genomics

package
v0.0.0-...-de2eba5 Latest Latest
Warning

This package is not in the latest version of its module.

 Go to latest Published: May 19, 2015 License: BSD-3-Clause Imports: 11 Imported by: 0

Documentation

Overview

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)

Index

Constants

View Source 
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"
)

OAuth2 scopes used by this API.

Variables

This section is empty.

Functions

This section is empty.

Types

type AlignReadGroupSetsRequest 

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"`
}

type AlignReadGroupSetsResponse 

type AlignReadGroupSetsResponse struct {
	// JobId: A job ID that can be used to get status information.
	JobId string `json:"jobId,omitempty"`
}

type Annotation 

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 map of additional data for this annotation.
	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"`
}

type AnnotationSet 

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 map of additional data for this annotation set.
	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 AnnotationSetsCreateCall 

type AnnotationSetsCreateCall struct {
	// contains filtered or unexported fields
}

func (*AnnotationSetsCreateCall) Do 

func (c *AnnotationSetsCreateCall) Do() (*AnnotationSet, error)

func (*AnnotationSetsCreateCall) Fields 

func (c *AnnotationSetsCreateCall) Fields(s ...googleapi.Field) *AnnotationSetsCreateCall

Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.

type AnnotationSetsDeleteCall 

type AnnotationSetsDeleteCall struct {
	// contains filtered or unexported fields
}

func (*AnnotationSetsDeleteCall) Do 

func (c *AnnotationSetsDeleteCall) Do() error

func (*AnnotationSetsDeleteCall) Fields 

func (c *AnnotationSetsDeleteCall) Fields(s ...googleapi.Field) *AnnotationSetsDeleteCall

Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.

type AnnotationSetsGetCall 

type AnnotationSetsGetCall struct {
	// contains filtered or unexported fields
}

func (*AnnotationSetsGetCall) Do 

func (c *AnnotationSetsGetCall) Do() (*AnnotationSet, error)

func (*AnnotationSetsGetCall) Fields 

func (c *AnnotationSetsGetCall) Fields(s ...googleapi.Field) *AnnotationSetsGetCall

Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.

type AnnotationSetsPatchCall 

type AnnotationSetsPatchCall struct {
	// contains filtered or unexported fields
}

func (*AnnotationSetsPatchCall) Do 

func (c *AnnotationSetsPatchCall) Do() (*AnnotationSet, error)

func (*AnnotationSetsPatchCall) Fields 

func (c *AnnotationSetsPatchCall) Fields(s ...googleapi.Field) *AnnotationSetsPatchCall

Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.

type AnnotationSetsSearchCall 

type AnnotationSetsSearchCall struct {
	// contains filtered or unexported fields
}

func (*AnnotationSetsSearchCall) Do 

func (c *AnnotationSetsSearchCall) Do() (*SearchAnnotationSetsResponse, error)

func (*AnnotationSetsSearchCall) Fields 

func (c *AnnotationSetsSearchCall) Fields(s ...googleapi.Field) *AnnotationSetsSearchCall

Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.

type AnnotationSetsService 

type AnnotationSetsService struct {
	// contains filtered or unexported fields
}

func NewAnnotationSetsService 

func NewAnnotationSetsService(s *Service) *AnnotationSetsService

func (*AnnotationSetsService) Create 

func (r *AnnotationSetsService) Create(annotationset *AnnotationSet) *AnnotationSetsCreateCall

Create: Creates a new annotation set. Caller must have WRITE permission for the associated dataset.

func (*AnnotationSetsService) Delete 

func (r *AnnotationSetsService) Delete(annotationSetId string) *AnnotationSetsDeleteCall

Delete: Deletes an annotation set. Caller must have WRITE permission for the associated annotation set.

func (*AnnotationSetsService) Get 

func (r *AnnotationSetsService) Get(annotationSetId string) *AnnotationSetsGetCall

Get: Gets an annotation set. Caller must have READ permission for the associated dataset.

func (*AnnotationSetsService) Patch 

func (r *AnnotationSetsService) Patch(annotationSetId string, annotationset *AnnotationSet) *AnnotationSetsPatchCall

Patch: Updates an annotation set. The update must respect all mutability restrictions and other invariants described on the annotation set resource. Caller must have WRITE permission for the associated dataset. This method supports patch semantics.

func (*AnnotationSetsService) Search 

func (r *AnnotationSetsService) Search(searchannotationsetsrequest *SearchAnnotationSetsRequest) *AnnotationSetsSearchCall

Search: Searches for annotation sets that match the given criteria. Results are returned in a deterministic order. Caller must have READ permission for the queried datasets.

func (*AnnotationSetsService) Update 

func (r *AnnotationSetsService) Update(annotationSetId string, annotationset *AnnotationSet) *AnnotationSetsUpdateCall

Update: Updates an annotation set. The update must respect all mutability restrictions and other invariants described on the annotation set resource. Caller must have WRITE permission for the associated dataset.

type AnnotationSetsUpdateCall 

type AnnotationSetsUpdateCall struct {
	// contains filtered or unexported fields
}

func (*AnnotationSetsUpdateCall) Do 

func (c *AnnotationSetsUpdateCall) Do() (*AnnotationSet, error)

func (*AnnotationSetsUpdateCall) Fields 

func (c *AnnotationSetsUpdateCall) Fields(s ...googleapi.Field) *AnnotationSetsUpdateCall

Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.

type AnnotationsBatchCreateCall 

type AnnotationsBatchCreateCall struct {
	// contains filtered or unexported fields
}

func (*AnnotationsBatchCreateCall) Do 

func (c *AnnotationsBatchCreateCall) Do() (*BatchAnnotationsResponse, error)

func (*AnnotationsBatchCreateCall) Fields 

func (c *AnnotationsBatchCreateCall) Fields(s ...googleapi.Field) *AnnotationsBatchCreateCall

Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.

type AnnotationsCreateCall 

type AnnotationsCreateCall struct {
	// contains filtered or unexported fields
}

func (*AnnotationsCreateCall) Do 

func (c *AnnotationsCreateCall) Do() (*Annotation, error)

func (*AnnotationsCreateCall) Fields 

func (c *AnnotationsCreateCall) Fields(s ...googleapi.Field) *AnnotationsCreateCall

Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.

type AnnotationsDeleteCall 

type AnnotationsDeleteCall struct {
	// contains filtered or unexported fields
}

func (*AnnotationsDeleteCall) Do 

func (c *AnnotationsDeleteCall) Do() error

func (*AnnotationsDeleteCall) Fields 

func (c *AnnotationsDeleteCall) Fields(s ...googleapi.Field) *AnnotationsDeleteCall

Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.

type AnnotationsGetCall 

type AnnotationsGetCall struct {
	// contains filtered or unexported fields
}

func (*AnnotationsGetCall) Do 

func (c *AnnotationsGetCall) Do() (*Annotation, error)

func (*AnnotationsGetCall) Fields 

func (c *AnnotationsGetCall) Fields(s ...googleapi.Field) *AnnotationsGetCall

Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.

type AnnotationsPatchCall 

type AnnotationsPatchCall struct {
	// contains filtered or unexported fields
}

func (*AnnotationsPatchCall) Do 

func (c *AnnotationsPatchCall) Do() (*Annotation, error)

func (*AnnotationsPatchCall) Fields 

func (c *AnnotationsPatchCall) Fields(s ...googleapi.Field) *AnnotationsPatchCall

Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.

type AnnotationsSearchCall 

type AnnotationsSearchCall struct {
	// contains filtered or unexported fields
}

func (*AnnotationsSearchCall) Do 

func (c *AnnotationsSearchCall) Do() (*SearchAnnotationsResponse, error)

func (*AnnotationsSearchCall) Fields 

func (c *AnnotationsSearchCall) Fields(s ...googleapi.Field) *AnnotationsSearchCall

Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.

type AnnotationsService 

type AnnotationsService struct {
	// contains filtered or unexported fields
}

func NewAnnotationsService 

func NewAnnotationsService(s *Service) *AnnotationsService

func (*AnnotationsService) BatchCreate 

func (r *AnnotationsService) BatchCreate(batchcreateannotationsrequest *BatchCreateAnnotationsRequest) *AnnotationsBatchCreateCall

BatchCreate: Creates one or more new annotations atomically. All annotations must belong to the same annotation set. Caller must have WRITE permission for this annotation set. For optimal performance, batch positionally adjacent annotations together.

If the request has a systemic issue, such as an attempt to write to an inaccessible annotation set, the entire RPC will fail accordingly. For lesser data issues, when possible an error will be isolated to the corresponding batch entry in the response; the remaining well formed annotations will be created normally.

func (*AnnotationsService) Create 

func (r *AnnotationsService) Create(annotation *Annotation) *AnnotationsCreateCall

Create: Creates a new annotation. Caller must have WRITE permission for the associated annotation set.

func (*AnnotationsService) Delete 

func (r *AnnotationsService) Delete(annotationId string) *AnnotationsDeleteCall

Delete: Deletes an annotation. Caller must have WRITE permission for the associated annotation set.

func (*AnnotationsService) Get 

func (r *AnnotationsService) Get(annotationId string) *AnnotationsGetCall

Get: Gets an annotation. Caller must have READ permission for the associated annotation set.

func (*AnnotationsService) Patch 

func (r *AnnotationsService) Patch(annotationId string, annotation *Annotation) *AnnotationsPatchCall

Patch: Updates an annotation. The update must respect all mutability restrictions and other invariants described on the annotation resource. Caller must have WRITE permission for the associated dataset. This method supports patch semantics.

func (*AnnotationsService) Search 

func (r *AnnotationsService) Search(searchannotationsrequest *SearchAnnotationsRequest) *AnnotationsSearchCall

Search: Searches for annotations that match the given criteria. Results are returned ordered by start position. Annotations that have matching start positions are ordered deterministically. Caller must have READ permission for the queried annotation sets.

func (*AnnotationsService) Update 

func (r *AnnotationsService) Update(annotationId string, annotation *Annotation) *AnnotationsUpdateCall

Update: Updates an annotation. The update must respect all mutability restrictions and other invariants described on the annotation resource. Caller must have WRITE permission for the associated dataset.

type AnnotationsUpdateCall 

type AnnotationsUpdateCall struct {
	// contains filtered or unexported fields
}

func (*AnnotationsUpdateCall) Do 

func (c *AnnotationsUpdateCall) Do() (*Annotation, error)

func (*AnnotationsUpdateCall) Fields 

func (c *AnnotationsUpdateCall) Fields(s ...googleapi.Field) *AnnotationsUpdateCall

Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.

type BatchAnnotationsResponse 

type BatchAnnotationsResponse struct {
	// Entries: The resulting per-annotation entries, ordered consistently
	// with the original request.
	Entries []*BatchAnnotationsResponseEntry `json:"entries,omitempty"`
}

type BatchAnnotationsResponseEntry 

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 

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 

type BatchCreateAnnotationsRequest struct {
	// Annotations: The annotations to be created. At most 4096 can be
	// specified in a single request.
	Annotations []*Annotation `json:"annotations,omitempty"`
}

type Call 

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 map of additional variant call information.
	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"`
}

type CallReadGroupSetsRequest 

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"`
}

type CallReadGroupSetsResponse 

type CallReadGroupSetsResponse struct {
	// JobId: A job ID that can be used to get status information.
	JobId string `json:"jobId,omitempty"`
}

type CallSet 

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 map of additional call set information.
	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"`
}

type CallsetsCreateCall 

type CallsetsCreateCall struct {
	// contains filtered or unexported fields
}

func (*CallsetsCreateCall) Do 

func (c *CallsetsCreateCall) Do() (*CallSet, error)

func (*CallsetsCreateCall) Fields 

func (c *CallsetsCreateCall) Fields(s ...googleapi.Field) *CallsetsCreateCall

Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.

type CallsetsDeleteCall 

type CallsetsDeleteCall struct {
	// contains filtered or unexported fields
}

func (*CallsetsDeleteCall) Do 

func (c *CallsetsDeleteCall) Do() error

func (*CallsetsDeleteCall) Fields 

func (c *CallsetsDeleteCall) Fields(s ...googleapi.Field) *CallsetsDeleteCall

Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.

type CallsetsGetCall 

type CallsetsGetCall struct {
	// contains filtered or unexported fields
}

func (*CallsetsGetCall) Do 

func (c *CallsetsGetCall) Do() (*CallSet, error)

func (*CallsetsGetCall) Fields 

func (c *CallsetsGetCall) Fields(s ...googleapi.Field) *CallsetsGetCall

Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.

type CallsetsPatchCall 

type CallsetsPatchCall struct {
	// contains filtered or unexported fields
}

func (*CallsetsPatchCall) Do 

func (c *CallsetsPatchCall) Do() (*CallSet, error)

func (*CallsetsPatchCall) Fields 

func (c *CallsetsPatchCall) Fields(s ...googleapi.Field) *CallsetsPatchCall

Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.

type CallsetsSearchCall 

type CallsetsSearchCall struct {
	// contains filtered or unexported fields
}

func (*CallsetsSearchCall) Do 

func (c *CallsetsSearchCall) Do() (*SearchCallSetsResponse, error)

func (*CallsetsSearchCall) Fields 

func (c *CallsetsSearchCall) Fields(s ...googleapi.Field) *CallsetsSearchCall

Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.

type CallsetsService 

type CallsetsService struct {
	// contains filtered or unexported fields
}

func NewCallsetsService 

func NewCallsetsService(s *Service) *CallsetsService

func (*CallsetsService) Create 

func (r *CallsetsService) Create(callset *CallSet) *CallsetsCreateCall

Create: Creates a new call set.

func (*CallsetsService) Delete 

func (r *CallsetsService) Delete(callSetId string) *CallsetsDeleteCall

Delete: Deletes a call set.

func (*CallsetsService) Get 

func (r *CallsetsService) Get(callSetId string) *CallsetsGetCall

Get: Gets a call set by ID.

func (*CallsetsService) Patch 

func (r *CallsetsService) Patch(callSetId string, callset *CallSet) *CallsetsPatchCall

Patch: Updates a call set. This method supports patch semantics.

func (*CallsetsService) Search 

func (r *CallsetsService) Search(searchcallsetsrequest *SearchCallSetsRequest) *CallsetsSearchCall

Search: Gets a list of call sets matching the criteria.

Implements GlobalAllianceApi.searchCallSets.

func (*CallsetsService) Update 

func (r *CallsetsService) Update(callSetId string, callset *CallSet) *CallsetsUpdateCall

Update: Updates a call set.

type CallsetsUpdateCall 

type CallsetsUpdateCall struct {
	// contains filtered or unexported fields
}

func (*CallsetsUpdateCall) Do 

func (c *CallsetsUpdateCall) Do() (*CallSet, error)

func (*CallsetsUpdateCall) Fields 

func (c *CallsetsUpdateCall) Fields(s ...googleapi.Field) *CallsetsUpdateCall

Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.

type CigarUnit 

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"`
}

type CoverageBucket 

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"`
}

type Dataset 

type Dataset struct {
	// 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"`
}

type DatasetsCreateCall 

type DatasetsCreateCall struct {
	// contains filtered or unexported fields
}

func (*DatasetsCreateCall) Do 

func (c *DatasetsCreateCall) Do() (*Dataset, error)

func (*DatasetsCreateCall) Fields 

func (c *DatasetsCreateCall) Fields(s ...googleapi.Field) *DatasetsCreateCall

Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.

type DatasetsDeleteCall 

type DatasetsDeleteCall struct {
	// contains filtered or unexported fields
}

func (*DatasetsDeleteCall) Do 

func (c *DatasetsDeleteCall) Do() error

func (*DatasetsDeleteCall) Fields 

func (c *DatasetsDeleteCall) Fields(s ...googleapi.Field) *DatasetsDeleteCall

Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.

type DatasetsGetCall 

type DatasetsGetCall struct {
	// contains filtered or unexported fields
}

func (*DatasetsGetCall) Do 

func (c *DatasetsGetCall) Do() (*Dataset, error)

func (*DatasetsGetCall) Fields 

func (c *DatasetsGetCall) Fields(s ...googleapi.Field) *DatasetsGetCall

Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.

type DatasetsListCall 

type DatasetsListCall struct {
	// contains filtered or unexported fields
}

func (*DatasetsListCall) Do 

func (c *DatasetsListCall) Do() (*ListDatasetsResponse, error)

func (*DatasetsListCall) Fields 

func (c *DatasetsListCall) Fields(s ...googleapi.Field) *DatasetsListCall

Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.

func (*DatasetsListCall) PageSize 

func (c *DatasetsListCall) PageSize(pageSize int64) *DatasetsListCall

PageSize sets the optional parameter "pageSize": The maximum number of results returned by this request. If unspecified, defaults to 50.

func (*DatasetsListCall) PageToken 

func (c *DatasetsListCall) PageToken(pageToken string) *DatasetsListCall

PageToken sets the optional parameter "pageToken": The continuation token, which is used to page through large result sets. To get the next page of results, set this parameter to the value of nextPageToken from the previous response.

func (*DatasetsListCall) ProjectNumber 

func (c *DatasetsListCall) ProjectNumber(projectNumber int64) *DatasetsListCall

ProjectNumber sets the optional parameter "projectNumber": The project to list datasets for.

type DatasetsPatchCall 

type DatasetsPatchCall struct {
	// contains filtered or unexported fields
}

func (*DatasetsPatchCall) Do 

func (c *DatasetsPatchCall) Do() (*Dataset, error)

func (*DatasetsPatchCall) Fields 

func (c *DatasetsPatchCall) Fields(s ...googleapi.Field) *DatasetsPatchCall

Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.

type DatasetsService 

type DatasetsService struct {
	// contains filtered or unexported fields
}

func NewDatasetsService 

func NewDatasetsService(s *Service) *DatasetsService

func (*DatasetsService) Create 

func (r *DatasetsService) Create(dataset *Dataset) *DatasetsCreateCall

Create: Creates a new dataset.

func (*DatasetsService) Delete 

func (r *DatasetsService) Delete(datasetId string) *DatasetsDeleteCall

Delete: Deletes a dataset.

func (*DatasetsService) Get 

func (r *DatasetsService) Get(datasetId string) *DatasetsGetCall

Get: Gets a dataset by ID.

func (*DatasetsService) List 

func (r *DatasetsService) List() *DatasetsListCall

List: Lists datasets within a project.

func (*DatasetsService) Patch 

func (r *DatasetsService) Patch(datasetId string, dataset *Dataset) *DatasetsPatchCall

Patch: Updates a dataset. This method supports patch semantics.

func (*DatasetsService) Undelete 

func (r *DatasetsService) Undelete(datasetId string) *DatasetsUndeleteCall

Undelete: Undeletes a dataset by restoring a dataset which was deleted via this API. This operation is only possible for a week after the deletion occurred.

func (*DatasetsService) Update 

func (r *DatasetsService) Update(datasetId string, dataset *Dataset) *DatasetsUpdateCall

Update: Updates a dataset.

type DatasetsUndeleteCall 

type DatasetsUndeleteCall struct {
	// contains filtered or unexported fields
}

func (*DatasetsUndeleteCall) Do 

func (c *DatasetsUndeleteCall) Do() (*Dataset, error)

func (*DatasetsUndeleteCall) Fields 

func (c *DatasetsUndeleteCall) Fields(s ...googleapi.Field) *DatasetsUndeleteCall

Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.

type DatasetsUpdateCall 

type DatasetsUpdateCall struct {
	// contains filtered or unexported fields
}

func (*DatasetsUpdateCall) Do 

func (c *DatasetsUpdateCall) Do() (*Dataset, error)

func (*DatasetsUpdateCall) Fields 

func (c *DatasetsUpdateCall) Fields(s ...googleapi.Field) *DatasetsUpdateCall

Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.

type ExperimentalCreateJobRequest 

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"`
}

type ExperimentalCreateJobResponse 

type ExperimentalCreateJobResponse struct {
	// JobId: A job ID that can be used to get status information.
	JobId string `json:"jobId,omitempty"`
}

type ExperimentalJobsCreateCall 

type ExperimentalJobsCreateCall struct {
	// contains filtered or unexported fields
}

func (*ExperimentalJobsCreateCall) Do 

func (c *ExperimentalJobsCreateCall) Do() (*ExperimentalCreateJobResponse, error)

func (*ExperimentalJobsCreateCall) Fields 

func (c *ExperimentalJobsCreateCall) Fields(s ...googleapi.Field) *ExperimentalJobsCreateCall

Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.

type ExperimentalJobsService 

type ExperimentalJobsService struct {
	// contains filtered or unexported fields
}

func NewExperimentalJobsService 

func NewExperimentalJobsService(s *Service) *ExperimentalJobsService

func (*ExperimentalJobsService) Create 

func (r *ExperimentalJobsService) Create(experimentalcreatejobrequest *ExperimentalCreateJobRequest) *ExperimentalJobsCreateCall

Create: Creates and asynchronously runs an ad-hoc job. This is an experimental call and may be removed or changed at any time.

type ExperimentalService 

type ExperimentalService struct {
	Jobs *ExperimentalJobsService
	// contains filtered or unexported fields
}

func NewExperimentalService 

func NewExperimentalService(s *Service) *ExperimentalService

type ExportReadGroupSetsRequest 

type ExportReadGroupSetsRequest struct {
	// ExportUri: 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: The Google Developers Console project number that owns
	// this export.
	ProjectNumber int64 `json:"projectNumber,omitempty,string"`

	// ReadGroupSetIds: 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"`
}

type ExportReadGroupSetsResponse 

type ExportReadGroupSetsResponse struct {
	// JobId: A job ID that can be used to get status information.
	JobId string `json:"jobId,omitempty"`
}

type ExportVariantSetRequest 

type ExportVariantSetRequest struct {
	// BigqueryDataset: The BigQuery dataset to export data to. Note that
	// this is distinct from the Genomics concept of "dataset".
	BigqueryDataset string `json:"bigqueryDataset,omitempty"`

	// BigqueryTable: 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: 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"`
}

type ExportVariantSetResponse 

type ExportVariantSetResponse struct {
	// JobId: A job ID that can be used to get status information.
	JobId string `json:"jobId,omitempty"`
}

type ExternalId 

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 

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"`
}

type ImportReadGroupSetsRequest 

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"`
}

type ImportReadGroupSetsResponse 

type ImportReadGroupSetsResponse struct {
	// JobId: A job ID that can be used to get status information.
	JobId string `json:"jobId,omitempty"`
}

type ImportVariantsRequest 

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"`

	// 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"`
}

type ImportVariantsResponse 

type ImportVariantsResponse struct {
	// JobId: A job ID that can be used to get status information.
	JobId string `json:"jobId,omitempty"`
}

type Int32Value 

type Int32Value struct {
	// Value: The int32 value.
	Value int64 `json:"value,omitempty"`
}

type InterleavedFastqSource 

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"`
}

type Job 

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"`
}

type JobRequest 

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"`
}

type JobsCancelCall 

type JobsCancelCall struct {
	// contains filtered or unexported fields
}

func (*JobsCancelCall) Do 

func (c *JobsCancelCall) Do() error

func (*JobsCancelCall) Fields 

func (c *JobsCancelCall) Fields(s ...googleapi.Field) *JobsCancelCall

Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.

type JobsGetCall 

type JobsGetCall struct {
	// contains filtered or unexported fields
}

func (*JobsGetCall) Do 

func (c *JobsGetCall) Do() (*Job, error)

func (*JobsGetCall) Fields 

func (c *JobsGetCall) Fields(s ...googleapi.Field) *JobsGetCall

Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.

type JobsSearchCall 

type JobsSearchCall struct {
	// contains filtered or unexported fields
}

func (*JobsSearchCall) Do 

func (c *JobsSearchCall) Do() (*SearchJobsResponse, error)

func (*JobsSearchCall) Fields 

func (c *JobsSearchCall) Fields(s ...googleapi.Field) *JobsSearchCall

Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.

type JobsService 

type JobsService struct {
	// contains filtered or unexported fields
}

func NewJobsService 

func NewJobsService(s *Service) *JobsService

func (*JobsService) Cancel 

func (r *JobsService) Cancel(jobId string) *JobsCancelCall

Cancel: Cancels a job by ID. Note that it is possible for partial results to be generated and stored for cancelled jobs.

func (*JobsService) Get 

func (r *JobsService) Get(jobId string) *JobsGetCall

Get: Gets a job by ID.

func (*JobsService) Search 

func (r *JobsService) Search(searchjobsrequest *SearchJobsRequest) *JobsSearchCall

Search: Gets a list of jobs matching the criteria.

type LinearAlignment 

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 

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 

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"`
}

type ListDatasetsResponse 

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 

type MergeVariantsRequest struct {
	// Variants: The variants to be merged with existing variants.
	Variants []*Variant `json:"variants,omitempty"`
}

type Metadata 

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: Remaining structured metadata key-value pairs.
	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"`
}

type PairedFastqSource 

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"`
}

type Position 

type Position struct {
	// Position: The 0-based offset from the start of the forward strand for
	// that reference.
	Position int64 `json:"position,omitempty,string"`

	// ReferenceName: The name of the reference in whatever reference set is
	// being used.
	ReferenceName string `json:"referenceName,omitempty"`

	// ReverseStrand: Whether this position is on the reverse strand, as
	// opposed to the forward strand.
	ReverseStrand *bool `json:"reverseStrand,omitempty"`
}

type QueryRange 

type QueryRange struct {
	// End: The end position of the range on the reference, 0-based
	// exclusive. If specified, referenceId or referenceName must also be
	// specified. If unset or 0, defaults to the length of the reference.
	End int64 `json:"end,omitempty,string"`

	// ReferenceId: The ID of the reference to query. At most one of
	// referenceId and referenceName should be specified.
	ReferenceId string `json:"referenceId,omitempty"`

	// ReferenceName: The name of the reference to query, within the
	// reference set associated with this query. At most one of referenceId
	// and referenceName pshould be specified.
	ReferenceName string `json:"referenceName,omitempty"`

	// Start: The start position of the range on the reference, 0-based
	// inclusive. If specified, referenceId or referenceName must also be
	// specified. Defaults to 0.
	Start int64 `json:"start,omitempty,string"`
}

type Range 

type Range struct {
	// End: The end position of the range on the reference, 0-based
	// exclusive. If specified, referenceName must also be specified.
	End int64 `json:"end,omitempty,string"`

	// ReferenceName: The reference sequence name, for example chr1, 1, or
	// chrX.
	ReferenceName string `json:"referenceName,omitempty"`

	// Start: The start position of the range on the reference, 0-based
	// inclusive. If specified, referenceName must also be specified.
	Start int64 `json:"start,omitempty,string"`
}

type RangePosition 

type RangePosition struct {
	// End: The end position of the range on the reference, 0-based
	// exclusive.
	End int64 `json:"end,omitempty,string"`

	// ReferenceId: The ID of the Google Genomics reference associated with
	// this range.
	ReferenceId string `json:"referenceId,omitempty"`

	// ReferenceName: The display name corresponding to the reference
	// specified by referenceId, for example chr1, 1, or chrX.
	ReferenceName string `json:"referenceName,omitempty"`

	// ReverseStrand: Whether this range refers to the reverse strand, as
	// opposed to the forward strand. Note that regardless of this field,
	// the start/end position of the range always refer to the forward
	// strand.
	ReverseStrand *bool `json:"reverseStrand,omitempty"`

	// Start: The start position of the range on the reference, 0-based
	// inclusive.
	Start int64 `json:"start,omitempty,string"`
}

type Read 

type Read struct {
	// AlignedQuality: The quality of the read sequence contained in this
	// alignment record. alignedSequence and alignedQuality may be shorter
	// than the full read sequence and quality. This will occur if the
	// alignment is part of a chimeric alignment, or if the read was
	// trimmed. When this occurs, the CIGAR for this read will begin/end
	// with a hard clip operator that will indicate the length of the
	// excised sequence.
	AlignedQuality []int64 `json:"alignedQuality,omitempty"`

	// AlignedSequence: The bases of the read sequence contained in this
	// alignment record, without CIGAR operations applied. alignedSequence
	// and alignedQuality may be shorter than the full read sequence and
	// quality. This will occur if the alignment is part of a chimeric
	// alignment, or if the read was trimmed. When this occurs, the CIGAR
	// for this read will begin/end with a hard clip operator that will
	// indicate the length of the excised sequence.
	AlignedSequence string `json:"alignedSequence,omitempty"`

	// Alignment: The linear alignment for this alignment record. This field
	// will be unset if the read is unmapped.
	Alignment *LinearAlignment `json:"alignment,omitempty"`

	// DuplicateFragment: The fragment is a PCR or optical duplicate (SAM
	// flag 0x400)
	DuplicateFragment *bool `json:"duplicateFragment,omitempty"`

	// FailedVendorQualityChecks: SAM flag 0x200
	FailedVendorQualityChecks *bool `json:"failedVendorQualityChecks,omitempty"`

	// FragmentLength: The observed length of the fragment, equivalent to
	// TLEN in SAM.
	FragmentLength int64 `json:"fragmentLength,omitempty"`

	// FragmentName: The fragment name. Equivalent to QNAME (query template
	// name) in SAM.
	FragmentName string `json:"fragmentName,omitempty"`

	// Id: The unique ID for this read. This is a generated unique ID, not
	// to be confused with fragmentName.
	Id string `json:"id,omitempty"`

	// Info: A map of additional read alignment information.
	Info map[string][]string `json:"info,omitempty"`

	// NextMatePosition: The position of the primary alignment of the
	// (readNumber+1)%numberReads read in the fragment. It replaces mate
	// position and mate strand in SAM. This field will be unset if that
	// read is unmapped or if the fragment only has a single read.
	NextMatePosition *Position `json:"nextMatePosition,omitempty"`

	// NumberReads: The number of reads in the fragment (extension to SAM
	// flag 0x1).
	NumberReads int64 `json:"numberReads,omitempty"`

	// ProperPlacement: The orientation and the distance between reads from
	// the fragment are consistent with the sequencing protocol (SAM flag
	// 0x2)
	ProperPlacement *bool `json:"properPlacement,omitempty"`

	// ReadGroupId: The ID of the read group this read belongs to. (Every
	// read must belong to exactly one read group.)
	ReadGroupId string `json:"readGroupId,omitempty"`

	// ReadGroupSetId: The ID of the read group set this read belongs to.
	// (Every read must belong to exactly one read group set.)
	ReadGroupSetId string `json:"readGroupSetId,omitempty"`

	// ReadNumber: The read number in sequencing. 0-based and less than
	// numberReads. This field replaces SAM flag 0x40 and 0x80.
	ReadNumber int64 `json:"readNumber,omitempty"`

	// SecondaryAlignment: Whether this alignment is secondary. Equivalent
	// to SAM flag 0x100. A secondary alignment represents an alternative to
	// the primary alignment for this read. Aligners may return secondary
	// alignments if a read can map ambiguously to multiple coordinates in
	// the genome. By convention, each read has one and only one alignment
	// where both secondaryAlignment and supplementaryAlignment are false.
	SecondaryAlignment *bool `json:"secondaryAlignment,omitempty"`

	// SupplementaryAlignment: Whether this alignment is supplementary.
	// Equivalent to SAM flag 0x800. Supplementary alignments are used in
	// the representation of a chimeric alignment. In a chimeric alignment,
	// a read is split into multiple linear alignments that map to different
	// reference contigs. The first linear alignment in the read will be
	// designated as the representative alignment; the remaining linear
	// alignments will be designated as supplementary alignments. These
	// alignments may have different mapping quality scores. In each linear
	// alignment in a chimeric alignment, the read will be hard clipped. The
	// alignedSequence and alignedQuality fields in the alignment record
	// will only represent the bases for its respective linear alignment.
	SupplementaryAlignment *bool `json:"supplementaryAlignment,omitempty"`
}

type ReadGroup 

type ReadGroup struct {
	// DatasetId: The ID of the dataset this read group belongs to.
	DatasetId string `json:"datasetId,omitempty"`

	// Description: A free-form text description of this read group.
	Description string `json:"description,omitempty"`

	// Experiment: The experiment used to generate this read group.
	Experiment *ReadGroupExperiment `json:"experiment,omitempty"`

	// Id: The generated unique read group ID. Note: This is different than
	// the @RG ID field in the SAM spec. For that value, see the name field.
	Id string `json:"id,omitempty"`

	// Info: A map of additional read group information.
	Info map[string][]string `json:"info,omitempty"`

	// Name: The read group name. This corresponds to the @RG ID field in
	// the SAM spec.
	Name string `json:"name,omitempty"`

	// PredictedInsertSize: The predicted insert size of this read group.
	// The insert size is the length the sequenced DNA fragment from
	// end-to-end, not including the adapters.
	PredictedInsertSize int64 `json:"predictedInsertSize,omitempty"`

	// Programs: The programs used to generate this read group. Programs are
	// always identical for all read groups within a read group set. For
	// this reason, only the first read group in a returned set will have
	// this field populated.
	Programs []*ReadGroupProgram `json:"programs,omitempty"`

	// ReferenceSetId: The reference set the reads in this read group are
	// aligned to. Required if there are any read alignments.
	ReferenceSetId string `json:"referenceSetId,omitempty"`

	// SampleId: The sample this read group's data was generated from. Note:
	// This is not an actual ID within this repository, but rather an
	// identifier for a sample which may be meaningful to some external
	// system.
	SampleId string `json:"sampleId,omitempty"`
}

type ReadGroupExperiment 

type ReadGroupExperiment struct {
	// InstrumentModel: The instrument model used as part of this
	// experiment. This maps to sequencing technology in BAM.
	InstrumentModel string `json:"instrumentModel,omitempty"`

	// LibraryId: The library used as part of this experiment. Note: This is
	// not an actual ID within this repository, but rather an identifier for
	// a library which may be meaningful to some external system.
	LibraryId string `json:"libraryId,omitempty"`

	// PlatformUnit: The platform unit used as part of this experiment e.g.
	// flowcell-barcode.lane for Illumina or slide for SOLiD. Corresponds to
	// the
	PlatformUnit string `json:"platformUnit,omitempty"`

	// SequencingCenter: The sequencing center used as part of this
	// experiment.
	SequencingCenter string `json:"sequencingCenter,omitempty"`
}

type ReadGroupProgram 

type ReadGroupProgram struct {
	// CommandLine: The command line used to run this program.
	CommandLine string `json:"commandLine,omitempty"`

	// Id: The user specified locally unique ID of the program. Used along
	// with prevProgramId to define an ordering between programs.
	Id string `json:"id,omitempty"`

	// Name: The name of the program.
	Name string `json:"name,omitempty"`

	// PrevProgramId: The ID of the program run before this one.
	PrevProgramId string `json:"prevProgramId,omitempty"`

	// Version: The version of the program run.
	Version string `json:"version,omitempty"`
}

type ReadGroupSet 

type ReadGroupSet struct {
	// DatasetId: The dataset ID.
	DatasetId string `json:"datasetId,omitempty"`

	// Filename: The filename of the original source file for this read
	// group set, if any.
	Filename string `json:"filename,omitempty"`

	// Id: The read group set ID.
	Id string `json:"id,omitempty"`

	// Info: A map of additional read group set information.
	Info map[string][]string `json:"info,omitempty"`

	// Name: The read group set name. By default this will be initialized to
	// the sample name of the sequenced data contained in this set.
	Name string `json:"name,omitempty"`

	// ReadGroups: The read groups in this set. There are typically 1-10
	// read groups in a read group set.
	ReadGroups []*ReadGroup `json:"readGroups,omitempty"`

	// ReferenceSetId: The reference set the reads in this read group set
	// are aligned to.
	ReferenceSetId string `json:"referenceSetId,omitempty"`
}

type ReadgroupsetsAlignCall 

type ReadgroupsetsAlignCall struct {
	// contains filtered or unexported fields
}

func (*ReadgroupsetsAlignCall) Do 

func (c *ReadgroupsetsAlignCall) Do() (*AlignReadGroupSetsResponse, error)

func (*ReadgroupsetsAlignCall) Fields 

func (c *ReadgroupsetsAlignCall) Fields(s ...googleapi.Field) *ReadgroupsetsAlignCall

Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.

type ReadgroupsetsCallCall 

type ReadgroupsetsCallCall struct {
	// contains filtered or unexported fields
}

func (*ReadgroupsetsCallCall) Do 

func (c *ReadgroupsetsCallCall) Do() (*CallReadGroupSetsResponse, error)

func (*ReadgroupsetsCallCall) Fields 

func (c *ReadgroupsetsCallCall) Fields(s ...googleapi.Field) *ReadgroupsetsCallCall

Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.

type ReadgroupsetsCoveragebucketsListCall 

type ReadgroupsetsCoveragebucketsListCall struct {
	// contains filtered or unexported fields
}

func (*ReadgroupsetsCoveragebucketsListCall) Do 

func (c *ReadgroupsetsCoveragebucketsListCall) Do() (*ListCoverageBucketsResponse, error)

func (*ReadgroupsetsCoveragebucketsListCall) Fields 

func (c *ReadgroupsetsCoveragebucketsListCall) Fields(s ...googleapi.Field) *ReadgroupsetsCoveragebucketsListCall

Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.

func (*ReadgroupsetsCoveragebucketsListCall) PageSize 

func (c *ReadgroupsetsCoveragebucketsListCall) PageSize(pageSize int64) *ReadgroupsetsCoveragebucketsListCall

PageSize sets the optional parameter "pageSize": The maximum number of results to return in a single page. If unspecified, defaults to 1024. The maximum value is 2048.

func (*ReadgroupsetsCoveragebucketsListCall) PageToken 

func (c *ReadgroupsetsCoveragebucketsListCall) PageToken(pageToken string) *ReadgroupsetsCoveragebucketsListCall

PageToken sets the optional parameter "pageToken": The continuation token, which is used to page through large result sets. To get the next page of results, set this parameter to the value of nextPageToken from the previous response.

func (*ReadgroupsetsCoveragebucketsListCall) RangeEnd 

func (c *ReadgroupsetsCoveragebucketsListCall) RangeEnd(rangeEnd int64) *ReadgroupsetsCoveragebucketsListCall

RangeEnd sets the optional parameter "range.end": The end position of the range on the reference, 0-based exclusive. If specified, referenceName must also be specified.

func (*ReadgroupsetsCoveragebucketsListCall) RangeReferenceName 

func (c *ReadgroupsetsCoveragebucketsListCall) RangeReferenceName(rangeReferenceName string) *ReadgroupsetsCoveragebucketsListCall

RangeReferenceName sets the optional parameter "range.referenceName": The reference sequence name, for example chr1, 1, or chrX.

func (*ReadgroupsetsCoveragebucketsListCall) RangeStart 

func (c *ReadgroupsetsCoveragebucketsListCall) RangeStart(rangeStart int64) *ReadgroupsetsCoveragebucketsListCall

RangeStart sets the optional parameter "range.start": The start position of the range on the reference, 0-based inclusive. If specified, referenceName must also be specified.

func (*ReadgroupsetsCoveragebucketsListCall) TargetBucketWidth 

func (c *ReadgroupsetsCoveragebucketsListCall) TargetBucketWidth(targetBucketWidth int64) *ReadgroupsetsCoveragebucketsListCall

TargetBucketWidth sets the optional parameter "targetBucketWidth": 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.

type ReadgroupsetsCoveragebucketsService 

type ReadgroupsetsCoveragebucketsService struct {
	// contains filtered or unexported fields
}

func NewReadgroupsetsCoveragebucketsService 

func NewReadgroupsetsCoveragebucketsService(s *Service) *ReadgroupsetsCoveragebucketsService

func (*ReadgroupsetsCoveragebucketsService) List 

func (r *ReadgroupsetsCoveragebucketsService) List(readGroupSetId string) *ReadgroupsetsCoveragebucketsListCall

List: Lists fixed width coverage buckets for a read group set, each of which correspond to a range of a reference sequence. Each bucket summarizes coverage information across its corresponding genomic range.

Coverage is defined as the number of reads which are aligned to a given base in the reference sequence. Coverage buckets are available at several precomputed bucket widths, enabling retrieval of various coverage 'zoom levels'. The caller must have READ permissions for the target read group set.

type ReadgroupsetsDeleteCall 

type ReadgroupsetsDeleteCall struct {
	// contains filtered or unexported fields
}

func (*ReadgroupsetsDeleteCall) Do 

func (c *ReadgroupsetsDeleteCall) Do() error

func (*ReadgroupsetsDeleteCall) Fields 

func (c *ReadgroupsetsDeleteCall) Fields(s ...googleapi.Field) *ReadgroupsetsDeleteCall

Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.

type ReadgroupsetsExportCall 

type ReadgroupsetsExportCall struct {
	// contains filtered or unexported fields
}

func (*ReadgroupsetsExportCall) Do 

func (c *ReadgroupsetsExportCall) Do() (*ExportReadGroupSetsResponse, error)

func (*ReadgroupsetsExportCall) Fields 

func (c *ReadgroupsetsExportCall) Fields(s ...googleapi.Field) *ReadgroupsetsExportCall

Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.

type ReadgroupsetsGetCall 

type ReadgroupsetsGetCall struct {
	// contains filtered or unexported fields
}

func (*ReadgroupsetsGetCall) Do 

func (c *ReadgroupsetsGetCall) Do() (*ReadGroupSet, error)

func (*ReadgroupsetsGetCall) Fields 

func (c *ReadgroupsetsGetCall) Fields(s ...googleapi.Field) *ReadgroupsetsGetCall

Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.

type ReadgroupsetsImportCall 

type ReadgroupsetsImportCall struct {
	// contains filtered or unexported fields
}

func (*ReadgroupsetsImportCall) Do 

func (c *ReadgroupsetsImportCall) Do() (*ImportReadGroupSetsResponse, error)

func (*ReadgroupsetsImportCall) Fields 

func (c *ReadgroupsetsImportCall) Fields(s ...googleapi.Field) *ReadgroupsetsImportCall

Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.

type ReadgroupsetsPatchCall 

type ReadgroupsetsPatchCall struct {
	// contains filtered or unexported fields
}

func (*ReadgroupsetsPatchCall) Do 

func (c *ReadgroupsetsPatchCall) Do() (*ReadGroupSet, error)

func (*ReadgroupsetsPatchCall) Fields 

func (c *ReadgroupsetsPatchCall) Fields(s ...googleapi.Field) *ReadgroupsetsPatchCall

Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.

type ReadgroupsetsSearchCall 

type ReadgroupsetsSearchCall struct {
	// contains filtered or unexported fields
}

func (*ReadgroupsetsSearchCall) Do 

func (c *ReadgroupsetsSearchCall) Do() (*SearchReadGroupSetsResponse, error)

func (*ReadgroupsetsSearchCall) Fields 

func (c *ReadgroupsetsSearchCall) Fields(s ...googleapi.Field) *ReadgroupsetsSearchCall

Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.

type ReadgroupsetsService 

type ReadgroupsetsService struct {
	Coveragebuckets *ReadgroupsetsCoveragebucketsService
	// contains filtered or unexported fields
}

func NewReadgroupsetsService 

func NewReadgroupsetsService(s *Service) *ReadgroupsetsService

func (*ReadgroupsetsService) Align 

func (r *ReadgroupsetsService) Align(alignreadgroupsetsrequest *AlignReadGroupSetsRequest) *ReadgroupsetsAlignCall

Align: Aligns read data from existing read group sets or files from Google Cloud Storage. See the alignment and variant calling documentation for more details.

func (*ReadgroupsetsService) Call 

func (r *ReadgroupsetsService) Call(callreadgroupsetsrequest *CallReadGroupSetsRequest) *ReadgroupsetsCallCall

Call: Calls variants on read data from existing read group sets or files from Google Cloud Storage. See the alignment and variant calling documentation for more details.

func (*ReadgroupsetsService) Delete 

func (r *ReadgroupsetsService) Delete(readGroupSetId string) *ReadgroupsetsDeleteCall

Delete: Deletes a read group set.

func (*ReadgroupsetsService) Export 

func (r *ReadgroupsetsService) Export(exportreadgroupsetsrequest *ExportReadGroupSetsRequest) *ReadgroupsetsExportCall

Export: Exports read group sets to a BAM file in Google Cloud Storage.

Note that currently there may be some differences between exported BAM files and the original BAM file at the time of import. In particular, comments in the input file header will not be preserved, some custom tags will be converted to strings, and original reference sequence order is not necessarily preserved.

func (*ReadgroupsetsService) Get 

func (r *ReadgroupsetsService) Get(readGroupSetId string) *ReadgroupsetsGetCall

Get: Gets a read group set by ID.

func (*ReadgroupsetsService) Import 

func (r *ReadgroupsetsService) Import(importreadgroupsetsrequest *ImportReadGroupSetsRequest) *ReadgroupsetsImportCall

Import: Creates read group sets by asynchronously importing the provided information.

Note that currently comments in the input file header are not imported and some custom tags will be converted to strings, rather than preserving tag types. The caller must have WRITE permissions to the dataset.

func (*ReadgroupsetsService) Patch 

func (r *ReadgroupsetsService) Patch(readGroupSetId string, readgroupset *ReadGroupSet) *ReadgroupsetsPatchCall

Patch: Updates a read group set. This method supports patch semantics.

func (*ReadgroupsetsService) Search 

func (r *ReadgroupsetsService) Search(searchreadgroupsetsrequest *SearchReadGroupSetsRequest) *ReadgroupsetsSearchCall

Search: Searches for read group sets matching the criteria.

Implements GlobalAllianceApi.searchReadGroupSets.

func (*ReadgroupsetsService) Update 

func (r *ReadgroupsetsService) Update(readGroupSetId string, readgroupset *ReadGroupSet) *ReadgroupsetsUpdateCall

Update: Updates a read group set.

type ReadgroupsetsUpdateCall 

type ReadgroupsetsUpdateCall struct {
	// contains filtered or unexported fields
}

func (*ReadgroupsetsUpdateCall) Do 

func (c *ReadgroupsetsUpdateCall) Do() (*ReadGroupSet, error)

func (*ReadgroupsetsUpdateCall) Fields 

func (c *ReadgroupsetsUpdateCall) Fields(s ...googleapi.Field) *ReadgroupsetsUpdateCall

Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.

type ReadsSearchCall 

type ReadsSearchCall struct {
	// contains filtered or unexported fields
}

func (*ReadsSearchCall) Do 

func (c *ReadsSearchCall) Do() (*SearchReadsResponse, error)

func (*ReadsSearchCall) Fields 

func (c *ReadsSearchCall) Fields(s ...googleapi.Field) *ReadsSearchCall

Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.

type ReadsService 

type ReadsService struct {
	// contains filtered or unexported fields
}

func NewReadsService 

func NewReadsService(s *Service) *ReadsService

func (*ReadsService) Search 

func (r *ReadsService) Search(searchreadsrequest *SearchReadsRequest) *ReadsSearchCall

Search: Gets a list of reads for one or more read group sets. Reads search operates over a genomic coordinate space of reference sequence & position defined over the reference sequences to which the requested read group sets are aligned.

If a target positional range is specified, search returns all reads whose alignment to the reference genome overlap the range. A query which specifies only read group set IDs yields all reads in those read group sets, including unmapped reads.

All reads returned (including reads on subsequent pages) are ordered by genomic coordinate (reference sequence & position). Reads with equivalent genomic coordinates are returned in a deterministic order.

Implements GlobalAllianceApi.searchReads.

type Reference 

type Reference struct {
	// Id: The Google generated immutable ID of the reference.
	Id string `json:"id,omitempty"`

	// Length: The length of this reference's sequence.
	Length int64 `json:"length,omitempty,string"`

	// Md5checksum: MD5 of the upper-case sequence excluding all whitespace
	// characters (this is equivalent to SQ:M5 in SAM). This value is
	// represented in lower case hexadecimal format.
	Md5checksum string `json:"md5checksum,omitempty"`

	// Name: The name of this reference, for example 22.
	Name string `json:"name,omitempty"`

	// NcbiTaxonId: ID from http://www.ncbi.nlm.nih.gov/taxonomy (e.g.
	// 9606->human) if not specified by the containing reference set.
	NcbiTaxonId int64 `json:"ncbiTaxonId,omitempty"`

	// SourceAccessions: All known corresponding accession IDs in INSDC
	// (GenBank/ENA/DDBJ) ideally with a version number, for example
	// GCF_000001405.26.
	SourceAccessions []string `json:"sourceAccessions,omitempty"`

	// SourceURI: The URI from which the sequence was obtained. Specifies a
	// FASTA format file/string with one name, sequence pair.
	SourceURI string `json:"sourceURI,omitempty"`
}

type ReferenceBound 

type ReferenceBound struct {
	// ReferenceName: The reference the bound is associate with.
	ReferenceName string `json:"referenceName,omitempty"`

	// UpperBound: An upper bound (inclusive) on the starting coordinate of
	// any variant in the reference sequence.
	UpperBound int64 `json:"upperBound,omitempty,string"`
}

type ReferenceSet 

type ReferenceSet struct {
	// AssemblyId: Public id of this reference set, such as GRCh37.
	AssemblyId string `json:"assemblyId,omitempty"`

	// Description: Free text description of this reference set.
	Description string `json:"description,omitempty"`

	// Id: The Google generated immutable ID of the reference set.
	Id string `json:"id,omitempty"`

	// Md5checksum: Order-independent MD5 checksum which identifies this
	// reference set. The checksum is computed by sorting all lower case
	// hexidecimal string reference.md5checksum (for all reference in this
	// set) in ascending lexicographic order, concatenating, and taking the
	// MD5 of that value. The resulting value is represented in lower case
	// hexadecimal format.
	Md5checksum string `json:"md5checksum,omitempty"`

	// NcbiTaxonId: ID from http://www.ncbi.nlm.nih.gov/taxonomy (e.g.
	// 9606->human) indicating the species which this assembly 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, e.g. EBV in a human reference
	// genome.
	NcbiTaxonId int64 `json:"ncbiTaxonId,omitempty"`

	// ReferenceIds: The IDs of the reference objects that are part of this
	// set. Reference.md5checksum must be unique within this set.
	ReferenceIds []string `json:"referenceIds,omitempty"`

	// SourceAccessions: All known corresponding accession IDs in INSDC
	// (GenBank/ENA/DDBJ) ideally with a version number, for example
	// NC_000001.11.
	SourceAccessions []string `json:"sourceAccessions,omitempty"`

	// SourceURI: The URI from which the references were obtained.
	SourceURI string `json:"sourceURI,omitempty"`
}

type ReferencesBasesListCall 

type ReferencesBasesListCall struct {
	// contains filtered or unexported fields
}

func (*ReferencesBasesListCall) Do 

func (c *ReferencesBasesListCall) Do() (*ListBasesResponse, error)

func (*ReferencesBasesListCall) End 

func (c *ReferencesBasesListCall) End(end int64) *ReferencesBasesListCall

End sets the optional parameter "end": The end position (0-based, exclusive) of this query. Defaults to the length of this reference.

func (*ReferencesBasesListCall) Fields 

func (c *ReferencesBasesListCall) Fields(s ...googleapi.Field) *ReferencesBasesListCall

Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.

func (*ReferencesBasesListCall) PageSize 

func (c *ReferencesBasesListCall) PageSize(pageSize int64) *ReferencesBasesListCall

PageSize sets the optional parameter "pageSize": Specifies the maximum number of bases to return in a single page.

func (*ReferencesBasesListCall) PageToken 

func (c *ReferencesBasesListCall) PageToken(pageToken string) *ReferencesBasesListCall

PageToken sets the optional parameter "pageToken": The continuation token, which is used to page through large result sets. To get the next page of results, set this parameter to the value of nextPageToken from the previous response.

func (*ReferencesBasesListCall) Start 

func (c *ReferencesBasesListCall) Start(start int64) *ReferencesBasesListCall

Start sets the optional parameter "start": The start position (0-based) of this query. Defaults to 0.

type ReferencesBasesService 

type ReferencesBasesService struct {
	// contains filtered or unexported fields
}

func NewReferencesBasesService 

func NewReferencesBasesService(s *Service) *ReferencesBasesService

func (*ReferencesBasesService) List 

func (r *ReferencesBasesService) List(referenceId string) *ReferencesBasesListCall

List: Lists the bases in a reference, optionally restricted to a range.

Implements GlobalAllianceApi.getReferenceBases.

type ReferencesGetCall 

type ReferencesGetCall struct {
	// contains filtered or unexported fields
}

func (*ReferencesGetCall) Do 

func (c *ReferencesGetCall) Do() (*Reference, error)

func (*ReferencesGetCall) Fields 

func (c *ReferencesGetCall) Fields(s ...googleapi.Field) *ReferencesGetCall

Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.

type ReferencesSearchCall 

type ReferencesSearchCall struct {
	// contains filtered or unexported fields
}

func (*ReferencesSearchCall) Do 

func (c *ReferencesSearchCall) Do() (*SearchReferencesResponse, error)

func (*ReferencesSearchCall) Fields 

func (c *ReferencesSearchCall) Fields(s ...googleapi.Field) *ReferencesSearchCall

Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.

type ReferencesService 

type ReferencesService struct {
	Bases *ReferencesBasesService
	// contains filtered or unexported fields
}

func NewReferencesService 

func NewReferencesService(s *Service) *ReferencesService

func (*ReferencesService) Get 

func (r *ReferencesService) Get(referenceId string) *ReferencesGetCall

Get: Gets a reference.

Implements GlobalAllianceApi.getReference.

func (*ReferencesService) Search 

func (r *ReferencesService) Search(searchreferencesrequest *SearchReferencesRequest) *ReferencesSearchCall

Search: Searches for references which match the given criteria.

Implements GlobalAllianceApi.searchReferences.

type ReferencesetsGetCall 

type ReferencesetsGetCall struct {
	// contains filtered or unexported fields
}

func (*ReferencesetsGetCall) Do 

func (c *ReferencesetsGetCall) Do() (*ReferenceSet, error)

func (*ReferencesetsGetCall) Fields 

func (c *ReferencesetsGetCall) Fields(s ...googleapi.Field) *ReferencesetsGetCall

Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.

type ReferencesetsSearchCall 

type ReferencesetsSearchCall struct {
	// contains filtered or unexported fields
}

func (*ReferencesetsSearchCall) Do 

func (c *ReferencesetsSearchCall) Do() (*SearchReferenceSetsResponse, error)

func (*ReferencesetsSearchCall) Fields 

func (c *ReferencesetsSearchCall) Fields(s ...googleapi.Field) *ReferencesetsSearchCall

Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.

type ReferencesetsService 

type ReferencesetsService struct {
	// contains filtered or unexported fields
}

func NewReferencesetsService 

func NewReferencesetsService(s *Service) *ReferencesetsService

func (*ReferencesetsService) Get 

func (r *ReferencesetsService) Get(referenceSetId string) *ReferencesetsGetCall

Get: Gets a reference set.

Implements GlobalAllianceApi.getReferenceSet.

func (*ReferencesetsService) Search 

func (r *ReferencesetsService) Search(searchreferencesetsrequest *SearchReferenceSetsRequest) *ReferencesetsSearchCall

Search: Searches for reference sets which match the given criteria.

Implements GlobalAllianceApi.searchReferenceSets.

type SearchAnnotationSetsRequest 

type SearchAnnotationSetsRequest struct {
	// DatasetIds: The dataset IDs to search within. Caller must have READ
	// access to these datasets.
	DatasetIds []string `json:"datasetIds,omitempty"`

	// Name: Only return annotations sets for which a substring of the name
	// matches this string (case insensitive).
	Name string `json:"name,omitempty"`

	// PageSize: Specifies number of results to return in a single page. If
	// unspecified, it will default to 128. The maximum value is 1024.
	PageSize int64 `json:"pageSize,omitempty"`

	// PageToken: The continuation token, which is used to page through
	// large result sets. To get the next page of results, set this
	// parameter to the value of nextPageToken from the previous response.
	PageToken string `json:"pageToken,omitempty"`

	// ReferenceSetId: If specified, only annotation sets associated with
	// the given reference set are returned.
	ReferenceSetId string `json:"referenceSetId,omitempty"`

	// Types: If specified, only annotation sets that have any of these
	// types are returned.
	Types []string `json:"types,omitempty"`
}

type SearchAnnotationSetsResponse 

type SearchAnnotationSetsResponse struct {
	// AnnotationSets: The matching annotation sets.
	AnnotationSets []*AnnotationSet `json:"annotationSets,omitempty"`

	// NextPageToken: The continuation token, which is used to page through
	// large result sets. Provide this value in a subsequent request to
	// return the next page of results. This field will be empty if there
	// aren't any additional results.
	NextPageToken string `json:"nextPageToken,omitempty"`
}

type SearchAnnotationsRequest 

type SearchAnnotationsRequest struct {
	// AnnotationSetIds: The annotation sets to search within. The caller
	// must have READ access to these annotation sets. Required. All queried
	// annotation sets must have the same type.
	AnnotationSetIds []string `json:"annotationSetIds,omitempty"`

	// PageSize: Specifies number of results to return in a single page. If
	// unspecified, it will default to 256. The maximum value is 2048.
	PageSize int64 `json:"pageSize,omitempty"`

	// PageToken: The continuation token, which is used to page through
	// large result sets. To get the next page of results, set this
	// parameter to the value of nextPageToken from the previous response.
	PageToken string `json:"pageToken,omitempty"`

	// Range: If specified, this query matches only annotations that overlap
	// this range.
	Range *QueryRange `json:"range,omitempty"`
}

type SearchAnnotationsResponse 

type SearchAnnotationsResponse struct {
	// Annotations: The matching annotations.
	Annotations []*Annotation `json:"annotations,omitempty"`

	// NextPageToken: The continuation token, which is used to page through
	// large result sets. Provide this value in a subsequent request to
	// return the next page of results. This field will be empty if there
	// aren't any additional results.
	NextPageToken string `json:"nextPageToken,omitempty"`
}

type SearchCallSetsRequest 

type SearchCallSetsRequest struct {
	// Name: Only return call sets for which a substring of the name matches
	// this string.
	Name string `json:"name,omitempty"`

	// PageSize: The maximum number of call sets to return. If unspecified,
	// defaults to 1000.
	PageSize int64 `json:"pageSize,omitempty"`

	// PageToken: The continuation token, which is used to page through
	// large result sets. To get the next page of results, set this
	// parameter to the value of nextPageToken from the previous response.
	PageToken string `json:"pageToken,omitempty"`

	// VariantSetIds: Restrict the query to call sets within the given
	// variant sets. At least one ID must be provided.
	VariantSetIds []string `json:"variantSetIds,omitempty"`
}

type SearchCallSetsResponse 

type SearchCallSetsResponse struct {
	// CallSets: The list of matching call sets.
	CallSets []*CallSet `json:"callSets,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 SearchJobsRequest 

type SearchJobsRequest struct {
	// CreatedAfter: If specified, only jobs created on or after this date,
	// given in milliseconds since Unix epoch, will be returned.
	CreatedAfter int64 `json:"createdAfter,omitempty,string"`

	// CreatedBefore: If specified, only jobs created prior to this date,
	// given in milliseconds since Unix epoch, will be returned.
	CreatedBefore int64 `json:"createdBefore,omitempty,string"`

	// PageSize: Specifies the number of results to return in a single page.
	// Defaults to 128. The maximum value is 256.
	PageSize int64 `json:"pageSize,omitempty"`

	// PageToken: The continuation token which is used to page through large
	// result sets. To get the next page of results, set this parameter to
	// the value of the nextPageToken from the previous response.
	PageToken string `json:"pageToken,omitempty"`

	// ProjectNumber: Required. Only return jobs which belong to this Google
	// Developers Console project.
	ProjectNumber int64 `json:"projectNumber,omitempty,string"`

	// Status: Only return jobs which have a matching status.
	Status []string `json:"status,omitempty"`
}

type SearchJobsResponse 

type SearchJobsResponse struct {
	// Jobs: The list of jobs results, ordered newest to oldest.
	Jobs []*Job `json:"jobs,omitempty"`

	// NextPageToken: The continuation token which is used to page through
	// large result sets. Provide this value is a subsequent request to
	// return the next page of results. This field will be empty if there
	// are no more results.
	NextPageToken string `json:"nextPageToken,omitempty"`
}

type SearchReadGroupSetsRequest 

type SearchReadGroupSetsRequest struct {
	// DatasetIds: Restricts this query to read group sets within the given
	// datasets. At least one ID must be provided.
	DatasetIds []string `json:"datasetIds,omitempty"`

	// Name: Only return read group sets for which a substring of the name
	// matches this string.
	Name string `json:"name,omitempty"`

	// PageSize: Specifies number of results to return in a single page. If
	// unspecified, it will default to 256. The maximum value is 1024.
	PageSize int64 `json:"pageSize,omitempty"`

	// PageToken: The continuation token, which is used to page through
	// large result sets. To get the next page of results, set this
	// parameter to the value of nextPageToken from the previous response.
	PageToken string `json:"pageToken,omitempty"`
}

type SearchReadGroupSetsResponse 

type SearchReadGroupSetsResponse 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"`

	// ReadGroupSets: The list of matching read group sets.
	ReadGroupSets []*ReadGroupSet `json:"readGroupSets,omitempty"`
}

type SearchReadsRequest 

type SearchReadsRequest struct {
	// End: The end position of the range on the reference, 0-based
	// exclusive. If specified, referenceName must also be specified.
	End int64 `json:"end,omitempty,string"`

	// PageSize: Specifies number of results to return in a single page. If
	// unspecified, it will default to 256. The maximum value is 2048.
	PageSize int64 `json:"pageSize,omitempty"`

	// PageToken: The continuation token, which is used to page through
	// large result sets. To get the next page of results, set this
	// parameter to the value of nextPageToken from the previous response.
	PageToken string `json:"pageToken,omitempty"`

	// ReadGroupIds: 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 `json:"readGroupIds,omitempty"`

	// ReadGroupSetIds: 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 `json:"readGroupSetIds,omitempty"`

	// ReferenceName: The reference sequence name, for example chr1, 1, or
	// chrX. If set to *, only unmapped reads are returned.
	ReferenceName string `json:"referenceName,omitempty"`

	// Start: The start position of the range on the reference, 0-based
	// inclusive. If specified, referenceName must also be specified.
	Start int64 `json:"start,omitempty,string"`
}

type SearchReadsResponse 

type SearchReadsResponse struct {
	// Alignments: 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 last and are
	// further sorted in ascending lexicographic order by fragment name.
	Alignments []*Read `json:"alignments,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 SearchReferenceSetsRequest 

type SearchReferenceSetsRequest struct {
	// Accessions: If present, return references for which the accession
	// matches any of these strings. Best to give a version number, for
	// example GCF_000001405.26. If only the main accession number is given
	// then all records with that main accession will be returned, whichever
	// version. Note that different versions will have different sequences.
	Accessions []string `json:"accessions,omitempty"`

	// AssemblyId: If present, return reference sets for which a substring
	// of their assemblyId matches this string (case insensitive).
	AssemblyId string `json:"assemblyId,omitempty"`

	// Md5checksums: If present, return references for which the md5checksum
	// matches. See ReferenceSet.md5checksum for details.
	Md5checksums []string `json:"md5checksums,omitempty"`

	// PageSize: Specifies the maximum number of results to return in a
	// single page.
	PageSize int64 `json:"pageSize,omitempty"`

	// PageToken: The continuation token, which is used to page through
	// large result sets. To get the next page of results, set this
	// parameter to the value of nextPageToken from the previous response.
	PageToken string `json:"pageToken,omitempty"`
}

type SearchReferenceSetsResponse 

type SearchReferenceSetsResponse 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"`

	// ReferenceSets: The matching references sets.
	ReferenceSets []*ReferenceSet `json:"referenceSets,omitempty"`
}

type SearchReferencesRequest 

type SearchReferencesRequest struct {
	// Accessions: If present, return references for which the accession
	// matches this string. Best to give a version number, for example
	// GCF_000001405.26. If only the main accession number is given then all
	// records with that main accession will be returned, whichever version.
	// Note that different versions will have different sequences.
	Accessions []string `json:"accessions,omitempty"`

	// Md5checksums: If present, return references for which the md5checksum
	// matches. See Reference.md5checksum for construction details.
	Md5checksums []string `json:"md5checksums,omitempty"`

	// PageSize: Specifies the maximum number of results to return in a
	// single page.
	PageSize int64 `json:"pageSize,omitempty"`

	// PageToken: The continuation token, which is used to page through
	// large result sets. To get the next page of results, set this
	// parameter to the value of nextPageToken from the previous response.
	PageToken string `json:"pageToken,omitempty"`

	// ReferenceSetId: If present, return only references which belong to
	// this reference set.
	ReferenceSetId string `json:"referenceSetId,omitempty"`
}

type SearchReferencesResponse 

type SearchReferencesResponse 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"`

	// References: The matching references.
	References []*Reference `json:"references,omitempty"`
}

type SearchVariantSetsRequest 

type SearchVariantSetsRequest struct {
	// DatasetIds: Exactly one dataset ID must be provided here. Only
	// variant sets which belong to this dataset will be returned.
	DatasetIds []string `json:"datasetIds,omitempty"`

	// PageSize: The maximum number of variant sets to return in a request.
	PageSize int64 `json:"pageSize,omitempty"`

	// PageToken: The continuation token, which is used to page through
	// large result sets. To get the next page of results, set this
	// parameter to the value of nextPageToken from the previous response.
	PageToken string `json:"pageToken,omitempty"`
}

type SearchVariantSetsResponse 

type SearchVariantSetsResponse 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"`

	// VariantSets: The variant sets belonging to the requested dataset.
	VariantSets []*VariantSet `json:"variantSets,omitempty"`
}

type SearchVariantsRequest 

type SearchVariantsRequest struct {
	// CallSetIds: Only return variant calls which belong to call sets with
	// these ids. Leaving this blank returns all variant calls. If a variant
	// has no calls belonging to any of these call sets, it won't be
	// returned at all. Currently, variants with no calls from any call set
	// will never be returned.
	CallSetIds []string `json:"callSetIds,omitempty"`

	// End: The end of the window, 0-based exclusive. If unspecified or 0,
	// defaults to the length of the reference.
	End int64 `json:"end,omitempty,string"`

	// MaxCalls: The maximum number of calls to return. However, at least
	// one variant will always be returned, even if it has more calls than
	// this limit. If unspecified, defaults to 5000.
	MaxCalls int64 `json:"maxCalls,omitempty"`

	// PageSize: The maximum number of variants to return. If unspecified,
	// defaults to 5000.
	PageSize int64 `json:"pageSize,omitempty"`

	// PageToken: The continuation token, which is used to page through
	// large result sets. To get the next page of results, set this
	// parameter to the value of nextPageToken from the previous response.
	PageToken string `json:"pageToken,omitempty"`

	// ReferenceName: Required. Only return variants in this reference
	// sequence.
	ReferenceName string `json:"referenceName,omitempty"`

	// Start: The beginning of the window (0-based, inclusive) for which
	// overlapping variants should be returned. If unspecified, defaults to
	// 0.
	Start int64 `json:"start,omitempty,string"`

	// VariantName: Only return variants which have exactly this name.
	VariantName string `json:"variantName,omitempty"`

	// VariantSetIds: At most one variant set ID must be provided. Only
	// variants from this variant set will be returned. If omitted, a call
	// set id must be included in the request.
	VariantSetIds []string `json:"variantSetIds,omitempty"`
}

type SearchVariantsResponse 

type SearchVariantsResponse 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"`

	// Variants: The list of matching Variants.
	Variants []*Variant `json:"variants,omitempty"`
}

type Service 

type Service struct {
	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
	// contains filtered or unexported fields
}

func New 

func New(client *http.Client) (*Service, error)

type Transcript 

type Transcript struct {
	// CodingSequence: The range of the coding sequence for this transcript,
	// if any. To determine the exact ranges of coding sequence, intersect
	// this range with those of the exons, if any. If there are any exons,
	// the codingSequence must start and end within them.
	//
	// Note that in some cases, the reference genome will not exactly match
	// the observed mRNA transcript e.g. due to variance in the source
	// genome from reference. In these cases, exon.frame will not
	// necessarily match the expected reference reading frame and coding
	// exon reference bases cannot necessarily be concatenated to produce
	// the original transcript mRNA.
	CodingSequence *TranscriptCodingSequence `json:"codingSequence,omitempty"`

	// Exons: The exons that compose this transcript. This field should be
	// unset for genomes where transcript splicing does not occur, for
	// example prokaryotes.
	//
	//
	// Introns are regions of the transcript that are not included in the
	// spliced RNA product. Though not explicitly modeled here, intron
	// ranges can be deduced; all regions of this transcript that are not
	// exons are introns.
	//
	//
	// Exonic sequences do not necessarily code for a translational product
	// (amino acids). Only the regions of exons bounded by the
	// codingSequence correspond to coding DNA sequence.
	//
	//
	// Exons are ordered by start position and may not overlap.
	Exons []*TranscriptExon `json:"exons,omitempty"`

	// GeneId: The annotation ID of the gene from which this transcript is
	// transcribed.
	GeneId string `json:"geneId,omitempty"`
}

type TranscriptCodingSequence 

type TranscriptCodingSequence struct {
	// End: The end of the coding sequence on this annotation's reference
	// sequence, 0-based exclusive. Note that this position is relative to
	// the reference start, and not the containing annotation start.
	End int64 `json:"end,omitempty,string"`

	// Start: The start of the coding sequence on this annotation's
	// reference sequence, 0-based inclusive. Note that this position is
	// relative to the reference start, and not the containing annotation
	// start.
	Start int64 `json:"start,omitempty,string"`
}

type TranscriptExon 

type TranscriptExon struct {
	// End: The end position of the exon on this annotation's reference
	// sequence, 0-based exclusive. Note that this is relative to the
	// reference start, and not the containing annotation start.
	End int64 `json:"end,omitempty,string"`

	// Frame: The frame of this exon. Contains a value of 0, 1, or 2, which
	// indicates the offset of the first coding base of the exon within the
	// reading frame of the coding DNA sequence, if any. This field is
	// dependent on the strandedness of this annotation (see
	// Annotation.position.reverseStrand). For forward stranded annotations,
	// this offset is relative to the exon.start. For reverse strand
	// annotations, this offset is relative to the exon.end-1.
	//
	// Unset if this exon does not intersect the coding sequence. Upon
	// creation of a transcript, the frame must be populated for all or none
	// of the coding exons.
	Frame *Int32Value `json:"frame,omitempty"`

	// Start: The start position of the exon on this annotation's reference
	// sequence, 0-based inclusive. Note that this is relative to the
	// reference start, and not the containing annotation start.
	Start int64 `json:"start,omitempty,string"`
}

type Variant 

type Variant struct {
	// AlternateBases: The bases that appear instead of the reference bases.
	AlternateBases []string `json:"alternateBases,omitempty"`

	// Calls: The variant calls for this particular variant. Each one
	// represents the determination of genotype with respect to this
	// variant.
	Calls []*Call `json:"calls,omitempty"`

	// Created: The date this variant was created, in milliseconds from the
	// epoch.
	Created int64 `json:"created,omitempty,string"`

	// End: The end position (0-based) of this variant. This corresponds to
	// the first base after the last base in the reference allele. So, the
	// length of the reference allele is (end - start). This is useful for
	// variants that don't explicitly give alternate bases, for example
	// large deletions.
	End int64 `json:"end,omitempty,string"`

	// Filter: A list of filters (normally quality filters) this variant has
	// failed. PASS indicates this variant has passed all filters.
	Filter []string `json:"filter,omitempty"`

	// Id: The Google generated ID of the variant, immutable.
	Id string `json:"id,omitempty"`

	// Info: A map of additional variant information.
	Info map[string][]string `json:"info,omitempty"`

	// Names: Names for the variant, for example a RefSNP ID.
	Names []string `json:"names,omitempty"`

	// Quality: A measure of how likely this variant is to be real. A higher
	// value is better.
	Quality float64 `json:"quality,omitempty"`

	// ReferenceBases: The reference bases for this variant. They start at
	// the given position.
	ReferenceBases string `json:"referenceBases,omitempty"`

	// ReferenceName: The reference on which this variant occurs. (such as
	// chr20 or X)
	ReferenceName string `json:"referenceName,omitempty"`

	// Start: The position at which this variant occurs (0-based). This
	// corresponds to the first base of the string of reference bases.
	Start int64 `json:"start,omitempty,string"`

	// VariantSetId: The ID of the variant set this variant belongs to.
	VariantSetId string `json:"variantSetId,omitempty"`
}

type VariantAnnotation 

type VariantAnnotation struct {
	// AlternateBases: The alternate allele for this variant. If multiple
	// alternate alleles exist at this location, create a separate variant
	// for each one, as they may represent distinct conditions.
	AlternateBases string `json:"alternateBases,omitempty"`

	// ClinicalSignificance: Describes the clinical significance of a
	// variant. It is adapted from the ClinVar controlled vocabulary for
	// clinical significance described at:
	// http://www.ncbi.nlm.nih.gov/clinvar/docs/clinsig/
	//
	// Possible values:
	//   "ASSOCIATION"
	//   "BENIGN"
	//   "CLINICAL_SIGNIFICANCE_UNSPECIFIED"
	//   "CONFERS_SENSITIVITY"
	//   "DRUG_RESPONSE"
	//   "HISTOCOMPATIBILITY"
	//   "LIKELY_BENIGN"
	//   "LIKELY_PATHOGENIC"
	//   "MULTIPLE_REPORTED"
	//   "OTHER"
	//   "PATHOGENIC"
	//   "PROTECTIVE"
	//   "RISK_FACTOR"
	//   "UNCERTAIN"
	ClinicalSignificance string `json:"clinicalSignificance,omitempty"`

	// Conditions: The set of conditions associated with this variant. A
	// condition describes the way a variant influences human health.
	Conditions []*VariantAnnotationCondition `json:"conditions,omitempty"`

	// Effect: Effect of the variant on the coding sequence.
	//
	// Possible values:
	//   "EFFECT_UNSPECIFIED"
	//   "FRAMESHIFT"
	//   "FRAME_PRESERVING_INDEL"
	//   "NONSYNONYMOUS_SNP"
	//   "OTHER"
	//   "SPLICE_SITE_DISRUPTION"
	//   "STOP_GAIN"
	//   "STOP_LOSS"
	//   "SYNONYMOUS_SNP"
	Effect string `json:"effect,omitempty"`

	// GeneId: Google annotation ID of the gene affected by this variant.
	// This should be provided when the variant is created.
	GeneId string `json:"geneId,omitempty"`

	// TranscriptIds: Google annotation IDs of the transcripts affected by
	// this variant. These should be provided when the variant is created.
	TranscriptIds []string `json:"transcriptIds,omitempty"`

	// Type: Type has been adapted from ClinVar's list of variant types.
	//
	// Possible values:
	//   "CNV"
	//   "DELETION"
	//   "INSERTION"
	//   "OTHER"
	//   "SNP"
	//   "STRUCTURAL"
	//   "SUBSTITUTION"
	//   "TYPE_UNSPECIFIED"
	Type string `json:"type,omitempty"`
}

type VariantAnnotationCondition 

type VariantAnnotationCondition struct {
	// ConceptId: The MedGen concept id associated with this gene. Search
	// for these IDs at http://www.ncbi.nlm.nih.gov/medgen/
	ConceptId string `json:"conceptId,omitempty"`

	// ExternalIds: The set of external IDs for this condition.
	ExternalIds []*ExternalId `json:"externalIds,omitempty"`

	// Names: A set of names for the condition.
	Names []string `json:"names,omitempty"`

	// OmimId: The OMIM id for this condition. Search for these IDs at
	// http://omim.org/
	OmimId string `json:"omimId,omitempty"`
}

type VariantSet 

type VariantSet struct {
	// DatasetId: The dataset to which this variant set belongs. Immutable.
	DatasetId string `json:"datasetId,omitempty"`

	// Id: The Google-generated ID of the variant set. Immutable.
	Id string `json:"id,omitempty"`

	// Metadata: The metadata associated with this variant set.
	Metadata []*Metadata `json:"metadata,omitempty"`

	// ReferenceBounds: A list of all references used by the variants in a
	// variant set with associated coordinate upper bounds for each one.
	ReferenceBounds []*ReferenceBound `json:"referenceBounds,omitempty"`
}

type VariantsCreateCall 

type VariantsCreateCall struct {
	// contains filtered or unexported fields
}

func (*VariantsCreateCall) Do 

func (c *VariantsCreateCall) Do() (*Variant, error)

func (*VariantsCreateCall) Fields 

func (c *VariantsCreateCall) Fields(s ...googleapi.Field) *VariantsCreateCall

Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.

type VariantsDeleteCall 

type VariantsDeleteCall struct {
	// contains filtered or unexported fields
}

func (*VariantsDeleteCall) Do 

func (c *VariantsDeleteCall) Do() error

func (*VariantsDeleteCall) Fields 

func (c *VariantsDeleteCall) Fields(s ...googleapi.Field) *VariantsDeleteCall

Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.

type VariantsGetCall 

type VariantsGetCall struct {
	// contains filtered or unexported fields
}

func (*VariantsGetCall) Do 

func (c *VariantsGetCall) Do() (*Variant, error)

func (*VariantsGetCall) Fields 

func (c *VariantsGetCall) Fields(s ...googleapi.Field) *VariantsGetCall

Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.

type VariantsSearchCall 

type VariantsSearchCall struct {
	// contains filtered or unexported fields
}

func (*VariantsSearchCall) Do 

func (c *VariantsSearchCall) Do() (*SearchVariantsResponse, error)

func (*VariantsSearchCall) Fields 

func (c *VariantsSearchCall) Fields(s ...googleapi.Field) *VariantsSearchCall

Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.

type VariantsService 

type VariantsService struct {
	// contains filtered or unexported fields
}

func NewVariantsService 

func NewVariantsService(s *Service) *VariantsService

func (*VariantsService) Create 

func (r *VariantsService) Create(variant *Variant) *VariantsCreateCall

Create: Creates a new variant.

func (*VariantsService) Delete 

func (r *VariantsService) Delete(variantId string) *VariantsDeleteCall

Delete: Deletes a variant.

func (*VariantsService) Get 

func (r *VariantsService) Get(variantId string) *VariantsGetCall

Get: Gets a variant by ID.

func (*VariantsService) Search 

func (r *VariantsService) Search(searchvariantsrequest *SearchVariantsRequest) *VariantsSearchCall

Search: Gets a list of variants matching the criteria.

Implements GlobalAllianceApi.searchVariants.

func (*VariantsService) Update 

func (r *VariantsService) Update(variantId string, variant *Variant) *VariantsUpdateCall

Update: Updates a variant's names and info fields. All other modifications are silently ignored. Returns the modified variant without its calls.

type VariantsUpdateCall 

type VariantsUpdateCall struct {
	// contains filtered or unexported fields
}

func (*VariantsUpdateCall) Do 

func (c *VariantsUpdateCall) Do() (*Variant, error)

func (*VariantsUpdateCall) Fields 

func (c *VariantsUpdateCall) Fields(s ...googleapi.Field) *VariantsUpdateCall

Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.

type VariantsetsDeleteCall 

type VariantsetsDeleteCall struct {
	// contains filtered or unexported fields
}

func (*VariantsetsDeleteCall) Do 

func (c *VariantsetsDeleteCall) Do() error

func (*VariantsetsDeleteCall) Fields 

func (c *VariantsetsDeleteCall) Fields(s ...googleapi.Field) *VariantsetsDeleteCall

Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.

type VariantsetsExportCall 

type VariantsetsExportCall struct {
	// contains filtered or unexported fields
}

func (*VariantsetsExportCall) Do 

func (c *VariantsetsExportCall) Do() (*ExportVariantSetResponse, error)

func (*VariantsetsExportCall) Fields 

func (c *VariantsetsExportCall) Fields(s ...googleapi.Field) *VariantsetsExportCall

Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.

type VariantsetsGetCall 

type VariantsetsGetCall struct {
	// contains filtered or unexported fields
}

func (*VariantsetsGetCall) Do 

func (c *VariantsetsGetCall) Do() (*VariantSet, error)

func (*VariantsetsGetCall) Fields 

func (c *VariantsetsGetCall) Fields(s ...googleapi.Field) *VariantsetsGetCall

Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.

type VariantsetsImportVariantsCall 

type VariantsetsImportVariantsCall struct {
	// contains filtered or unexported fields
}

func (*VariantsetsImportVariantsCall) Do 

func (c *VariantsetsImportVariantsCall) Do() (*ImportVariantsResponse, error)

func (*VariantsetsImportVariantsCall) Fields 

func (c *VariantsetsImportVariantsCall) Fields(s ...googleapi.Field) *VariantsetsImportVariantsCall

Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.

type VariantsetsMergeVariantsCall 

type VariantsetsMergeVariantsCall struct {
	// contains filtered or unexported fields
}

func (*VariantsetsMergeVariantsCall) Do 

func (c *VariantsetsMergeVariantsCall) Do() error

func (*VariantsetsMergeVariantsCall) Fields 

func (c *VariantsetsMergeVariantsCall) Fields(s ...googleapi.Field) *VariantsetsMergeVariantsCall

Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.

type VariantsetsPatchCall 

type VariantsetsPatchCall struct {
	// contains filtered or unexported fields
}

func (*VariantsetsPatchCall) Do 

func (c *VariantsetsPatchCall) Do() (*VariantSet, error)

func (*VariantsetsPatchCall) Fields 

func (c *VariantsetsPatchCall) Fields(s ...googleapi.Field) *VariantsetsPatchCall

Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.

type VariantsetsSearchCall 

type VariantsetsSearchCall struct {
	// contains filtered or unexported fields
}

func (*VariantsetsSearchCall) Do 

func (c *VariantsetsSearchCall) Do() (*SearchVariantSetsResponse, error)

func (*VariantsetsSearchCall) Fields 

func (c *VariantsetsSearchCall) Fields(s ...googleapi.Field) *VariantsetsSearchCall

Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.

type VariantsetsService 

type VariantsetsService struct {
	// contains filtered or unexported fields
}

func NewVariantsetsService 

func NewVariantsetsService(s *Service) *VariantsetsService

func (*VariantsetsService) Delete 

func (r *VariantsetsService) Delete(variantSetId string) *VariantsetsDeleteCall

Delete: Deletes the contents of a variant set. The variant set object is not deleted.

func (*VariantsetsService) Export 

func (r *VariantsetsService) Export(variantSetId string, exportvariantsetrequest *ExportVariantSetRequest) *VariantsetsExportCall

Export: Exports variant set data to an external destination.

func (*VariantsetsService) Get 

func (r *VariantsetsService) Get(variantSetId string) *VariantsetsGetCall

Get: Gets a variant set by ID.

func (*VariantsetsService) ImportVariants 

func (r *VariantsetsService) ImportVariants(variantSetId string, importvariantsrequest *ImportVariantsRequest) *VariantsetsImportVariantsCall

ImportVariants: Creates variant data by asynchronously importing the provided information.

The variants for import will be merged with any existing data and each other according to the behavior of mergeVariants. In particular, this means for merged VCF variants that have conflicting INFO fields, some data will be arbitrarily discarded. As a special case, for single-sample VCF files, QUAL and FILTER fields will be moved to the call level; these are sometimes interpreted in a call-specific context. Imported VCF headers are appended to the metadata already in a variant set.

func (*VariantsetsService) MergeVariants 

func (r *VariantsetsService) MergeVariants(variantSetId string, mergevariantsrequest *MergeVariantsRequest) *VariantsetsMergeVariantsCall

MergeVariants: Merges the given variants with existing variants. Each variant will be merged with an existing variant that matches its reference sequence, start, end, reference bases, and alternative bases. If no such variant exists, a new one will be created.

When variants are merged, the call information from the new variant is added to the existing variant, and other fields (such as key/value pairs) are discarded.

func (*VariantsetsService) Patch 

func (r *VariantsetsService) Patch(variantSetId string, variantset *VariantSet) *VariantsetsPatchCall

Patch: Updates a variant set's metadata. All other modifications are silently ignored. This method supports patch semantics.

func (*VariantsetsService) Search 

func (r *VariantsetsService) Search(searchvariantsetsrequest *SearchVariantSetsRequest) *VariantsetsSearchCall

Search: Returns a list of all variant sets matching search criteria.

Implements GlobalAllianceApi.searchVariantSets.

func (*VariantsetsService) Update 

func (r *VariantsetsService) Update(variantSetId string, variantset *VariantSet) *VariantsetsUpdateCall

Update: Updates a variant set's metadata. All other modifications are silently ignored.

type VariantsetsUpdateCall 

type VariantsetsUpdateCall struct {
	// contains filtered or unexported fields
}

func (*VariantsetsUpdateCall) Do 

func (c *VariantsetsUpdateCall) Do() (*VariantSet, error)

func (*VariantsetsUpdateCall) Fields 

func (c *VariantsetsUpdateCall) Fields(s ...googleapi.Field) *VariantsetsUpdateCall

Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.

Source Files

View all Source files

Jump to

Keyboard shortcuts

? : This menu
/ : Search site
f or F : Jump to
y or Y : Canonical URL
go.dev uses cookies from Google to deliver and enhance the quality of its services and to analyze traffic. Learn more.