/
reads.pb.go
1769 lines (1608 loc) · 74.7 KB
/
reads.pb.go
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// Code generated by protoc-gen-go. DO NOT EDIT.
// source: google/genomics/v1/reads.proto
package genomics
import (
fmt "fmt"
proto "github.com/golang/protobuf/proto"
empty "github.com/golang/protobuf/ptypes/empty"
_ "google.golang.org/genproto/googleapis/api/annotations"
longrunning "google.golang.org/genproto/googleapis/longrunning"
field_mask "google.golang.org/genproto/protobuf/field_mask"
math "math"
)
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
// This is a compile-time assertion to ensure that this generated file
// is compatible with the proto package it is being compiled against.
// A compilation error at this line likely means your copy of the
// proto package needs to be updated.
const _ = proto.ProtoPackageIsVersion2 // please upgrade the proto package
type ImportReadGroupSetsRequest_PartitionStrategy int32
const (
ImportReadGroupSetsRequest_PARTITION_STRATEGY_UNSPECIFIED ImportReadGroupSetsRequest_PartitionStrategy = 0
// In most cases, this strategy yields one read group set per file. This is
// the default behavior.
//
// Allocate one read group set per file per sample. For BAM files, read
// groups are considered to share a sample if they have identical sample
// names. Furthermore, all reads for each file which do not belong to a read
// group, if any, will be grouped into a single read group set per-file.
ImportReadGroupSetsRequest_PER_FILE_PER_SAMPLE ImportReadGroupSetsRequest_PartitionStrategy = 1
// Includes all read groups in all imported files into a single read group
// set. Requires that the headers for all imported files are equivalent. All
// reads which do not belong to a read group, if any, will be grouped into a
// separate read group set.
ImportReadGroupSetsRequest_MERGE_ALL ImportReadGroupSetsRequest_PartitionStrategy = 2
)
var ImportReadGroupSetsRequest_PartitionStrategy_name = map[int32]string{
0: "PARTITION_STRATEGY_UNSPECIFIED",
1: "PER_FILE_PER_SAMPLE",
2: "MERGE_ALL",
}
var ImportReadGroupSetsRequest_PartitionStrategy_value = map[string]int32{
"PARTITION_STRATEGY_UNSPECIFIED": 0,
"PER_FILE_PER_SAMPLE": 1,
"MERGE_ALL": 2,
}
func (x ImportReadGroupSetsRequest_PartitionStrategy) String() string {
return proto.EnumName(ImportReadGroupSetsRequest_PartitionStrategy_name, int32(x))
}
func (ImportReadGroupSetsRequest_PartitionStrategy) EnumDescriptor() ([]byte, []int) {
return fileDescriptor_6b02d5d0c80a106c, []int{2, 0}
}
// The read group set search request.
type SearchReadGroupSetsRequest struct {
// Restricts this query to read group sets within the given datasets. At least
// one ID must be provided.
DatasetIds []string `protobuf:"bytes,1,rep,name=dataset_ids,json=datasetIds,proto3" json:"dataset_ids,omitempty"`
// Only return read group sets for which a substring of the name matches this
// string.
Name string `protobuf:"bytes,3,opt,name=name,proto3" json:"name,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,2,opt,name=page_token,json=pageToken,proto3" json:"page_token,omitempty"`
// The maximum number of results to return in a single page. If unspecified,
// defaults to 256. The maximum value is 1024.
PageSize int32 `protobuf:"varint,4,opt,name=page_size,json=pageSize,proto3" json:"page_size,omitempty"`
XXX_NoUnkeyedLiteral struct{} `json:"-"`
XXX_unrecognized []byte `json:"-"`
XXX_sizecache int32 `json:"-"`
}
func (m *SearchReadGroupSetsRequest) Reset() { *m = SearchReadGroupSetsRequest{} }
func (m *SearchReadGroupSetsRequest) String() string { return proto.CompactTextString(m) }
func (*SearchReadGroupSetsRequest) ProtoMessage() {}
func (*SearchReadGroupSetsRequest) Descriptor() ([]byte, []int) {
return fileDescriptor_6b02d5d0c80a106c, []int{0}
}
func (m *SearchReadGroupSetsRequest) XXX_Unmarshal(b []byte) error {
return xxx_messageInfo_SearchReadGroupSetsRequest.Unmarshal(m, b)
}
func (m *SearchReadGroupSetsRequest) XXX_Marshal(b []byte, deterministic bool) ([]byte, error) {
return xxx_messageInfo_SearchReadGroupSetsRequest.Marshal(b, m, deterministic)
}
func (m *SearchReadGroupSetsRequest) XXX_Merge(src proto.Message) {
xxx_messageInfo_SearchReadGroupSetsRequest.Merge(m, src)
}
func (m *SearchReadGroupSetsRequest) XXX_Size() int {
return xxx_messageInfo_SearchReadGroupSetsRequest.Size(m)
}
func (m *SearchReadGroupSetsRequest) XXX_DiscardUnknown() {
xxx_messageInfo_SearchReadGroupSetsRequest.DiscardUnknown(m)
}
var xxx_messageInfo_SearchReadGroupSetsRequest proto.InternalMessageInfo
func (m *SearchReadGroupSetsRequest) GetDatasetIds() []string {
if m != nil {
return m.DatasetIds
}
return nil
}
func (m *SearchReadGroupSetsRequest) GetName() string {
if m != nil {
return m.Name
}
return ""
}
func (m *SearchReadGroupSetsRequest) GetPageToken() string {
if m != nil {
return m.PageToken
}
return ""
}
func (m *SearchReadGroupSetsRequest) GetPageSize() int32 {
if m != nil {
return m.PageSize
}
return 0
}
// The read group set search response.
type SearchReadGroupSetsResponse struct {
// The list of matching read group sets.
ReadGroupSets []*ReadGroupSet `protobuf:"bytes,1,rep,name=read_group_sets,json=readGroupSets,proto3" json:"read_group_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,proto3" json:"next_page_token,omitempty"`
XXX_NoUnkeyedLiteral struct{} `json:"-"`
XXX_unrecognized []byte `json:"-"`
XXX_sizecache int32 `json:"-"`
}
func (m *SearchReadGroupSetsResponse) Reset() { *m = SearchReadGroupSetsResponse{} }
func (m *SearchReadGroupSetsResponse) String() string { return proto.CompactTextString(m) }
func (*SearchReadGroupSetsResponse) ProtoMessage() {}
func (*SearchReadGroupSetsResponse) Descriptor() ([]byte, []int) {
return fileDescriptor_6b02d5d0c80a106c, []int{1}
}
func (m *SearchReadGroupSetsResponse) XXX_Unmarshal(b []byte) error {
return xxx_messageInfo_SearchReadGroupSetsResponse.Unmarshal(m, b)
}
func (m *SearchReadGroupSetsResponse) XXX_Marshal(b []byte, deterministic bool) ([]byte, error) {
return xxx_messageInfo_SearchReadGroupSetsResponse.Marshal(b, m, deterministic)
}
func (m *SearchReadGroupSetsResponse) XXX_Merge(src proto.Message) {
xxx_messageInfo_SearchReadGroupSetsResponse.Merge(m, src)
}
func (m *SearchReadGroupSetsResponse) XXX_Size() int {
return xxx_messageInfo_SearchReadGroupSetsResponse.Size(m)
}
func (m *SearchReadGroupSetsResponse) XXX_DiscardUnknown() {
xxx_messageInfo_SearchReadGroupSetsResponse.DiscardUnknown(m)
}
var xxx_messageInfo_SearchReadGroupSetsResponse proto.InternalMessageInfo
func (m *SearchReadGroupSetsResponse) GetReadGroupSets() []*ReadGroupSet {
if m != nil {
return m.ReadGroupSets
}
return nil
}
func (m *SearchReadGroupSetsResponse) GetNextPageToken() string {
if m != nil {
return m.NextPageToken
}
return ""
}
// The read group set import request.
type ImportReadGroupSetsRequest struct {
// Required. The ID of the dataset these read group sets will belong to. The
// caller must have WRITE permissions to this dataset.
DatasetId string `protobuf:"bytes,1,opt,name=dataset_id,json=datasetId,proto3" json:"dataset_id,omitempty"`
// The reference set to which the imported read group sets are aligned to, if
// any. The reference names of this reference set must be a superset of those
// found in the imported file headers. If no reference set id is provided, a
// best effort is made to associate with a matching reference set.
ReferenceSetId string `protobuf:"bytes,4,opt,name=reference_set_id,json=referenceSetId,proto3" json:"reference_set_id,omitempty"`
// A list of URIs pointing at [BAM
// files](https://samtools.github.io/hts-specs/SAMv1.pdf)
// in Google Cloud Storage.
// Those URIs can include wildcards (*), but do not add or remove
// matching files before import has completed.
//
// Note that Google Cloud Storage object listing is only eventually
// consistent: files added may be not be immediately visible to
// everyone. Thus, if using a wildcard it is preferable not to start
// the import immediately after the files are created.
SourceUris []string `protobuf:"bytes,2,rep,name=source_uris,json=sourceUris,proto3" json:"source_uris,omitempty"`
// The partition strategy describes how read groups are partitioned into read
// group sets.
PartitionStrategy ImportReadGroupSetsRequest_PartitionStrategy `protobuf:"varint,5,opt,name=partition_strategy,json=partitionStrategy,proto3,enum=google.genomics.v1.ImportReadGroupSetsRequest_PartitionStrategy" json:"partition_strategy,omitempty"`
XXX_NoUnkeyedLiteral struct{} `json:"-"`
XXX_unrecognized []byte `json:"-"`
XXX_sizecache int32 `json:"-"`
}
func (m *ImportReadGroupSetsRequest) Reset() { *m = ImportReadGroupSetsRequest{} }
func (m *ImportReadGroupSetsRequest) String() string { return proto.CompactTextString(m) }
func (*ImportReadGroupSetsRequest) ProtoMessage() {}
func (*ImportReadGroupSetsRequest) Descriptor() ([]byte, []int) {
return fileDescriptor_6b02d5d0c80a106c, []int{2}
}
func (m *ImportReadGroupSetsRequest) XXX_Unmarshal(b []byte) error {
return xxx_messageInfo_ImportReadGroupSetsRequest.Unmarshal(m, b)
}
func (m *ImportReadGroupSetsRequest) XXX_Marshal(b []byte, deterministic bool) ([]byte, error) {
return xxx_messageInfo_ImportReadGroupSetsRequest.Marshal(b, m, deterministic)
}
func (m *ImportReadGroupSetsRequest) XXX_Merge(src proto.Message) {
xxx_messageInfo_ImportReadGroupSetsRequest.Merge(m, src)
}
func (m *ImportReadGroupSetsRequest) XXX_Size() int {
return xxx_messageInfo_ImportReadGroupSetsRequest.Size(m)
}
func (m *ImportReadGroupSetsRequest) XXX_DiscardUnknown() {
xxx_messageInfo_ImportReadGroupSetsRequest.DiscardUnknown(m)
}
var xxx_messageInfo_ImportReadGroupSetsRequest proto.InternalMessageInfo
func (m *ImportReadGroupSetsRequest) GetDatasetId() string {
if m != nil {
return m.DatasetId
}
return ""
}
func (m *ImportReadGroupSetsRequest) GetReferenceSetId() string {
if m != nil {
return m.ReferenceSetId
}
return ""
}
func (m *ImportReadGroupSetsRequest) GetSourceUris() []string {
if m != nil {
return m.SourceUris
}
return nil
}
func (m *ImportReadGroupSetsRequest) GetPartitionStrategy() ImportReadGroupSetsRequest_PartitionStrategy {
if m != nil {
return m.PartitionStrategy
}
return ImportReadGroupSetsRequest_PARTITION_STRATEGY_UNSPECIFIED
}
// The read group set import response.
type ImportReadGroupSetsResponse struct {
// IDs of the read group sets that were created.
ReadGroupSetIds []string `protobuf:"bytes,1,rep,name=read_group_set_ids,json=readGroupSetIds,proto3" json:"read_group_set_ids,omitempty"`
XXX_NoUnkeyedLiteral struct{} `json:"-"`
XXX_unrecognized []byte `json:"-"`
XXX_sizecache int32 `json:"-"`
}
func (m *ImportReadGroupSetsResponse) Reset() { *m = ImportReadGroupSetsResponse{} }
func (m *ImportReadGroupSetsResponse) String() string { return proto.CompactTextString(m) }
func (*ImportReadGroupSetsResponse) ProtoMessage() {}
func (*ImportReadGroupSetsResponse) Descriptor() ([]byte, []int) {
return fileDescriptor_6b02d5d0c80a106c, []int{3}
}
func (m *ImportReadGroupSetsResponse) XXX_Unmarshal(b []byte) error {
return xxx_messageInfo_ImportReadGroupSetsResponse.Unmarshal(m, b)
}
func (m *ImportReadGroupSetsResponse) XXX_Marshal(b []byte, deterministic bool) ([]byte, error) {
return xxx_messageInfo_ImportReadGroupSetsResponse.Marshal(b, m, deterministic)
}
func (m *ImportReadGroupSetsResponse) XXX_Merge(src proto.Message) {
xxx_messageInfo_ImportReadGroupSetsResponse.Merge(m, src)
}
func (m *ImportReadGroupSetsResponse) XXX_Size() int {
return xxx_messageInfo_ImportReadGroupSetsResponse.Size(m)
}
func (m *ImportReadGroupSetsResponse) XXX_DiscardUnknown() {
xxx_messageInfo_ImportReadGroupSetsResponse.DiscardUnknown(m)
}
var xxx_messageInfo_ImportReadGroupSetsResponse proto.InternalMessageInfo
func (m *ImportReadGroupSetsResponse) GetReadGroupSetIds() []string {
if m != nil {
return m.ReadGroupSetIds
}
return nil
}
// The read group set export request.
type ExportReadGroupSetRequest struct {
// Required. The Google Cloud project ID that owns this
// export. The caller must have WRITE access to this project.
ProjectId string `protobuf:"bytes,1,opt,name=project_id,json=projectId,proto3" json:"project_id,omitempty"`
// Required. A Google Cloud Storage URI for the exported BAM file.
// The currently authenticated user must have write access to the new file.
// An error will be returned if the URI already contains data.
ExportUri string `protobuf:"bytes,2,opt,name=export_uri,json=exportUri,proto3" json:"export_uri,omitempty"`
// Required. The ID of the read group set to export. The caller must have
// READ access to this read group set.
ReadGroupSetId string `protobuf:"bytes,3,opt,name=read_group_set_id,json=readGroupSetId,proto3" json:"read_group_set_id,omitempty"`
// The reference names to export. If this is not specified, all reference
// sequences, including unmapped reads, are exported.
// Use `*` to export only unmapped reads.
ReferenceNames []string `protobuf:"bytes,4,rep,name=reference_names,json=referenceNames,proto3" json:"reference_names,omitempty"`
XXX_NoUnkeyedLiteral struct{} `json:"-"`
XXX_unrecognized []byte `json:"-"`
XXX_sizecache int32 `json:"-"`
}
func (m *ExportReadGroupSetRequest) Reset() { *m = ExportReadGroupSetRequest{} }
func (m *ExportReadGroupSetRequest) String() string { return proto.CompactTextString(m) }
func (*ExportReadGroupSetRequest) ProtoMessage() {}
func (*ExportReadGroupSetRequest) Descriptor() ([]byte, []int) {
return fileDescriptor_6b02d5d0c80a106c, []int{4}
}
func (m *ExportReadGroupSetRequest) XXX_Unmarshal(b []byte) error {
return xxx_messageInfo_ExportReadGroupSetRequest.Unmarshal(m, b)
}
func (m *ExportReadGroupSetRequest) XXX_Marshal(b []byte, deterministic bool) ([]byte, error) {
return xxx_messageInfo_ExportReadGroupSetRequest.Marshal(b, m, deterministic)
}
func (m *ExportReadGroupSetRequest) XXX_Merge(src proto.Message) {
xxx_messageInfo_ExportReadGroupSetRequest.Merge(m, src)
}
func (m *ExportReadGroupSetRequest) XXX_Size() int {
return xxx_messageInfo_ExportReadGroupSetRequest.Size(m)
}
func (m *ExportReadGroupSetRequest) XXX_DiscardUnknown() {
xxx_messageInfo_ExportReadGroupSetRequest.DiscardUnknown(m)
}
var xxx_messageInfo_ExportReadGroupSetRequest proto.InternalMessageInfo
func (m *ExportReadGroupSetRequest) GetProjectId() string {
if m != nil {
return m.ProjectId
}
return ""
}
func (m *ExportReadGroupSetRequest) GetExportUri() string {
if m != nil {
return m.ExportUri
}
return ""
}
func (m *ExportReadGroupSetRequest) GetReadGroupSetId() string {
if m != nil {
return m.ReadGroupSetId
}
return ""
}
func (m *ExportReadGroupSetRequest) GetReferenceNames() []string {
if m != nil {
return m.ReferenceNames
}
return nil
}
type UpdateReadGroupSetRequest struct {
// The ID of the read group set to be updated. The caller must have WRITE
// permissions to the dataset associated with this read group set.
ReadGroupSetId string `protobuf:"bytes,1,opt,name=read_group_set_id,json=readGroupSetId,proto3" json:"read_group_set_id,omitempty"`
// The new read group set data. See `updateMask` for details on mutability of
// fields.
ReadGroupSet *ReadGroupSet `protobuf:"bytes,2,opt,name=read_group_set,json=readGroupSet,proto3" json:"read_group_set,omitempty"`
// An optional mask specifying which fields to update. Supported fields:
//
// * [name][google.genomics.v1.ReadGroupSet.name].
// * [referenceSetId][google.genomics.v1.ReadGroupSet.reference_set_id].
//
// Leaving `updateMask` unset is equivalent to specifying all mutable
// fields.
UpdateMask *field_mask.FieldMask `protobuf:"bytes,3,opt,name=update_mask,json=updateMask,proto3" json:"update_mask,omitempty"`
XXX_NoUnkeyedLiteral struct{} `json:"-"`
XXX_unrecognized []byte `json:"-"`
XXX_sizecache int32 `json:"-"`
}
func (m *UpdateReadGroupSetRequest) Reset() { *m = UpdateReadGroupSetRequest{} }
func (m *UpdateReadGroupSetRequest) String() string { return proto.CompactTextString(m) }
func (*UpdateReadGroupSetRequest) ProtoMessage() {}
func (*UpdateReadGroupSetRequest) Descriptor() ([]byte, []int) {
return fileDescriptor_6b02d5d0c80a106c, []int{5}
}
func (m *UpdateReadGroupSetRequest) XXX_Unmarshal(b []byte) error {
return xxx_messageInfo_UpdateReadGroupSetRequest.Unmarshal(m, b)
}
func (m *UpdateReadGroupSetRequest) XXX_Marshal(b []byte, deterministic bool) ([]byte, error) {
return xxx_messageInfo_UpdateReadGroupSetRequest.Marshal(b, m, deterministic)
}
func (m *UpdateReadGroupSetRequest) XXX_Merge(src proto.Message) {
xxx_messageInfo_UpdateReadGroupSetRequest.Merge(m, src)
}
func (m *UpdateReadGroupSetRequest) XXX_Size() int {
return xxx_messageInfo_UpdateReadGroupSetRequest.Size(m)
}
func (m *UpdateReadGroupSetRequest) XXX_DiscardUnknown() {
xxx_messageInfo_UpdateReadGroupSetRequest.DiscardUnknown(m)
}
var xxx_messageInfo_UpdateReadGroupSetRequest proto.InternalMessageInfo
func (m *UpdateReadGroupSetRequest) GetReadGroupSetId() string {
if m != nil {
return m.ReadGroupSetId
}
return ""
}
func (m *UpdateReadGroupSetRequest) GetReadGroupSet() *ReadGroupSet {
if m != nil {
return m.ReadGroupSet
}
return nil
}
func (m *UpdateReadGroupSetRequest) GetUpdateMask() *field_mask.FieldMask {
if m != nil {
return m.UpdateMask
}
return nil
}
type DeleteReadGroupSetRequest struct {
// The ID of the read group set to be deleted. The caller must have WRITE
// permissions to the dataset associated with this read group set.
ReadGroupSetId string `protobuf:"bytes,1,opt,name=read_group_set_id,json=readGroupSetId,proto3" json:"read_group_set_id,omitempty"`
XXX_NoUnkeyedLiteral struct{} `json:"-"`
XXX_unrecognized []byte `json:"-"`
XXX_sizecache int32 `json:"-"`
}
func (m *DeleteReadGroupSetRequest) Reset() { *m = DeleteReadGroupSetRequest{} }
func (m *DeleteReadGroupSetRequest) String() string { return proto.CompactTextString(m) }
func (*DeleteReadGroupSetRequest) ProtoMessage() {}
func (*DeleteReadGroupSetRequest) Descriptor() ([]byte, []int) {
return fileDescriptor_6b02d5d0c80a106c, []int{6}
}
func (m *DeleteReadGroupSetRequest) XXX_Unmarshal(b []byte) error {
return xxx_messageInfo_DeleteReadGroupSetRequest.Unmarshal(m, b)
}
func (m *DeleteReadGroupSetRequest) XXX_Marshal(b []byte, deterministic bool) ([]byte, error) {
return xxx_messageInfo_DeleteReadGroupSetRequest.Marshal(b, m, deterministic)
}
func (m *DeleteReadGroupSetRequest) XXX_Merge(src proto.Message) {
xxx_messageInfo_DeleteReadGroupSetRequest.Merge(m, src)
}
func (m *DeleteReadGroupSetRequest) XXX_Size() int {
return xxx_messageInfo_DeleteReadGroupSetRequest.Size(m)
}
func (m *DeleteReadGroupSetRequest) XXX_DiscardUnknown() {
xxx_messageInfo_DeleteReadGroupSetRequest.DiscardUnknown(m)
}
var xxx_messageInfo_DeleteReadGroupSetRequest proto.InternalMessageInfo
func (m *DeleteReadGroupSetRequest) GetReadGroupSetId() string {
if m != nil {
return m.ReadGroupSetId
}
return ""
}
type GetReadGroupSetRequest struct {
// The ID of the read group set.
ReadGroupSetId string `protobuf:"bytes,1,opt,name=read_group_set_id,json=readGroupSetId,proto3" json:"read_group_set_id,omitempty"`
XXX_NoUnkeyedLiteral struct{} `json:"-"`
XXX_unrecognized []byte `json:"-"`
XXX_sizecache int32 `json:"-"`
}
func (m *GetReadGroupSetRequest) Reset() { *m = GetReadGroupSetRequest{} }
func (m *GetReadGroupSetRequest) String() string { return proto.CompactTextString(m) }
func (*GetReadGroupSetRequest) ProtoMessage() {}
func (*GetReadGroupSetRequest) Descriptor() ([]byte, []int) {
return fileDescriptor_6b02d5d0c80a106c, []int{7}
}
func (m *GetReadGroupSetRequest) XXX_Unmarshal(b []byte) error {
return xxx_messageInfo_GetReadGroupSetRequest.Unmarshal(m, b)
}
func (m *GetReadGroupSetRequest) XXX_Marshal(b []byte, deterministic bool) ([]byte, error) {
return xxx_messageInfo_GetReadGroupSetRequest.Marshal(b, m, deterministic)
}
func (m *GetReadGroupSetRequest) XXX_Merge(src proto.Message) {
xxx_messageInfo_GetReadGroupSetRequest.Merge(m, src)
}
func (m *GetReadGroupSetRequest) XXX_Size() int {
return xxx_messageInfo_GetReadGroupSetRequest.Size(m)
}
func (m *GetReadGroupSetRequest) XXX_DiscardUnknown() {
xxx_messageInfo_GetReadGroupSetRequest.DiscardUnknown(m)
}
var xxx_messageInfo_GetReadGroupSetRequest proto.InternalMessageInfo
func (m *GetReadGroupSetRequest) GetReadGroupSetId() string {
if m != nil {
return m.ReadGroupSetId
}
return ""
}
type ListCoverageBucketsRequest struct {
// Required. The ID of the read group set over which coverage is requested.
ReadGroupSetId string `protobuf:"bytes,1,opt,name=read_group_set_id,json=readGroupSetId,proto3" json:"read_group_set_id,omitempty"`
// The name of the reference to query, within the reference set associated
// with this query. Optional.
ReferenceName string `protobuf:"bytes,3,opt,name=reference_name,json=referenceName,proto3" json:"reference_name,omitempty"`
// The start position of the range on the reference, 0-based inclusive. If
// specified, `referenceName` must also be specified. Defaults to 0.
Start int64 `protobuf:"varint,4,opt,name=start,proto3" json:"start,omitempty"`
// The end position of the range on the reference, 0-based exclusive. If
// specified, `referenceName` must also be specified. If unset or 0, defaults
// to the length of the reference.
End int64 `protobuf:"varint,5,opt,name=end,proto3" json:"end,omitempty"`
// The desired width of each reported coverage bucket in base pairs. This
// will be rounded down to the nearest precomputed bucket width; the value
// of which is returned as `bucketWidth` in the response. Defaults
// to infinity (each bucket spans an entire reference sequence) or the length
// of the target range, if specified. The smallest precomputed
// `bucketWidth` is currently 2048 base pairs; this is subject to
// change.
TargetBucketWidth int64 `protobuf:"varint,6,opt,name=target_bucket_width,json=targetBucketWidth,proto3" json:"target_bucket_width,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,7,opt,name=page_token,json=pageToken,proto3" json:"page_token,omitempty"`
// The maximum number of results to return in a single page. If unspecified,
// defaults to 1024. The maximum value is 2048.
PageSize int32 `protobuf:"varint,8,opt,name=page_size,json=pageSize,proto3" json:"page_size,omitempty"`
XXX_NoUnkeyedLiteral struct{} `json:"-"`
XXX_unrecognized []byte `json:"-"`
XXX_sizecache int32 `json:"-"`
}
func (m *ListCoverageBucketsRequest) Reset() { *m = ListCoverageBucketsRequest{} }
func (m *ListCoverageBucketsRequest) String() string { return proto.CompactTextString(m) }
func (*ListCoverageBucketsRequest) ProtoMessage() {}
func (*ListCoverageBucketsRequest) Descriptor() ([]byte, []int) {
return fileDescriptor_6b02d5d0c80a106c, []int{8}
}
func (m *ListCoverageBucketsRequest) XXX_Unmarshal(b []byte) error {
return xxx_messageInfo_ListCoverageBucketsRequest.Unmarshal(m, b)
}
func (m *ListCoverageBucketsRequest) XXX_Marshal(b []byte, deterministic bool) ([]byte, error) {
return xxx_messageInfo_ListCoverageBucketsRequest.Marshal(b, m, deterministic)
}
func (m *ListCoverageBucketsRequest) XXX_Merge(src proto.Message) {
xxx_messageInfo_ListCoverageBucketsRequest.Merge(m, src)
}
func (m *ListCoverageBucketsRequest) XXX_Size() int {
return xxx_messageInfo_ListCoverageBucketsRequest.Size(m)
}
func (m *ListCoverageBucketsRequest) XXX_DiscardUnknown() {
xxx_messageInfo_ListCoverageBucketsRequest.DiscardUnknown(m)
}
var xxx_messageInfo_ListCoverageBucketsRequest proto.InternalMessageInfo
func (m *ListCoverageBucketsRequest) GetReadGroupSetId() string {
if m != nil {
return m.ReadGroupSetId
}
return ""
}
func (m *ListCoverageBucketsRequest) GetReferenceName() string {
if m != nil {
return m.ReferenceName
}
return ""
}
func (m *ListCoverageBucketsRequest) GetStart() int64 {
if m != nil {
return m.Start
}
return 0
}
func (m *ListCoverageBucketsRequest) GetEnd() int64 {
if m != nil {
return m.End
}
return 0
}
func (m *ListCoverageBucketsRequest) GetTargetBucketWidth() int64 {
if m != nil {
return m.TargetBucketWidth
}
return 0
}
func (m *ListCoverageBucketsRequest) GetPageToken() string {
if m != nil {
return m.PageToken
}
return ""
}
func (m *ListCoverageBucketsRequest) GetPageSize() int32 {
if m != nil {
return m.PageSize
}
return 0
}
// A bucket over which read coverage has been precomputed. A bucket corresponds
// to a specific range of the reference sequence.
type CoverageBucket struct {
// The genomic coordinate range spanned by this bucket.
Range *Range `protobuf:"bytes,1,opt,name=range,proto3" json:"range,omitempty"`
// The average number of reads which are aligned to each individual
// reference base in this bucket.
MeanCoverage float32 `protobuf:"fixed32,2,opt,name=mean_coverage,json=meanCoverage,proto3" json:"mean_coverage,omitempty"`
XXX_NoUnkeyedLiteral struct{} `json:"-"`
XXX_unrecognized []byte `json:"-"`
XXX_sizecache int32 `json:"-"`
}
func (m *CoverageBucket) Reset() { *m = CoverageBucket{} }
func (m *CoverageBucket) String() string { return proto.CompactTextString(m) }
func (*CoverageBucket) ProtoMessage() {}
func (*CoverageBucket) Descriptor() ([]byte, []int) {
return fileDescriptor_6b02d5d0c80a106c, []int{9}
}
func (m *CoverageBucket) XXX_Unmarshal(b []byte) error {
return xxx_messageInfo_CoverageBucket.Unmarshal(m, b)
}
func (m *CoverageBucket) XXX_Marshal(b []byte, deterministic bool) ([]byte, error) {
return xxx_messageInfo_CoverageBucket.Marshal(b, m, deterministic)
}
func (m *CoverageBucket) XXX_Merge(src proto.Message) {
xxx_messageInfo_CoverageBucket.Merge(m, src)
}
func (m *CoverageBucket) XXX_Size() int {
return xxx_messageInfo_CoverageBucket.Size(m)
}
func (m *CoverageBucket) XXX_DiscardUnknown() {
xxx_messageInfo_CoverageBucket.DiscardUnknown(m)
}
var xxx_messageInfo_CoverageBucket proto.InternalMessageInfo
func (m *CoverageBucket) GetRange() *Range {
if m != nil {
return m.Range
}
return nil
}
func (m *CoverageBucket) GetMeanCoverage() float32 {
if m != nil {
return m.MeanCoverage
}
return 0
}
type ListCoverageBucketsResponse struct {
// The length of each coverage bucket in base pairs. Note that buckets at the
// end of a reference sequence may be shorter. This value is omitted if the
// bucket width is infinity (the default behaviour, with no range or
// `targetBucketWidth`).
BucketWidth int64 `protobuf:"varint,1,opt,name=bucket_width,json=bucketWidth,proto3" json:"bucket_width,omitempty"`
// The coverage buckets. The list of buckets is sparse; a bucket with 0
// overlapping reads is not returned. A bucket never crosses more than one
// reference sequence. Each bucket has width `bucketWidth`, unless
// its end is the end of the reference sequence.
CoverageBuckets []*CoverageBucket `protobuf:"bytes,2,rep,name=coverage_buckets,json=coverageBuckets,proto3" json:"coverage_buckets,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,proto3" json:"next_page_token,omitempty"`
XXX_NoUnkeyedLiteral struct{} `json:"-"`
XXX_unrecognized []byte `json:"-"`
XXX_sizecache int32 `json:"-"`
}
func (m *ListCoverageBucketsResponse) Reset() { *m = ListCoverageBucketsResponse{} }
func (m *ListCoverageBucketsResponse) String() string { return proto.CompactTextString(m) }
func (*ListCoverageBucketsResponse) ProtoMessage() {}
func (*ListCoverageBucketsResponse) Descriptor() ([]byte, []int) {
return fileDescriptor_6b02d5d0c80a106c, []int{10}
}
func (m *ListCoverageBucketsResponse) XXX_Unmarshal(b []byte) error {
return xxx_messageInfo_ListCoverageBucketsResponse.Unmarshal(m, b)
}
func (m *ListCoverageBucketsResponse) XXX_Marshal(b []byte, deterministic bool) ([]byte, error) {
return xxx_messageInfo_ListCoverageBucketsResponse.Marshal(b, m, deterministic)
}
func (m *ListCoverageBucketsResponse) XXX_Merge(src proto.Message) {
xxx_messageInfo_ListCoverageBucketsResponse.Merge(m, src)
}
func (m *ListCoverageBucketsResponse) XXX_Size() int {
return xxx_messageInfo_ListCoverageBucketsResponse.Size(m)
}
func (m *ListCoverageBucketsResponse) XXX_DiscardUnknown() {
xxx_messageInfo_ListCoverageBucketsResponse.DiscardUnknown(m)
}
var xxx_messageInfo_ListCoverageBucketsResponse proto.InternalMessageInfo
func (m *ListCoverageBucketsResponse) GetBucketWidth() int64 {
if m != nil {
return m.BucketWidth
}
return 0
}
func (m *ListCoverageBucketsResponse) GetCoverageBuckets() []*CoverageBucket {
if m != nil {
return m.CoverageBuckets
}
return nil
}
func (m *ListCoverageBucketsResponse) GetNextPageToken() string {
if m != nil {
return m.NextPageToken
}
return ""
}
// The read search request.
type SearchReadsRequest struct {
// The IDs of the read groups sets within which to search for reads. All
// specified read group sets must be aligned against a common set of reference
// sequences; this defines the genomic coordinates for the query. Must specify
// one of `readGroupSetIds` or `readGroupIds`.
ReadGroupSetIds []string `protobuf:"bytes,1,rep,name=read_group_set_ids,json=readGroupSetIds,proto3" json:"read_group_set_ids,omitempty"`
// The IDs of the read groups within which to search for reads. All specified
// read groups must belong to the same read group sets. Must specify one of
// `readGroupSetIds` or `readGroupIds`.
ReadGroupIds []string `protobuf:"bytes,5,rep,name=read_group_ids,json=readGroupIds,proto3" json:"read_group_ids,omitempty"`
// The reference sequence name, for example `chr1`, `1`, or `chrX`. If set to
// `*`, only unmapped reads are returned. If unspecified, all reads (mapped
// and unmapped) are returned.
ReferenceName string `protobuf:"bytes,7,opt,name=reference_name,json=referenceName,proto3" json:"reference_name,omitempty"`
// The start position of the range on the reference, 0-based inclusive. If
// specified, `referenceName` must also be specified.
Start int64 `protobuf:"varint,8,opt,name=start,proto3" json:"start,omitempty"`
// The end position of the range on the reference, 0-based exclusive. If
// specified, `referenceName` must also be specified.
End int64 `protobuf:"varint,9,opt,name=end,proto3" 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,3,opt,name=page_token,json=pageToken,proto3" json:"page_token,omitempty"`
// The maximum number of results to return in a single page. If unspecified,
// defaults to 256. The maximum value is 2048.
PageSize int32 `protobuf:"varint,4,opt,name=page_size,json=pageSize,proto3" json:"page_size,omitempty"`
XXX_NoUnkeyedLiteral struct{} `json:"-"`
XXX_unrecognized []byte `json:"-"`
XXX_sizecache int32 `json:"-"`
}
func (m *SearchReadsRequest) Reset() { *m = SearchReadsRequest{} }
func (m *SearchReadsRequest) String() string { return proto.CompactTextString(m) }
func (*SearchReadsRequest) ProtoMessage() {}
func (*SearchReadsRequest) Descriptor() ([]byte, []int) {
return fileDescriptor_6b02d5d0c80a106c, []int{11}
}
func (m *SearchReadsRequest) XXX_Unmarshal(b []byte) error {
return xxx_messageInfo_SearchReadsRequest.Unmarshal(m, b)
}
func (m *SearchReadsRequest) XXX_Marshal(b []byte, deterministic bool) ([]byte, error) {
return xxx_messageInfo_SearchReadsRequest.Marshal(b, m, deterministic)
}
func (m *SearchReadsRequest) XXX_Merge(src proto.Message) {
xxx_messageInfo_SearchReadsRequest.Merge(m, src)
}
func (m *SearchReadsRequest) XXX_Size() int {
return xxx_messageInfo_SearchReadsRequest.Size(m)
}
func (m *SearchReadsRequest) XXX_DiscardUnknown() {
xxx_messageInfo_SearchReadsRequest.DiscardUnknown(m)
}
var xxx_messageInfo_SearchReadsRequest proto.InternalMessageInfo
func (m *SearchReadsRequest) GetReadGroupSetIds() []string {
if m != nil {
return m.ReadGroupSetIds
}
return nil
}
func (m *SearchReadsRequest) GetReadGroupIds() []string {
if m != nil {
return m.ReadGroupIds
}
return nil
}
func (m *SearchReadsRequest) GetReferenceName() string {
if m != nil {
return m.ReferenceName
}
return ""
}
func (m *SearchReadsRequest) GetStart() int64 {
if m != nil {
return m.Start
}
return 0
}
func (m *SearchReadsRequest) GetEnd() int64 {
if m != nil {
return m.End
}
return 0
}
func (m *SearchReadsRequest) GetPageToken() string {
if m != nil {
return m.PageToken
}
return ""
}
func (m *SearchReadsRequest) GetPageSize() int32 {
if m != nil {
return m.PageSize
}
return 0
}
// The read search response.
type SearchReadsResponse struct {
// The list of matching alignments sorted by mapped genomic coordinate,
// if any, ascending in position within the same reference. Unmapped reads,
// which have no position, are returned contiguously and are sorted in
// ascending lexicographic order by fragment name.
Alignments []*Read `protobuf:"bytes,1,rep,name=alignments,proto3" json:"alignments,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,proto3" json:"next_page_token,omitempty"`
XXX_NoUnkeyedLiteral struct{} `json:"-"`
XXX_unrecognized []byte `json:"-"`
XXX_sizecache int32 `json:"-"`
}
func (m *SearchReadsResponse) Reset() { *m = SearchReadsResponse{} }
func (m *SearchReadsResponse) String() string { return proto.CompactTextString(m) }
func (*SearchReadsResponse) ProtoMessage() {}
func (*SearchReadsResponse) Descriptor() ([]byte, []int) {
return fileDescriptor_6b02d5d0c80a106c, []int{12}
}
func (m *SearchReadsResponse) XXX_Unmarshal(b []byte) error {
return xxx_messageInfo_SearchReadsResponse.Unmarshal(m, b)
}
func (m *SearchReadsResponse) XXX_Marshal(b []byte, deterministic bool) ([]byte, error) {
return xxx_messageInfo_SearchReadsResponse.Marshal(b, m, deterministic)
}
func (m *SearchReadsResponse) XXX_Merge(src proto.Message) {
xxx_messageInfo_SearchReadsResponse.Merge(m, src)
}
func (m *SearchReadsResponse) XXX_Size() int {
return xxx_messageInfo_SearchReadsResponse.Size(m)
}
func (m *SearchReadsResponse) XXX_DiscardUnknown() {
xxx_messageInfo_SearchReadsResponse.DiscardUnknown(m)
}
var xxx_messageInfo_SearchReadsResponse proto.InternalMessageInfo
func (m *SearchReadsResponse) GetAlignments() []*Read {
if m != nil {
return m.Alignments
}
return nil
}
func (m *SearchReadsResponse) GetNextPageToken() string {
if m != nil {
return m.NextPageToken
}
return ""
}
// The stream reads request.
type StreamReadsRequest struct {
// The Google Cloud project ID which will be billed
// for this access. The caller must have WRITE access to this project.
// Required.
ProjectId string `protobuf:"bytes,1,opt,name=project_id,json=projectId,proto3" json:"project_id,omitempty"`
// The ID of the read group set from which to stream reads.
ReadGroupSetId string `protobuf:"bytes,2,opt,name=read_group_set_id,json=readGroupSetId,proto3" json:"read_group_set_id,omitempty"`
// The reference sequence name, for example `chr1`,
// `1`, or `chrX`. If set to *, only unmapped reads are
// returned.
ReferenceName string `protobuf:"bytes,3,opt,name=reference_name,json=referenceName,proto3" json:"reference_name,omitempty"`
// The start position of the range on the reference, 0-based inclusive. If
// specified, `referenceName` must also be specified.
Start int64 `protobuf:"varint,4,opt,name=start,proto3" json:"start,omitempty"`
// The end position of the range on the reference, 0-based exclusive. If
// specified, `referenceName` must also be specified.
End int64 `protobuf:"varint,5,opt,name=end,proto3" json:"end,omitempty"`
// Restricts results to a shard containing approximately `1/totalShards`
// of the normal response payload for this query. Results from a sharded
// request are disjoint from those returned by all queries which differ only
// in their shard parameter. A shard may yield 0 results; this is especially
// likely for large values of `totalShards`.
//
// Valid values are `[0, totalShards)`.
Shard int32 `protobuf:"varint,6,opt,name=shard,proto3" json:"shard,omitempty"`
// Specifying `totalShards` causes a disjoint subset of the normal response
// payload to be returned for each query with a unique `shard` parameter
// specified. A best effort is made to yield equally sized shards. Sharding
// can be used to distribute processing amongst workers, where each worker is
// assigned a unique `shard` number and all workers specify the same
// `totalShards` number. The union of reads returned for all sharded queries
// `[0, totalShards)` is equal to those returned by a single unsharded query.
//
// Queries for different values of `totalShards` with common divisors will
// share shard boundaries. For example, streaming `shard` 2 of 5
// `totalShards` yields the same results as streaming `shard`s 4 and 5 of 10
// `totalShards`. This property can be leveraged for adaptive retries.
TotalShards int32 `protobuf:"varint,7,opt,name=total_shards,json=totalShards,proto3" json:"total_shards,omitempty"`
XXX_NoUnkeyedLiteral struct{} `json:"-"`
XXX_unrecognized []byte `json:"-"`
XXX_sizecache int32 `json:"-"`
}
func (m *StreamReadsRequest) Reset() { *m = StreamReadsRequest{} }
func (m *StreamReadsRequest) String() string { return proto.CompactTextString(m) }
func (*StreamReadsRequest) ProtoMessage() {}
func (*StreamReadsRequest) Descriptor() ([]byte, []int) {
return fileDescriptor_6b02d5d0c80a106c, []int{13}
}
func (m *StreamReadsRequest) XXX_Unmarshal(b []byte) error {
return xxx_messageInfo_StreamReadsRequest.Unmarshal(m, b)
}
func (m *StreamReadsRequest) XXX_Marshal(b []byte, deterministic bool) ([]byte, error) {
return xxx_messageInfo_StreamReadsRequest.Marshal(b, m, deterministic)
}
func (m *StreamReadsRequest) XXX_Merge(src proto.Message) {
xxx_messageInfo_StreamReadsRequest.Merge(m, src)
}
func (m *StreamReadsRequest) XXX_Size() int {
return xxx_messageInfo_StreamReadsRequest.Size(m)
}
func (m *StreamReadsRequest) XXX_DiscardUnknown() {
xxx_messageInfo_StreamReadsRequest.DiscardUnknown(m)
}
var xxx_messageInfo_StreamReadsRequest proto.InternalMessageInfo
func (m *StreamReadsRequest) GetProjectId() string {
if m != nil {
return m.ProjectId
}
return ""