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genomics-gen.go
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genomics-gen.go
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// Package genomics provides access to the Genomics API.
//
// See https://developers.google.com/genomics/v1beta2/reference
//
// Usage example:
//
// import "google.golang.org/api/genomics/v1beta2"
// ...
// genomicsService, err := genomics.New(oauthHttpClient)
package genomics
import (
"bytes"
"encoding/json"
"errors"
"fmt"
"golang.org/x/net/context"
"google.golang.org/api/googleapi"
"io"
"net/http"
"net/url"
"strconv"
"strings"
)
// Always reference these packages, just in case the auto-generated code
// below doesn't.
var _ = bytes.NewBuffer
var _ = strconv.Itoa
var _ = fmt.Sprintf
var _ = json.NewDecoder
var _ = io.Copy
var _ = url.Parse
var _ = googleapi.Version
var _ = errors.New
var _ = strings.Replace
var _ = context.Background
const apiId = "genomics:v1beta2"
const apiName = "genomics"
const apiVersion = "v1beta2"
const basePath = "https://www.googleapis.com/genomics/v1beta2/"
// OAuth2 scopes used by this API.
const (
// View and manage your data in Google BigQuery
BigqueryScope = "https://www.googleapis.com/auth/bigquery"
// View and manage your data across Google Cloud Platform services
CloudPlatformScope = "https://www.googleapis.com/auth/cloud-platform"
// Manage your data in Google Cloud Storage
DevstorageReadWriteScope = "https://www.googleapis.com/auth/devstorage.read_write"
// View and manage Genomics data
GenomicsScope = "https://www.googleapis.com/auth/genomics"
// View Genomics data
GenomicsReadonlyScope = "https://www.googleapis.com/auth/genomics.readonly"
)
func New(client *http.Client) (*Service, error) {
if client == nil {
return nil, errors.New("client is nil")
}
s := &Service{client: client, BasePath: basePath}
s.AnnotationSets = NewAnnotationSetsService(s)
s.Annotations = NewAnnotationsService(s)
s.Callsets = NewCallsetsService(s)
s.Datasets = NewDatasetsService(s)
s.Experimental = NewExperimentalService(s)
s.Jobs = NewJobsService(s)
s.Readgroupsets = NewReadgroupsetsService(s)
s.Reads = NewReadsService(s)
s.References = NewReferencesService(s)
s.Referencesets = NewReferencesetsService(s)
s.Variants = NewVariantsService(s)
s.Variantsets = NewVariantsetsService(s)
return s, nil
}
type Service struct {
client *http.Client
BasePath string // API endpoint base URL
UserAgent string // optional additional User-Agent fragment
AnnotationSets *AnnotationSetsService
Annotations *AnnotationsService
Callsets *CallsetsService
Datasets *DatasetsService
Experimental *ExperimentalService
Jobs *JobsService
Readgroupsets *ReadgroupsetsService
Reads *ReadsService
References *ReferencesService
Referencesets *ReferencesetsService
Variants *VariantsService
Variantsets *VariantsetsService
}
func (s *Service) userAgent() string {
if s.UserAgent == "" {
return googleapi.UserAgent
}
return googleapi.UserAgent + " " + s.UserAgent
}
func NewAnnotationSetsService(s *Service) *AnnotationSetsService {
rs := &AnnotationSetsService{s: s}
return rs
}
type AnnotationSetsService struct {
s *Service
}
func NewAnnotationsService(s *Service) *AnnotationsService {
rs := &AnnotationsService{s: s}
return rs
}
type AnnotationsService struct {
s *Service
}
func NewCallsetsService(s *Service) *CallsetsService {
rs := &CallsetsService{s: s}
return rs
}
type CallsetsService struct {
s *Service
}
func NewDatasetsService(s *Service) *DatasetsService {
rs := &DatasetsService{s: s}
return rs
}
type DatasetsService struct {
s *Service
}
func NewExperimentalService(s *Service) *ExperimentalService {
rs := &ExperimentalService{s: s}
rs.Jobs = NewExperimentalJobsService(s)
return rs
}
type ExperimentalService struct {
s *Service
Jobs *ExperimentalJobsService
}
func NewExperimentalJobsService(s *Service) *ExperimentalJobsService {
rs := &ExperimentalJobsService{s: s}
return rs
}
type ExperimentalJobsService struct {
s *Service
}
func NewJobsService(s *Service) *JobsService {
rs := &JobsService{s: s}
return rs
}
type JobsService struct {
s *Service
}
func NewReadgroupsetsService(s *Service) *ReadgroupsetsService {
rs := &ReadgroupsetsService{s: s}
rs.Coveragebuckets = NewReadgroupsetsCoveragebucketsService(s)
return rs
}
type ReadgroupsetsService struct {
s *Service
Coveragebuckets *ReadgroupsetsCoveragebucketsService
}
func NewReadgroupsetsCoveragebucketsService(s *Service) *ReadgroupsetsCoveragebucketsService {
rs := &ReadgroupsetsCoveragebucketsService{s: s}
return rs
}
type ReadgroupsetsCoveragebucketsService struct {
s *Service
}
func NewReadsService(s *Service) *ReadsService {
rs := &ReadsService{s: s}
return rs
}
type ReadsService struct {
s *Service
}
func NewReferencesService(s *Service) *ReferencesService {
rs := &ReferencesService{s: s}
rs.Bases = NewReferencesBasesService(s)
return rs
}
type ReferencesService struct {
s *Service
Bases *ReferencesBasesService
}
func NewReferencesBasesService(s *Service) *ReferencesBasesService {
rs := &ReferencesBasesService{s: s}
return rs
}
type ReferencesBasesService struct {
s *Service
}
func NewReferencesetsService(s *Service) *ReferencesetsService {
rs := &ReferencesetsService{s: s}
return rs
}
type ReferencesetsService struct {
s *Service
}
func NewVariantsService(s *Service) *VariantsService {
rs := &VariantsService{s: s}
return rs
}
type VariantsService struct {
s *Service
}
func NewVariantsetsService(s *Service) *VariantsetsService {
rs := &VariantsetsService{s: s}
return rs
}
type VariantsetsService struct {
s *Service
}
// AlignReadGroupSetsRequest: The read group set align request.
type AlignReadGroupSetsRequest struct {
// BamSourceUris: The BAM source files for alignment. Exactly one of
// readGroupSetId, bamSourceUris, interleavedFastqSource or
// pairedFastqSource must be provided. The caller must have READ
// permissions for these files.
BamSourceUris []string `json:"bamSourceUris,omitempty"`
// DatasetId: Required. The ID of the dataset the newly aligned read
// group sets will belong to. The caller must have WRITE permissions to
// this dataset.
DatasetId string `json:"datasetId,omitempty"`
// InterleavedFastqSource: The interleaved FASTQ source files for
// alignment, where both members of each pair of reads are found on
// consecutive records within the same FASTQ file. Exactly one of
// readGroupSetId, bamSourceUris, interleavedFastqSource or
// pairedFastqSource must be provided.
InterleavedFastqSource *InterleavedFastqSource `json:"interleavedFastqSource,omitempty"`
// PairedFastqSource: The paired end FASTQ source files for alignment,
// where each member of a pair of reads are found in separate files.
// Exactly one of readGroupSetId, bamSourceUris, interleavedFastqSource
// or pairedFastqSource must be provided.
PairedFastqSource *PairedFastqSource `json:"pairedFastqSource,omitempty"`
// ReadGroupSetId: The ID of the read group set which will be aligned. A
// new read group set will be generated to hold the aligned data, the
// originals will not be modified. The caller must have READ permissions
// for this read group set. Exactly one of readGroupSetId,
// bamSourceUris, interleavedFastqSource or pairedFastqSource must be
// provided.
ReadGroupSetId string `json:"readGroupSetId,omitempty"`
}
// AlignReadGroupSetsResponse: The read group set align response.
type AlignReadGroupSetsResponse struct {
// JobId: A job ID that can be used to get status information.
JobId string `json:"jobId,omitempty"`
}
// Annotation: An annotation describes a region of reference genome. The
// value of an annotation may be one of several canonical types,
// supplemented by arbitrary info tags. A variant annotation is
// represented by one or more of these canonical types. An annotation is
// not inherently associated with a specific sample or individual
// (though a client could choose to use annotations in this way).
// Example canonical annotation types are 'Gene' and 'Variant'.
type Annotation struct {
// AnnotationSetId: The ID of the containing annotation set.
AnnotationSetId string `json:"annotationSetId,omitempty"`
// Id: The generated unique ID for this annotation.
Id string `json:"id,omitempty"`
// Info: A string which maps to an array of values.
Info map[string][]string `json:"info,omitempty"`
// Name: The display name of this annotation.
Name string `json:"name,omitempty"`
// Position: The position of this annotation on the reference sequence.
Position *RangePosition `json:"position,omitempty"`
// Transcript: A transcript value represents the assertion that a
// particular region of the reference genome may be transcribed as RNA.
// An alternative splicing pattern would be represented as a separate
// transcript object. This field is only set for annotations of type
// TRANSCRIPT.
Transcript *Transcript `json:"transcript,omitempty"`
// Type: The data type for this annotation. Must match the containing
// annotation set's type.
//
// Possible values:
// "GENE"
// "GENERIC"
// "TRANSCRIPT"
// "VARIANT"
Type string `json:"type,omitempty"`
// Variant: A variant annotation, which describes the effect of a
// variant on the genome, the coding sequence, and/or higher level
// consequences at the organism level e.g. pathogenicity. This field is
// only set for annotations of type VARIANT.
Variant *VariantAnnotation `json:"variant,omitempty"`
}
// AnnotationSet: An annotation set is a logical grouping of annotations
// that share consistent type information and provenance. Examples of
// annotation sets include 'all genes from refseq', and 'all variant
// annotations from ClinVar'.
type AnnotationSet struct {
// DatasetId: The ID of the containing dataset.
DatasetId string `json:"datasetId,omitempty"`
// Id: The generated unique ID for this annotation set.
Id string `json:"id,omitempty"`
// Info: A string which maps to an array of values.
Info map[string][]string `json:"info,omitempty"`
// Name: The display name for this annotation set.
Name string `json:"name,omitempty"`
// ReferenceSetId: The ID of the reference set that defines the
// coordinate space for this set's annotations.
ReferenceSetId string `json:"referenceSetId,omitempty"`
// SourceUri: The source URI describing the file from which this
// annotation set was generated, if any.
SourceUri string `json:"sourceUri,omitempty"`
// Type: The type of annotations contained within this set.
//
// Possible values:
// "GENE"
// "GENERIC"
// "TRANSCRIPT"
// "VARIANT"
Type string `json:"type,omitempty"`
}
type BatchAnnotationsResponse struct {
// Entries: The resulting per-annotation entries, ordered consistently
// with the original request.
Entries []*BatchAnnotationsResponseEntry `json:"entries,omitempty"`
}
type BatchAnnotationsResponseEntry struct {
// Annotation: The annotation, if any.
Annotation *Annotation `json:"annotation,omitempty"`
// Status: The resulting status for this annotation operation.
Status *BatchAnnotationsResponseEntryStatus `json:"status,omitempty"`
}
type BatchAnnotationsResponseEntryStatus struct {
// Code: The HTTP status code for this operation.
Code int64 `json:"code,omitempty"`
// Message: Error message for this status, if any.
Message string `json:"message,omitempty"`
}
type BatchCreateAnnotationsRequest struct {
// Annotations: The annotations to be created. At most 4096 can be
// specified in a single request.
Annotations []*Annotation `json:"annotations,omitempty"`
}
// Call: A call represents the determination of genotype with respect to
// a particular variant. It may include associated information such as
// quality and phasing. For example, a call might assign a probability
// of 0.32 to the occurrence of a SNP named rs1234 in a call set with
// the name NA12345.
type Call struct {
// CallSetId: The ID of the call set this variant call belongs to.
CallSetId string `json:"callSetId,omitempty"`
// CallSetName: The name of the call set this variant call belongs to.
CallSetName string `json:"callSetName,omitempty"`
// Genotype: The genotype of this variant call. Each value represents
// either the value of the referenceBases field or a 1-based index into
// alternateBases. If a variant had a referenceBases value of T and an
// alternateBases value of ["A", "C"], and the genotype was [2, 1], that
// would mean the call represented the heterozygous value CA for this
// variant. If the genotype was instead [0, 1], the represented value
// would be TA. Ordering of the genotype values is important if the
// phaseset is present. If a genotype is not called (that is, a . is
// present in the GT string) -1 is returned.
Genotype []int64 `json:"genotype,omitempty"`
// GenotypeLikelihood: The genotype likelihoods for this variant call.
// Each array entry represents how likely a specific genotype is for
// this call. The value ordering is defined by the GL tag in the VCF
// spec. If Phred-scaled genotype likelihood scores (PL) are available
// and log10(P) genotype likelihood scores (GL) are not, PL scores are
// converted to GL scores. If both are available, PL scores are stored
// in info.
GenotypeLikelihood []float64 `json:"genotypeLikelihood,omitempty"`
// Info: A string which maps to an array of values.
Info map[string][]string `json:"info,omitempty"`
// Phaseset: If this field is present, this variant call's genotype
// ordering implies the phase of the bases and is consistent with any
// other variant calls in the same reference sequence which have the
// same phaseset value. When importing data from VCF, if the genotype
// data was phased but no phase set was specified this field will be set
// to *.
Phaseset string `json:"phaseset,omitempty"`
}
// CallReadGroupSetsRequest: The read group set call request.
type CallReadGroupSetsRequest struct {
// DatasetId: Required. The ID of the dataset the called variants will
// belong to. The caller must have WRITE permissions to this dataset.
DatasetId string `json:"datasetId,omitempty"`
// ReadGroupSetId: The IDs of the read group sets which will be called.
// The caller must have READ permissions for these read group sets. One
// of readGroupSetId or sourceUris must be provided.
ReadGroupSetId string `json:"readGroupSetId,omitempty"`
// SourceUris: A list of URIs pointing at BAM files in Google Cloud
// Storage which will be called. FASTQ files are not allowed. The caller
// must have READ permissions for these files. One of readGroupSetId or
// sourceUris must be provided.
SourceUris []string `json:"sourceUris,omitempty"`
}
// CallReadGroupSetsResponse: The read group set call response.
type CallReadGroupSetsResponse struct {
// JobId: A job ID that can be used to get status information.
JobId string `json:"jobId,omitempty"`
}
// CallSet: A call set is a collection of variant calls, typically for
// one sample. It belongs to a variant set.
type CallSet struct {
// Created: The date this call set was created in milliseconds from the
// epoch.
Created int64 `json:"created,omitempty,string"`
// Id: The Google generated ID of the call set, immutable.
Id string `json:"id,omitempty"`
// Info: A string which maps to an array of values.
Info map[string][]string `json:"info,omitempty"`
// Name: The call set name.
Name string `json:"name,omitempty"`
// SampleId: The sample ID this call set corresponds to.
SampleId string `json:"sampleId,omitempty"`
// VariantSetIds: The IDs of the variant sets this call set belongs to.
VariantSetIds []string `json:"variantSetIds,omitempty"`
}
// CigarUnit: A single CIGAR operation.
type CigarUnit struct {
// Possible values:
// "ALIGNMENT_MATCH"
// "CLIP_HARD"
// "CLIP_SOFT"
// "DELETE"
// "INSERT"
// "OPERATION_UNSPECIFIED"
// "PAD"
// "SEQUENCE_MATCH"
// "SEQUENCE_MISMATCH"
// "SKIP"
Operation string `json:"operation,omitempty"`
// OperationLength: The number of bases that the operation runs for.
// Required.
OperationLength int64 `json:"operationLength,omitempty,string"`
// ReferenceSequence: referenceSequence is only used at mismatches
// (SEQUENCE_MISMATCH) and deletions (DELETE). Filling this field
// replaces SAM's MD tag. If the relevant information is not available,
// this field is unset.
ReferenceSequence string `json:"referenceSequence,omitempty"`
}
// CoverageBucket: A bucket over which read coverage has been
// precomputed. A bucket corresponds to a specific range of the
// reference sequence.
type CoverageBucket struct {
// MeanCoverage: The average number of reads which are aligned to each
// individual reference base in this bucket.
MeanCoverage float64 `json:"meanCoverage,omitempty"`
// Range: The genomic coordinate range spanned by this bucket.
Range *Range `json:"range,omitempty"`
}
// Dataset: A Dataset is a collection of genomic data.
type Dataset struct {
// CreateTime: The time this dataset was created, in seconds from the
// epoch.
CreateTime int64 `json:"createTime,omitempty,string"`
// Id: The Google generated ID of the dataset, immutable.
Id string `json:"id,omitempty"`
// IsPublic: Flag indicating whether or not a dataset is publicly
// viewable. If a dataset is not public, it inherits viewing permissions
// from its project.
IsPublic *bool `json:"isPublic,omitempty"`
// Name: The dataset name.
Name string `json:"name,omitempty"`
// ProjectNumber: The Google Developers Console project number that this
// dataset belongs to.
ProjectNumber int64 `json:"projectNumber,omitempty,string"`
}
// ExperimentalCreateJobRequest: The job creation request.
type ExperimentalCreateJobRequest struct {
// Align: Specifies whether or not to run the alignment pipeline. Either
// align or callVariants must be set.
Align bool `json:"align,omitempty"`
// CallVariants: Specifies whether or not to run the variant calling
// pipeline. Either align or callVariants must be set.
CallVariants bool `json:"callVariants,omitempty"`
// GcsOutputPath: Specifies where to copy the results of certain
// pipelines. This should be in the form of gs://bucket/path.
GcsOutputPath string `json:"gcsOutputPath,omitempty"`
// PairedSourceUris: A list of Google Cloud Storage URIs of paired end
// .fastq files to operate upon. If specified, this represents the
// second file of each paired .fastq file. The first file of each pair
// should be specified in sourceUris.
PairedSourceUris []string `json:"pairedSourceUris,omitempty"`
// ProjectNumber: Required. The Google Cloud Project ID with which to
// associate the request.
ProjectNumber int64 `json:"projectNumber,omitempty,string"`
// SourceUris: A list of Google Cloud Storage URIs of data files to
// operate upon. These can be .bam, interleaved .fastq, or paired
// .fastq. If specifying paired .fastq files, the first of each pair of
// files should be listed here, and the second of each pair should be
// listed in pairedSourceUris.
SourceUris []string `json:"sourceUris,omitempty"`
}
// ExperimentalCreateJobResponse: The job creation response.
type ExperimentalCreateJobResponse struct {
// JobId: A job ID that can be used to get status information.
JobId string `json:"jobId,omitempty"`
}
// ExportReadGroupSetsRequest: The read group set export request.
type ExportReadGroupSetsRequest struct {
// ExportUri: Required. A Google Cloud Storage URI for the exported BAM
// file. The currently authenticated user must have write access to the
// new file. An error will be returned if the URI already contains data.
ExportUri string `json:"exportUri,omitempty"`
// ProjectNumber: Required. The Google Developers Console project number
// that owns this export.
ProjectNumber int64 `json:"projectNumber,omitempty,string"`
// ReadGroupSetIds: Required. The IDs of the read group sets to export.
ReadGroupSetIds []string `json:"readGroupSetIds,omitempty"`
// ReferenceNames: The reference names to export. If this is not
// specified, all reference sequences, including unmapped reads, are
// exported. Use * to export only unmapped reads.
ReferenceNames []string `json:"referenceNames,omitempty"`
}
// ExportReadGroupSetsResponse: The read group set export response.
type ExportReadGroupSetsResponse struct {
// JobId: A job ID that can be used to get status information.
JobId string `json:"jobId,omitempty"`
}
// ExportVariantSetRequest: The variant data export request.
type ExportVariantSetRequest struct {
// BigqueryDataset: Required. The BigQuery dataset to export data to.
// This dataset must already exist. Note that this is distinct from the
// Genomics concept of "dataset".
BigqueryDataset string `json:"bigqueryDataset,omitempty"`
// BigqueryTable: Required. The BigQuery table to export data to. If the
// table doesn't exist, it will be created. If it already exists, it
// will be overwritten.
BigqueryTable string `json:"bigqueryTable,omitempty"`
// CallSetIds: If provided, only variant call information from the
// specified call sets will be exported. By default all variant calls
// are exported.
CallSetIds []string `json:"callSetIds,omitempty"`
// Format: The format for the exported data.
//
// Possible values:
// "BIGQUERY"
Format string `json:"format,omitempty"`
// ProjectNumber: Required. The Google Cloud project number that owns
// the destination BigQuery dataset. The caller must have WRITE access
// to this project. This project will also own the resulting export job.
ProjectNumber int64 `json:"projectNumber,omitempty,string"`
}
// ExportVariantSetResponse: The variant data export response.
type ExportVariantSetResponse struct {
// JobId: A job ID that can be used to get status information.
JobId string `json:"jobId,omitempty"`
}
type ExternalId struct {
// Id: The id used by the source of this data.
Id string `json:"id,omitempty"`
// SourceName: The name of the source of this data.
SourceName string `json:"sourceName,omitempty"`
}
type FastqMetadata struct {
// LibraryName: Optionally specifies the library name for alignment from
// FASTQ.
LibraryName string `json:"libraryName,omitempty"`
// PlatformName: Optionally specifies the platform name for alignment
// from FASTQ. For example: CAPILLARY, LS454, ILLUMINA, SOLID, HELICOS,
// IONTORRENT, PACBIO.
PlatformName string `json:"platformName,omitempty"`
// PlatformUnit: Optionally specifies the platform unit for alignment
// from FASTQ. For example: flowcell-barcode.lane for Illumina or slide
// for SOLID.
PlatformUnit string `json:"platformUnit,omitempty"`
// ReadGroupName: Optionally specifies the read group name for alignment
// from FASTQ.
ReadGroupName string `json:"readGroupName,omitempty"`
// SampleName: Optionally specifies the sample name for alignment from
// FASTQ.
SampleName string `json:"sampleName,omitempty"`
}
// ImportReadGroupSetsRequest: The read group set import request.
type ImportReadGroupSetsRequest struct {
// DatasetId: Required. The ID of the dataset these read group sets will
// belong to. The caller must have WRITE permissions to this dataset.
DatasetId string `json:"datasetId,omitempty"`
// PartitionStrategy: The partition strategy describes how read groups
// are partitioned into read group sets.
//
// Possible values:
// "MERGE_ALL"
// "PER_FILE_PER_SAMPLE"
PartitionStrategy string `json:"partitionStrategy,omitempty"`
// ReferenceSetId: The reference set to which the imported read group
// sets are aligned to, if any. The reference names of this reference
// set must be a superset of those found in the imported file headers.
// If no reference set id is provided, a best effort is made to
// associate with a matching reference set.
ReferenceSetId string `json:"referenceSetId,omitempty"`
// SourceUris: A list of URIs pointing at BAM files in Google Cloud
// Storage.
SourceUris []string `json:"sourceUris,omitempty"`
}
// ImportReadGroupSetsResponse: The read group set import response.
type ImportReadGroupSetsResponse struct {
// JobId: A job ID that can be used to get status information.
JobId string `json:"jobId,omitempty"`
}
// ImportVariantsRequest: The variant data import request.
type ImportVariantsRequest struct {
// Format: The format of the variant data being imported. If
// unspecified, defaults to to "VCF".
//
// Possible values:
// "COMPLETE_GENOMICS"
// "VCF"
Format string `json:"format,omitempty"`
// NormalizeReferenceNames: Convert reference names to the canonical
// representation. hg19 haploytypes (those reference names containing
// "_hap") are not modified in any way. All other reference names are
// modified according to the following rules: The reference name is
// capitalized. The "chr" prefix is dropped for all autosomes and sex
// chromsomes. For example "chr17" becomes "17" and "chrX" becomes "X".
// All mitochondrial chromosomes ("chrM", "chrMT", etc) become "MT".
NormalizeReferenceNames bool `json:"normalizeReferenceNames,omitempty"`
// SourceUris: A list of URIs referencing variant files in Google Cloud
// Storage. URIs can include wildcards as described here. Note that
// recursive wildcards ('**') are not supported.
SourceUris []string `json:"sourceUris,omitempty"`
}
// ImportVariantsResponse: The variant data import response.
type ImportVariantsResponse struct {
// JobId: A job ID that can be used to get status information.
JobId string `json:"jobId,omitempty"`
}
// Int32Value: Wrapper message for `int32`.
//
// The JSON representation for `Int32Value` is JSON number.
type Int32Value struct {
// Value: The int32 value.
Value int64 `json:"value,omitempty"`
}
// InterleavedFastqSource: Describes an interleaved FASTQ file source
// for alignment.
type InterleavedFastqSource struct {
// Metadata: Optionally specifies the metadata to be associated with the
// final aligned read group set.
Metadata *FastqMetadata `json:"metadata,omitempty"`
// SourceUris: A list of URIs pointing at interleaved FASTQ files in
// Google Cloud Storage which will be aligned. The caller must have READ
// permissions for these files.
SourceUris []string `json:"sourceUris,omitempty"`
}
// Job: A Job represents an ongoing process that can be monitored for
// status information.
type Job struct {
// Created: The date this job was created, in milliseconds from the
// epoch.
Created int64 `json:"created,omitempty,string"`
// DetailedStatus: A more detailed description of this job's current
// status.
DetailedStatus string `json:"detailedStatus,omitempty"`
// Errors: Any errors that occurred during processing.
Errors []string `json:"errors,omitempty"`
// Id: The job ID.
Id string `json:"id,omitempty"`
// ImportedIds: If this Job represents an import, this field will
// contain the IDs of the objects that were successfully imported.
ImportedIds []string `json:"importedIds,omitempty"`
// ProjectNumber: The Google Developers Console project number to which
// this job belongs.
ProjectNumber int64 `json:"projectNumber,omitempty,string"`
// Request: A summarized representation of the original service request.
Request *JobRequest `json:"request,omitempty"`
// Status: The status of this job.
//
// Possible values:
// "CANCELED"
// "FAILURE"
// "NEW"
// "PENDING"
// "RUNNING"
// "SUCCESS"
// "UNKNOWN_STATUS"
Status string `json:"status,omitempty"`
// Warnings: Any warnings that occurred during processing.
Warnings []string `json:"warnings,omitempty"`
}
// JobRequest: A summary representation of the service request that
// spawned the job.
type JobRequest struct {
// Destination: The data destination of the request, for example, a
// Google BigQuery Table or Dataset ID.
Destination []string `json:"destination,omitempty"`
// Source: The data source of the request, for example, a Google Cloud
// Storage object path or Readset ID.
Source []string `json:"source,omitempty"`
// Type: The original request type.
//
// Possible values:
// "ALIGN_READSETS"
// "CALL_READSETS"
// "EXPERIMENTAL_CREATE_JOB"
// "EXPORT_READSETS"
// "EXPORT_VARIANTS"
// "IMPORT_READSETS"
// "IMPORT_VARIANTS"
// "UNKNOWN_TYPE"
Type string `json:"type,omitempty"`
}
// KeyValue: Used to hold basic key value information.
type KeyValue struct {
// Key: A string which maps to an array of values.
Key string `json:"key,omitempty"`
// Value: The string values.
Value []string `json:"value,omitempty"`
}
// LinearAlignment: A linear alignment can be represented by one CIGAR
// string. Describes the mapped position and local alignment of the read
// to the reference.
type LinearAlignment struct {
// Cigar: Represents the local alignment of this sequence (alignment
// matches, indels, etc) against the reference.
Cigar []*CigarUnit `json:"cigar,omitempty"`
// MappingQuality: The mapping quality of this alignment. Represents how
// likely the read maps to this position as opposed to other locations.
MappingQuality int64 `json:"mappingQuality,omitempty"`
// Position: The position of this alignment.
Position *Position `json:"position,omitempty"`
}
type ListBasesResponse struct {
// NextPageToken: The continuation token, which is used to page through
// large result sets. Provide this value in a subsequent request to
// return the next page of results. This field will be empty if there
// aren't any additional results.
NextPageToken string `json:"nextPageToken,omitempty"`
// Offset: The offset position (0-based) of the given sequence from the
// start of this Reference. This value will differ for each page in a
// paginated request.
Offset int64 `json:"offset,omitempty,string"`
// Sequence: A substring of the bases that make up this reference.
Sequence string `json:"sequence,omitempty"`
}
type ListCoverageBucketsResponse struct {
// BucketWidth: The length of each coverage bucket in base pairs. Note
// that buckets at the end of a reference sequence may be shorter. This
// value is omitted if the bucket width is infinity (the default
// behaviour, with no range or targetBucketWidth).
BucketWidth int64 `json:"bucketWidth,omitempty,string"`
// CoverageBuckets: The coverage buckets. The list of buckets is sparse;
// a bucket with 0 overlapping reads is not returned. A bucket never
// crosses more than one reference sequence. Each bucket has width
// bucketWidth, unless its end is the end of the reference sequence.
CoverageBuckets []*CoverageBucket `json:"coverageBuckets,omitempty"`
// NextPageToken: The continuation token, which is used to page through
// large result sets. Provide this value in a subsequent request to
// return the next page of results. This field will be empty if there
// aren't any additional results.
NextPageToken string `json:"nextPageToken,omitempty"`
}
// ListDatasetsResponse: The dataset list response.
type ListDatasetsResponse struct {
// Datasets: The list of matching Datasets.
Datasets []*Dataset `json:"datasets,omitempty"`
// NextPageToken: The continuation token, which is used to page through
// large result sets. Provide this value in a subsequent request to
// return the next page of results. This field will be empty if there
// aren't any additional results.
NextPageToken string `json:"nextPageToken,omitempty"`
}
type MergeVariantsRequest struct {
// Variants: The variants to be merged with existing variants.
Variants []*Variant `json:"variants,omitempty"`
}
// Metadata: Metadata describes a single piece of variant call metadata.
// These data include a top level key and either a single value string
// (value) or a list of key-value pairs (info.) Value and info are
// mutually exclusive.
type Metadata struct {
// Description: A textual description of this metadata.
Description string `json:"description,omitempty"`
// Id: User-provided ID field, not enforced by this API. Two or more
// pieces of structured metadata with identical id and key fields are
// considered equivalent.
Id string `json:"id,omitempty"`
// Info: A string which maps to an array of values.
Info map[string][]string `json:"info,omitempty"`
// Key: The top-level key.
Key string `json:"key,omitempty"`
// Number: The number of values that can be included in a field
// described by this metadata.
Number string `json:"number,omitempty"`
// Type: The type of data. Possible types include: Integer, Float, Flag,
// Character, and String.
//
// Possible values:
// "CHARACTER"
// "FLAG"
// "FLOAT"
// "INTEGER"
// "STRING"
// "UNKNOWN_TYPE"
Type string `json:"type,omitempty"`
// Value: The value field for simple metadata
Value string `json:"value,omitempty"`
}
// PairedFastqSource: Describes a paired-end FASTQ file source for
// alignment.
type PairedFastqSource struct {
// FirstSourceUris: A list of URIs pointing at paired end FASTQ files in
// Google Cloud Storage which will be aligned. The first of each paired
// file should be specified here, in an order that matches the second of
// each paired file specified in secondSourceUris. For example:
// firstSourceUris: [file1_1.fq, file2_1.fq], secondSourceUris:
// [file1_2.fq, file2_2.fq]. The caller must have READ permissions for
// these files.
FirstSourceUris []string `json:"firstSourceUris,omitempty"`
// Metadata: Optionally specifies the metadata to be associated with the
// final aligned read group set.
Metadata *FastqMetadata `json:"metadata,omitempty"`
// SecondSourceUris: A list of URIs pointing at paired end FASTQ files
// in Google Cloud Storage which will be aligned. The second of each
// paired file should be specified here, in an order that matches the
// first of each paired file specified in firstSourceUris. For example:
// firstSourceUris: [file1_1.fq, file2_1.fq], secondSourceUris:
// [file1_2.fq, file2_2.fq]. The caller must have READ permissions for
// these files.
SecondSourceUris []string `json:"secondSourceUris,omitempty"`
}
// Position: An abstraction for referring to a genomic position, in
// relation to some already known reference. For now, represents a
// genomic position as a reference name, a base number on that reference
// (0-based), and a determination of forward or reverse strand.
type Position struct {
// Position: The 0-based offset from the start of the forward strand for
// that reference.
Position int64 `json:"position,omitempty,string"`