}

1414
vendor/google.golang.org/genproto/googleapis/genomics/v1/reads.pb.go generated vendored Normal file
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864
vendor/google.golang.org/genproto/googleapis/genomics/v1/references.pb.go generated vendored Normal file
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@ -0,0 +1,864 @@
// Code generated by protoc-gen-go. DO NOT EDIT.
// source: google/genomics/v1/references.proto
package genomics
import proto "github.com/golang/protobuf/proto"
import fmt "fmt"
import math "math"
import _ "google.golang.org/genproto/googleapis/api/annotations"
import (
context "golang.org/x/net/context"
grpc "google.golang.org/grpc"
)
// Reference imports to suppress errors if they are not otherwise used.
var _ = proto.Marshal
var _ = fmt.Errorf
var _ = math.Inf
// A reference is a canonical assembled DNA sequence, intended to act as a
// reference coordinate space for other genomic annotations. A single reference
// might represent the human chromosome 1 or mitochandrial DNA, for instance. A
// reference belongs to one or more reference sets.
//
// For more genomics resource definitions, see [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
type Reference struct {
// The server-generated reference ID, unique across all references.
Id string `protobuf:"bytes,1,opt,name=id" json:"id,omitempty"`
// The length of this reference's sequence.
Length int64 `protobuf:"varint,2,opt,name=length" json:"length,omitempty"`
// 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 `protobuf:"bytes,3,opt,name=md5checksum" json:"md5checksum,omitempty"`
// The name of this reference, for example `22`.
Name string `protobuf:"bytes,4,opt,name=name" json:"name,omitempty"`
// The URI from which the sequence was obtained. Typically specifies a FASTA
// format file.
SourceUri string `protobuf:"bytes,5,opt,name=source_uri,json=sourceUri" json:"source_uri,omitempty"`
// All known corresponding accession IDs in INSDC (GenBank/ENA/DDBJ) ideally
// with a version number, for example `GCF_000001405.26`.
SourceAccessions []string `protobuf:"bytes,6,rep,name=source_accessions,json=sourceAccessions" json:"source_accessions,omitempty"`
// ID from http://www.ncbi.nlm.nih.gov/taxonomy. For example, 9606 for human.
NcbiTaxonId int32 `protobuf:"varint,7,opt,name=ncbi_taxon_id,json=ncbiTaxonId" json:"ncbi_taxon_id,omitempty"`
}
func (m *Reference) Reset() { *m = Reference{} }
func (m *Reference) String() string { return proto.CompactTextString(m) }
func (*Reference) ProtoMessage() {}
func (*Reference) Descriptor() ([]byte, []int) { return fileDescriptor10, []int{0} }
func (m *Reference) GetId() string {
if m != nil {
return m.Id
}
return ""
}
func (m *Reference) GetLength() int64 {
if m != nil {
return m.Length
}
return 0
}
func (m *Reference) GetMd5Checksum() string {
if m != nil {
return m.Md5Checksum
}
return ""
}
func (m *Reference) GetName() string {
if m != nil {
return m.Name
}
return ""
}
func (m *Reference) GetSourceUri() string {
if m != nil {
return m.SourceUri
}
return ""
}
func (m *Reference) GetSourceAccessions() []string {
if m != nil {
return m.SourceAccessions
}
return nil
}
func (m *Reference) GetNcbiTaxonId() int32 {
if m != nil {
return m.NcbiTaxonId
}
return 0
}
// A reference set is a set of references which typically comprise a reference
// assembly for a species, such as `GRCh38` which is representative
// of the human genome. A reference set defines a common coordinate space for
// comparing reference-aligned experimental data. A reference set contains 1 or
// more references.
//
// For more genomics resource definitions, see [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
type ReferenceSet struct {
// The server-generated reference set ID, unique across all reference sets.
Id string `protobuf:"bytes,1,opt,name=id" json:"id,omitempty"`
// The IDs of the reference objects that are part of this set.
// `Reference.md5checksum` must be unique within this set.
ReferenceIds []string `protobuf:"bytes,2,rep,name=reference_ids,json=referenceIds" json:"reference_ids,omitempty"`
// 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 `protobuf:"bytes,3,opt,name=md5checksum" json:"md5checksum,omitempty"`
// 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 int32 `protobuf:"varint,4,opt,name=ncbi_taxon_id,json=ncbiTaxonId" json:"ncbi_taxon_id,omitempty"`
// Free text description of this reference set.
Description string `protobuf:"bytes,5,opt,name=description" json:"description,omitempty"`
// Public id of this reference set, such as `GRCh37`.
AssemblyId string `protobuf:"bytes,6,opt,name=assembly_id,json=assemblyId" json:"assembly_id,omitempty"`
// The URI from which the references were obtained.
SourceUri string `protobuf:"bytes,7,opt,name=source_uri,json=sourceUri" json:"source_uri,omitempty"`
// All known corresponding accession IDs in INSDC (GenBank/ENA/DDBJ) ideally
// with a version number, for example `NC_000001.11`.
SourceAccessions []string `protobuf:"bytes,8,rep,name=source_accessions,json=sourceAccessions" json:"source_accessions,omitempty"`
}
func (m *ReferenceSet) Reset() { *m = ReferenceSet{} }
func (m *ReferenceSet) String() string { return proto.CompactTextString(m) }
func (*ReferenceSet) ProtoMessage() {}
func (*ReferenceSet) Descriptor() ([]byte, []int) { return fileDescriptor10, []int{1} }
func (m *ReferenceSet) GetId() string {
if m != nil {
return m.Id
}
return ""
}
func (m *ReferenceSet) GetReferenceIds() []string {
if m != nil {
return m.ReferenceIds
}
return nil
}
func (m *ReferenceSet) GetMd5Checksum() string {
if m != nil {
return m.Md5Checksum
}
return ""
}
func (m *ReferenceSet) GetNcbiTaxonId() int32 {
if m != nil {
return m.NcbiTaxonId
}
return 0
}
func (m *ReferenceSet) GetDescription() string {
if m != nil {
return m.Description
}
return ""
}
func (m *ReferenceSet) GetAssemblyId() string {
if m != nil {
return m.AssemblyId
}
return ""
}
func (m *ReferenceSet) GetSourceUri() string {
if m != nil {
return m.SourceUri
}
return ""
}
func (m *ReferenceSet) GetSourceAccessions() []string {
if m != nil {
return m.SourceAccessions
}
return nil
}
type SearchReferenceSetsRequest struct {
// If present, return reference sets for which the
// [md5checksum][google.genomics.v1.ReferenceSet.md5checksum] matches exactly.
Md5Checksums []string `protobuf:"bytes,1,rep,name=md5checksums" json:"md5checksums,omitempty"`
// If present, return reference sets for which a prefix of any of
// [sourceAccessions][google.genomics.v1.ReferenceSet.source_accessions]
// match any of these strings. Accession numbers typically have a main number
// and a version, for example `NC_000001.11`.
Accessions []string `protobuf:"bytes,2,rep,name=accessions" json:"accessions,omitempty"`
// If present, return reference sets for which a substring of their
// `assemblyId` matches this string (case insensitive).
AssemblyId string `protobuf:"bytes,3,opt,name=assembly_id,json=assemblyId" json:"assembly_id,omitempty"`
// 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 `protobuf:"bytes,4,opt,name=page_token,json=pageToken" json:"page_token,omitempty"`
// The maximum number of results to return in a single page. If unspecified,
// defaults to 1024. The maximum value is 4096.
PageSize int32 `protobuf:"varint,5,opt,name=page_size,json=pageSize" json:"page_size,omitempty"`
}
func (m *SearchReferenceSetsRequest) Reset() { *m = SearchReferenceSetsRequest{} }
func (m *SearchReferenceSetsRequest) String() string { return proto.CompactTextString(m) }
func (*SearchReferenceSetsRequest) ProtoMessage() {}
func (*SearchReferenceSetsRequest) Descriptor() ([]byte, []int) { return fileDescriptor10, []int{2} }
func (m *SearchReferenceSetsRequest) GetMd5Checksums() []string {
if m != nil {
return m.Md5Checksums
}
return nil
}
func (m *SearchReferenceSetsRequest) GetAccessions() []string {
if m != nil {
return m.Accessions
}
return nil
}
func (m *SearchReferenceSetsRequest) GetAssemblyId() string {
if m != nil {
return m.AssemblyId
}
return ""
}
func (m *SearchReferenceSetsRequest) GetPageToken() string {
if m != nil {
return m.PageToken
}
return ""
}
func (m *SearchReferenceSetsRequest) GetPageSize() int32 {
if m != nil {
return m.PageSize
}
return 0
}
type SearchReferenceSetsResponse struct {
// The matching references sets.
ReferenceSets []*ReferenceSet `protobuf:"bytes,1,rep,name=reference_sets,json=referenceSets" json:"reference_sets,omitempty"`
// 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 `protobuf:"bytes,2,opt,name=next_page_token,json=nextPageToken" json:"next_page_token,omitempty"`
}
func (m *SearchReferenceSetsResponse) Reset() { *m = SearchReferenceSetsResponse{} }
func (m *SearchReferenceSetsResponse) String() string { return proto.CompactTextString(m) }
func (*SearchReferenceSetsResponse) ProtoMessage() {}
func (*SearchReferenceSetsResponse) Descriptor() ([]byte, []int) { return fileDescriptor10, []int{3} }
func (m *SearchReferenceSetsResponse) GetReferenceSets() []*ReferenceSet {
if m != nil {
return m.ReferenceSets
}
return nil
}
func (m *SearchReferenceSetsResponse) GetNextPageToken() string {
if m != nil {
return m.NextPageToken
}
return ""
}
type GetReferenceSetRequest struct {
// The ID of the reference set.
ReferenceSetId string `protobuf:"bytes,1,opt,name=reference_set_id,json=referenceSetId" json:"reference_set_id,omitempty"`
}
func (m *GetReferenceSetRequest) Reset() { *m = GetReferenceSetRequest{} }
func (m *GetReferenceSetRequest) String() string { return proto.CompactTextString(m) }
func (*GetReferenceSetRequest) ProtoMessage() {}
func (*GetReferenceSetRequest) Descriptor() ([]byte, []int) { return fileDescriptor10, []int{4} }
func (m *GetReferenceSetRequest) GetReferenceSetId() string {
if m != nil {
return m.ReferenceSetId
}
return ""
}
type SearchReferencesRequest struct {
// If present, return references for which the
// [md5checksum][google.genomics.v1.Reference.md5checksum] matches exactly.
Md5Checksums []string `protobuf:"bytes,1,rep,name=md5checksums" json:"md5checksums,omitempty"`
// If present, return references for which a prefix of any of
// [sourceAccessions][google.genomics.v1.Reference.source_accessions] match
// any of these strings. Accession numbers typically have a main number and a
// version, for example `GCF_000001405.26`.
Accessions []string `protobuf:"bytes,2,rep,name=accessions" json:"accessions,omitempty"`
// If present, return only references which belong to this reference set.
ReferenceSetId string `protobuf:"bytes,3,opt,name=reference_set_id,json=referenceSetId" json:"reference_set_id,omitempty"`
// 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 `protobuf:"bytes,4,opt,name=page_token,json=pageToken" json:"page_token,omitempty"`
// The maximum number of results to return in a single page. If unspecified,
// defaults to 1024. The maximum value is 4096.
PageSize int32 `protobuf:"varint,5,opt,name=page_size,json=pageSize" json:"page_size,omitempty"`
}
func (m *SearchReferencesRequest) Reset() { *m = SearchReferencesRequest{} }
func (m *SearchReferencesRequest) String() string { return proto.CompactTextString(m) }
func (*SearchReferencesRequest) ProtoMessage() {}
func (*SearchReferencesRequest) Descriptor() ([]byte, []int) { return fileDescriptor10, []int{5} }
func (m *SearchReferencesRequest) GetMd5Checksums() []string {
if m != nil {
return m.Md5Checksums
}
return nil
}
func (m *SearchReferencesRequest) GetAccessions() []string {
if m != nil {
return m.Accessions
}
return nil
}
func (m *SearchReferencesRequest) GetReferenceSetId() string {
if m != nil {
return m.ReferenceSetId
}
return ""
}
func (m *SearchReferencesRequest) GetPageToken() string {
if m != nil {
return m.PageToken
}
return ""
}
func (m *SearchReferencesRequest) GetPageSize() int32 {
if m != nil {
return m.PageSize
}
return 0
}
type SearchReferencesResponse struct {
// The matching references.
References []*Reference `protobuf:"bytes,1,rep,name=references" json:"references,omitempty"`
// 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 `protobuf:"bytes,2,opt,name=next_page_token,json=nextPageToken" json:"next_page_token,omitempty"`
}
func (m *SearchReferencesResponse) Reset() { *m = SearchReferencesResponse{} }
func (m *SearchReferencesResponse) String() string { return proto.CompactTextString(m) }
func (*SearchReferencesResponse) ProtoMessage() {}
func (*SearchReferencesResponse) Descriptor() ([]byte, []int) { return fileDescriptor10, []int{6} }
func (m *SearchReferencesResponse) GetReferences() []*Reference {
if m != nil {
return m.References
}
return nil
}
func (m *SearchReferencesResponse) GetNextPageToken() string {
if m != nil {
return m.NextPageToken
}
return ""
}
type GetReferenceRequest struct {
// The ID of the reference.
ReferenceId string `protobuf:"bytes,1,opt,name=reference_id,json=referenceId" json:"reference_id,omitempty"`
}
func (m *GetReferenceRequest) Reset() { *m = GetReferenceRequest{} }
func (m *GetReferenceRequest) String() string { return proto.CompactTextString(m) }
func (*GetReferenceRequest) ProtoMessage() {}
func (*GetReferenceRequest) Descriptor() ([]byte, []int) { return fileDescriptor10, []int{7} }
func (m *GetReferenceRequest) GetReferenceId() string {
if m != nil {
return m.ReferenceId
}
return ""
}
type ListBasesRequest struct {
// The ID of the reference.
ReferenceId string `protobuf:"bytes,1,opt,name=reference_id,json=referenceId" json:"reference_id,omitempty"`
// The start position (0-based) of this query. Defaults to 0.
Start int64 `protobuf:"varint,2,opt,name=start" json:"start,omitempty"`
// The end position (0-based, exclusive) of this query. Defaults to the length
// of this reference.
End int64 `protobuf:"varint,3,opt,name=end" json:"end,omitempty"`
// 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 `protobuf:"bytes,4,opt,name=page_token,json=pageToken" json:"page_token,omitempty"`
// The maximum number of bases to return in a single page. If unspecified,
// defaults to 200Kbp (kilo base pairs). The maximum value is 10Mbp (mega base
// pairs).
PageSize int32 `protobuf:"varint,5,opt,name=page_size,json=pageSize" json:"page_size,omitempty"`
}
func (m *ListBasesRequest) Reset() { *m = ListBasesRequest{} }
func (m *ListBasesRequest) String() string { return proto.CompactTextString(m) }
func (*ListBasesRequest) ProtoMessage() {}
func (*ListBasesRequest) Descriptor() ([]byte, []int) { return fileDescriptor10, []int{8} }
func (m *ListBasesRequest) GetReferenceId() string {
if m != nil {
return m.ReferenceId
}
return ""
}
func (m *ListBasesRequest) GetStart() int64 {
if m != nil {
return m.Start
}
return 0
}
func (m *ListBasesRequest) GetEnd() int64 {
if m != nil {
return m.End
}
return 0
}
func (m *ListBasesRequest) GetPageToken() string {
if m != nil {
return m.PageToken
}
return ""
}
func (m *ListBasesRequest) GetPageSize() int32 {
if m != nil {
return m.PageSize
}
return 0
}
type ListBasesResponse struct {
// 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 `protobuf:"varint,1,opt,name=offset" json:"offset,omitempty"`
// A substring of the bases that make up this reference.
Sequence string `protobuf:"bytes,2,opt,name=sequence" json:"sequence,omitempty"`
// 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 `protobuf:"bytes,3,opt,name=next_page_token,json=nextPageToken" json:"next_page_token,omitempty"`
}
func (m *ListBasesResponse) Reset() { *m = ListBasesResponse{} }
func (m *ListBasesResponse) String() string { return proto.CompactTextString(m) }
func (*ListBasesResponse) ProtoMessage() {}
func (*ListBasesResponse) Descriptor() ([]byte, []int) { return fileDescriptor10, []int{9} }
func (m *ListBasesResponse) GetOffset() int64 {
if m != nil {
return m.Offset
}
return 0
}
func (m *ListBasesResponse) GetSequence() string {
if m != nil {
return m.Sequence
}
return ""
}
func (m *ListBasesResponse) GetNextPageToken() string {
if m != nil {
return m.NextPageToken
}
return ""
}
func init() {
proto.RegisterType((*Reference)(nil), "google.genomics.v1.Reference")
proto.RegisterType((*ReferenceSet)(nil), "google.genomics.v1.ReferenceSet")
proto.RegisterType((*SearchReferenceSetsRequest)(nil), "google.genomics.v1.SearchReferenceSetsRequest")
proto.RegisterType((*SearchReferenceSetsResponse)(nil), "google.genomics.v1.SearchReferenceSetsResponse")
proto.RegisterType((*GetReferenceSetRequest)(nil), "google.genomics.v1.GetReferenceSetRequest")
proto.RegisterType((*SearchReferencesRequest)(nil), "google.genomics.v1.SearchReferencesRequest")
proto.RegisterType((*SearchReferencesResponse)(nil), "google.genomics.v1.SearchReferencesResponse")
proto.RegisterType((*GetReferenceRequest)(nil), "google.genomics.v1.GetReferenceRequest")
proto.RegisterType((*ListBasesRequest)(nil), "google.genomics.v1.ListBasesRequest")
proto.RegisterType((*ListBasesResponse)(nil), "google.genomics.v1.ListBasesResponse")
}
// Reference imports to suppress errors if they are not otherwise used.
var _ context.Context
var _ grpc.ClientConn
// This is a compile-time assertion to ensure that this generated file
// is compatible with the grpc package it is being compiled against.
const _ = grpc.SupportPackageIsVersion4
// Client API for ReferenceServiceV1 service
type ReferenceServiceV1Client interface {
// Searches for reference sets which match the given criteria.
//
// For the definitions of references and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
//
// Implements
// [GlobalAllianceApi.searchReferenceSets](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/referencemethods.avdl#L71)
SearchReferenceSets(ctx context.Context, in *SearchReferenceSetsRequest, opts ...grpc.CallOption) (*SearchReferenceSetsResponse, error)
// Gets a reference set.
//
// For the definitions of references and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
//
// Implements
// [GlobalAllianceApi.getReferenceSet](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/referencemethods.avdl#L83).
GetReferenceSet(ctx context.Context, in *GetReferenceSetRequest, opts ...grpc.CallOption) (*ReferenceSet, error)
// Searches for references which match the given criteria.
//
// For the definitions of references and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
//
// Implements
// [GlobalAllianceApi.searchReferences](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/referencemethods.avdl#L146).
SearchReferences(ctx context.Context, in *SearchReferencesRequest, opts ...grpc.CallOption) (*SearchReferencesResponse, error)
// Gets a reference.
//
// For the definitions of references and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
//
// Implements
// [GlobalAllianceApi.getReference](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/referencemethods.avdl#L158).
GetReference(ctx context.Context, in *GetReferenceRequest, opts ...grpc.CallOption) (*Reference, error)
// Lists the bases in a reference, optionally restricted to a range.
//
// For the definitions of references and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
//
// Implements
// [GlobalAllianceApi.getReferenceBases](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/referencemethods.avdl#L221).
ListBases(ctx context.Context, in *ListBasesRequest, opts ...grpc.CallOption) (*ListBasesResponse, error)
}
type referenceServiceV1Client struct {
cc *grpc.ClientConn
}
func NewReferenceServiceV1Client(cc *grpc.ClientConn) ReferenceServiceV1Client {
return &referenceServiceV1Client{cc}
}
func (c *referenceServiceV1Client) SearchReferenceSets(ctx context.Context, in *SearchReferenceSetsRequest, opts ...grpc.CallOption) (*SearchReferenceSetsResponse, error) {
out := new(SearchReferenceSetsResponse)
err := grpc.Invoke(ctx, "/google.genomics.v1.ReferenceServiceV1/SearchReferenceSets", in, out, c.cc, opts...)
if err != nil {
return nil, err
}
return out, nil
}
func (c *referenceServiceV1Client) GetReferenceSet(ctx context.Context, in *GetReferenceSetRequest, opts ...grpc.CallOption) (*ReferenceSet, error) {
out := new(ReferenceSet)
err := grpc.Invoke(ctx, "/google.genomics.v1.ReferenceServiceV1/GetReferenceSet", in, out, c.cc, opts...)
if err != nil {
return nil, err
}
return out, nil
}
func (c *referenceServiceV1Client) SearchReferences(ctx context.Context, in *SearchReferencesRequest, opts ...grpc.CallOption) (*SearchReferencesResponse, error) {
out := new(SearchReferencesResponse)
err := grpc.Invoke(ctx, "/google.genomics.v1.ReferenceServiceV1/SearchReferences", in, out, c.cc, opts...)
if err != nil {
return nil, err
}
return out, nil
}
func (c *referenceServiceV1Client) GetReference(ctx context.Context, in *GetReferenceRequest, opts ...grpc.CallOption) (*Reference, error) {
out := new(Reference)
err := grpc.Invoke(ctx, "/google.genomics.v1.ReferenceServiceV1/GetReference", in, out, c.cc, opts...)
if err != nil {
return nil, err
}
return out, nil
}
func (c *referenceServiceV1Client) ListBases(ctx context.Context, in *ListBasesRequest, opts ...grpc.CallOption) (*ListBasesResponse, error) {
out := new(ListBasesResponse)
err := grpc.Invoke(ctx, "/google.genomics.v1.ReferenceServiceV1/ListBases", in, out, c.cc, opts...)
if err != nil {
return nil, err
}
return out, nil
}
// Server API for ReferenceServiceV1 service
type ReferenceServiceV1Server interface {
// Searches for reference sets which match the given criteria.
//
// For the definitions of references and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
//
// Implements
// [GlobalAllianceApi.searchReferenceSets](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/referencemethods.avdl#L71)
SearchReferenceSets(context.Context, *SearchReferenceSetsRequest) (*SearchReferenceSetsResponse, error)
// Gets a reference set.
//
// For the definitions of references and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
//
// Implements
// [GlobalAllianceApi.getReferenceSet](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/referencemethods.avdl#L83).
GetReferenceSet(context.Context, *GetReferenceSetRequest) (*ReferenceSet, error)
// Searches for references which match the given criteria.
//
// For the definitions of references and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
//
// Implements
// [GlobalAllianceApi.searchReferences](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/referencemethods.avdl#L146).
SearchReferences(context.Context, *SearchReferencesRequest) (*SearchReferencesResponse, error)
// Gets a reference.
//
// For the definitions of references and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
//
// Implements
// [GlobalAllianceApi.getReference](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/referencemethods.avdl#L158).
GetReference(context.Context, *GetReferenceRequest) (*Reference, error)
// Lists the bases in a reference, optionally restricted to a range.
//
// For the definitions of references and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
//
// Implements
// [GlobalAllianceApi.getReferenceBases](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/referencemethods.avdl#L221).
ListBases(context.Context, *ListBasesRequest) (*ListBasesResponse, error)
}
func RegisterReferenceServiceV1Server(s *grpc.Server, srv ReferenceServiceV1Server) {
s.RegisterService(&_ReferenceServiceV1_serviceDesc, srv)
}
func _ReferenceServiceV1_SearchReferenceSets_Handler(srv interface{}, ctx context.Context, dec func(interface{}) error, interceptor grpc.UnaryServerInterceptor) (interface{}, error) {
in := new(SearchReferenceSetsRequest)
if err := dec(in); err != nil {
return nil, err
}
if interceptor == nil {
return srv.(ReferenceServiceV1Server).SearchReferenceSets(ctx, in)
}
info := &grpc.UnaryServerInfo{
Server: srv,
FullMethod: "/google.genomics.v1.ReferenceServiceV1/SearchReferenceSets",
}
handler := func(ctx context.Context, req interface{}) (interface{}, error) {
return srv.(ReferenceServiceV1Server).SearchReferenceSets(ctx, req.(*SearchReferenceSetsRequest))
}
return interceptor(ctx, in, info, handler)
}
func _ReferenceServiceV1_GetReferenceSet_Handler(srv interface{}, ctx context.Context, dec func(interface{}) error, interceptor grpc.UnaryServerInterceptor) (interface{}, error) {
in := new(GetReferenceSetRequest)
if err := dec(in); err != nil {
return nil, err
}
if interceptor == nil {
return srv.(ReferenceServiceV1Server).GetReferenceSet(ctx, in)
}
info := &grpc.UnaryServerInfo{
Server: srv,
FullMethod: "/google.genomics.v1.ReferenceServiceV1/GetReferenceSet",
}
handler := func(ctx context.Context, req interface{}) (interface{}, error) {
return srv.(ReferenceServiceV1Server).GetReferenceSet(ctx, req.(*GetReferenceSetRequest))
}
return interceptor(ctx, in, info, handler)
}
func _ReferenceServiceV1_SearchReferences_Handler(srv interface{}, ctx context.Context, dec func(interface{}) error, interceptor grpc.UnaryServerInterceptor) (interface{}, error) {
in := new(SearchReferencesRequest)
if err := dec(in); err != nil {
return nil, err
}
if interceptor == nil {
return srv.(ReferenceServiceV1Server).SearchReferences(ctx, in)
}
info := &grpc.UnaryServerInfo{
Server: srv,
FullMethod: "/google.genomics.v1.ReferenceServiceV1/SearchReferences",
}
handler := func(ctx context.Context, req interface{}) (interface{}, error) {
return srv.(ReferenceServiceV1Server).SearchReferences(ctx, req.(*SearchReferencesRequest))
}
return interceptor(ctx, in, info, handler)
}
func _ReferenceServiceV1_GetReference_Handler(srv interface{}, ctx context.Context, dec func(interface{}) error, interceptor grpc.UnaryServerInterceptor) (interface{}, error) {
in := new(GetReferenceRequest)
if err := dec(in); err != nil {
return nil, err
}
if interceptor == nil {
return srv.(ReferenceServiceV1Server).GetReference(ctx, in)
}
info := &grpc.UnaryServerInfo{
Server: srv,
FullMethod: "/google.genomics.v1.ReferenceServiceV1/GetReference",
}
handler := func(ctx context.Context, req interface{}) (interface{}, error) {
return srv.(ReferenceServiceV1Server).GetReference(ctx, req.(*GetReferenceRequest))
}
return interceptor(ctx, in, info, handler)
}
func _ReferenceServiceV1_ListBases_Handler(srv interface{}, ctx context.Context, dec func(interface{}) error, interceptor grpc.UnaryServerInterceptor) (interface{}, error) {
in := new(ListBasesRequest)
if err := dec(in); err != nil {
return nil, err
}
if interceptor == nil {
return srv.(ReferenceServiceV1Server).ListBases(ctx, in)
}
info := &grpc.UnaryServerInfo{
Server: srv,
FullMethod: "/google.genomics.v1.ReferenceServiceV1/ListBases",
}
handler := func(ctx context.Context, req interface{}) (interface{}, error) {
return srv.(ReferenceServiceV1Server).ListBases(ctx, req.(*ListBasesRequest))
}
return interceptor(ctx, in, info, handler)
}
var _ReferenceServiceV1_serviceDesc = grpc.ServiceDesc{
ServiceName: "google.genomics.v1.ReferenceServiceV1",
HandlerType: (*ReferenceServiceV1Server)(nil),
Methods: []grpc.MethodDesc{
{
MethodName: "SearchReferenceSets",
Handler: _ReferenceServiceV1_SearchReferenceSets_Handler,
},
{
MethodName: "GetReferenceSet",
Handler: _ReferenceServiceV1_GetReferenceSet_Handler,
},
{
MethodName: "SearchReferences",
Handler: _ReferenceServiceV1_SearchReferences_Handler,
},
{
MethodName: "GetReference",
Handler: _ReferenceServiceV1_GetReference_Handler,
},
{
MethodName: "ListBases",
Handler: _ReferenceServiceV1_ListBases_Handler,
},
},
Streams: []grpc.StreamDesc{},
Metadata: "google/genomics/v1/references.proto",
}
func init() { proto.RegisterFile("google/genomics/v1/references.proto", fileDescriptor10) }
var fileDescriptor10 = []byte{
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}

2808
vendor/google.golang.org/genproto/googleapis/genomics/v1/variants.pb.go generated vendored Normal file
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1838
vendor/google.golang.org/genproto/googleapis/genomics/v1alpha2/pipelines.pb.go generated vendored Normal file
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