Network.Google.Genomics.Types

Service Configuration

genomicsService :: Service

Default request referring to version v1 of the Genomics API. This contains the host and root path used as a starting point for constructing service requests.

OAuth Scopes

genomicsScope :: OAuthScope

View and manage Genomics data

cloudPlatformScope :: OAuthScope

View and manage your data across Google Cloud Platform services

genomicsReadonlyScope :: OAuthScope

View Genomics data

devstorageReadWriteScope :: OAuthScope

Manage your data in Google Cloud Storage

bigqueryScope :: OAuthScope

View and manage your data in Google BigQuery

ReadInfo

data ReadInfo

A map of additional read alignment information. This must be of the form map (string key mapping to a list of string values).

See: readInfo smart constructor.

Instances

Eq ReadInfo

Data ReadInfo

Show ReadInfo

Generic ReadInfo

ToJSON ReadInfo

FromJSON ReadInfo

type Rep ReadInfo

readInfo

Arguments

:: HashMap Text [JSONValue]

riAddtional

-> ReadInfo

Creates a value of ReadInfo with the minimum fields required to make a request.

Use one of the following lenses to modify other fields as desired:

• riAddtional

riAddtional :: Lens' ReadInfo (HashMap Text [JSONValue])

Status

data Status

The `Status` type defines a logical error model that is suitable for different programming environments, including REST APIs and RPC APIs. It is used by gRPC. The error model is designed to be: - Simple to use and understand for most users - Flexible enough to meet unexpected needs # Overview The `Status` message contains three pieces of data: error code, error message, and error details. The error code should be an enum value of google.rpc.Code, but it may accept additional error codes if needed. The error message should be a developer-facing English message that helps developers *understand* and *resolve* the error. If a localized user-facing error message is needed, put the localized message in the error details or localize it in the client. The optional error details may contain arbitrary information about the error. There is a predefined set of error detail types in the package `google.rpc` which can be used for common error conditions. # Language mapping The `Status` message is the logical representation of the error model, but it is not necessarily the actual wire format. When the `Status` message is exposed in different client libraries and different wire protocols, it can be mapped differently. For example, it will likely be mapped to some exceptions in Java, but more likely mapped to some error codes in C. # Other uses The error model and the `Status` message can be used in a variety of environments, either with or without APIs, to provide a consistent developer experience across different environments. Example uses of this error model include: - Partial errors. If a service needs to return partial errors to the client, it may embed the `Status` in the normal response to indicate the partial errors. - Workflow errors. A typical workflow has multiple steps. Each step may have a `Status` message for error reporting purpose. - Batch operations. If a client uses batch request and batch response, the `Status` message should be used directly inside batch response, one for each error sub-response. - Asynchronous operations. If an API call embeds asynchronous operation results in its response, the status of those operations should be represented directly using the `Status` message. - Logging. If some API errors are stored in logs, the message `Status` could be used directly after any stripping needed for security/privacy reasons.

See: status smart constructor.

Instances

Eq Status

Data Status

Show Status

Generic Status

ToJSON Status

FromJSON Status

type Rep Status

status :: Status

Creates a value of Status with the minimum fields required to make a request.

Use one of the following lenses to modify other fields as desired:

• sDetails
• sCode
• sMessage

sDetails :: Lens' Status [StatusDetailsItem]

A list of messages that carry the error details. There will be a common set of message types for APIs to use.

sCode :: Lens' Status (Maybe Int32)

The status code, which should be an enum value of google.rpc.Code.

sMessage :: Lens' Status (Maybe Text)

A developer-facing error message, which should be in English. Any user-facing error message should be localized and sent in the google.rpc.Status.details field, or localized by the client.

OperationSchema

data OperationSchema

An OperationMetadata object. This will always be returned with the Operation.

See: operationSchema smart constructor.

Instances

Eq OperationSchema

Data OperationSchema

Show OperationSchema

Generic OperationSchema

ToJSON OperationSchema

FromJSON OperationSchema

type Rep OperationSchema

operationSchema

Arguments

:: HashMap Text JSONValue

osAddtional

-> OperationSchema

Creates a value of OperationSchema with the minimum fields required to make a request.

Use one of the following lenses to modify other fields as desired:

• osAddtional

osAddtional :: Lens' OperationSchema (HashMap Text JSONValue)

Properties of the object. Contains field 'ype with type URL.

Variant

data Variant

A variant represents a change in DNA sequence relative to a reference sequence. For example, a variant could represent a SNP or an insertion. Variants belong to a variant set. Each of the calls on a variant represent a determination of genotype with respect to that variant. For example, a call might assign probability of 0.32 to the occurrence of a SNP named rs1234 in a sample named NA12345. A call belongs to a call set, which contains related calls typically from one sample.

See: variant smart constructor.

Instances

Eq Variant

Data Variant

Show Variant

Generic Variant

ToJSON Variant

FromJSON Variant

type Rep Variant

variant :: Variant

Creates a value of Variant with the minimum fields required to make a request.

Use one of the following lenses to modify other fields as desired:

• vVariantSetId
• vCreated
• vStart
• vAlternateBases
• vReferenceName
• vNames
• vEnd
• vReferenceBases
• vId
• vQuality
• vFilter
• vInfo
• vCalls

vVariantSetId :: Lens' Variant (Maybe Text)

The ID of the variant set this variant belongs to.

vCreated :: Lens' Variant (Maybe Int64)

The date this variant was created, in milliseconds from the epoch.

vStart :: Lens' Variant (Maybe Int64)

The position at which this variant occurs (0-based). This corresponds to the first base of the string of reference bases.

vAlternateBases :: Lens' Variant [Text]

The bases that appear instead of the reference bases.

vReferenceName :: Lens' Variant (Maybe Text)

The reference on which this variant occurs. (such as `chr20` or `X`)

vNames :: Lens' Variant [Text]

Names for the variant, for example a RefSNP ID.

vEnd :: Lens' Variant (Maybe Int64)

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.

vReferenceBases :: Lens' Variant (Maybe Text)

The reference bases for this variant. They start at the given position.

vId :: Lens' Variant (Maybe Text)

The server-generated variant ID, unique across all variants.

vQuality :: Lens' Variant (Maybe Double)

A measure of how likely this variant is to be real. A higher value is better.

vFilter :: Lens' Variant [Text]

A list of filters (normally quality filters) this variant has failed. `PASS` indicates this variant has passed all filters.

vInfo :: Lens' Variant (Maybe VariantInfo)

A map of additional variant information. This must be of the form map (string key mapping to a list of string values).

vCalls :: Lens' Variant [VariantCall]

The variant calls for this particular variant. Each one represents the determination of genotype with respect to this variant.

ListBasesResponse

data ListBasesResponse

Instances

Eq ListBasesResponse

Data ListBasesResponse

Show ListBasesResponse

Generic ListBasesResponse

ToJSON ListBasesResponse

FromJSON ListBasesResponse

type Rep ListBasesResponse

listBasesResponse :: ListBasesResponse

Creates a value of ListBasesResponse with the minimum fields required to make a request.

Use one of the following lenses to modify other fields as desired:

• lbrNextPageToken
• lbrOffSet
• lbrSequence

lbrNextPageToken :: Lens' ListBasesResponse (Maybe Text)

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.

lbrOffSet :: Lens' ListBasesResponse (Maybe Int64)

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.

lbrSequence :: Lens' ListBasesResponse (Maybe Text)

A substring of the bases that make up this reference.

ListOperationsResponse

data ListOperationsResponse

The response message for Operations.ListOperations.

See: listOperationsResponse smart constructor.

Instances

Eq ListOperationsResponse

Data ListOperationsResponse

Show ListOperationsResponse

Generic ListOperationsResponse

ToJSON ListOperationsResponse

FromJSON ListOperationsResponse

type Rep ListOperationsResponse

listOperationsResponse :: ListOperationsResponse

Creates a value of ListOperationsResponse with the minimum fields required to make a request.

Use one of the following lenses to modify other fields as desired:

• lorNextPageToken
• lorOperations

lorNextPageToken :: Lens' ListOperationsResponse (Maybe Text)

The standard List next-page token.

lorOperations :: Lens' ListOperationsResponse [Operation]

A list of operations that matches the specified filter in the request.

GetIAMPolicyRequest

data GetIAMPolicyRequest

Request message for `GetIamPolicy` method.

See: getIAMPolicyRequest smart constructor.

Instances

Eq GetIAMPolicyRequest

Data GetIAMPolicyRequest

Show GetIAMPolicyRequest

Generic GetIAMPolicyRequest

ToJSON GetIAMPolicyRequest

FromJSON GetIAMPolicyRequest

type Rep GetIAMPolicyRequest

getIAMPolicyRequest :: GetIAMPolicyRequest

Creates a value of GetIAMPolicyRequest with the minimum fields required to make a request.

CancelOperationRequest

data CancelOperationRequest

The request message for Operations.CancelOperation.

See: cancelOperationRequest smart constructor.

Instances

Eq CancelOperationRequest

Data CancelOperationRequest

Show CancelOperationRequest

Generic CancelOperationRequest

ToJSON CancelOperationRequest

FromJSON CancelOperationRequest

type Rep CancelOperationRequest

cancelOperationRequest :: CancelOperationRequest

Creates a value of CancelOperationRequest with the minimum fields required to make a request.

DataSet

data DataSet

A Dataset is a collection of genomic data.

See: dataSet smart constructor.

Instances

Eq DataSet

Data DataSet

Show DataSet

Generic DataSet

ToJSON DataSet

FromJSON DataSet

type Rep DataSet

dataSet :: DataSet

Creates a value of DataSet with the minimum fields required to make a request.

Use one of the following lenses to modify other fields as desired:

• dsName
• dsId
• dsProjectId
• dsCreateTime

dsName :: Lens' DataSet (Maybe Text)

The dataset name.

dsId :: Lens' DataSet (Maybe Text)

The server-generated dataset ID, unique across all datasets.

dsProjectId :: Lens' DataSet (Maybe Text)

The Google Developers Console project ID that this dataset belongs to.

dsCreateTime :: Lens' DataSet (Maybe Text)

The time this dataset was created, in seconds from the epoch.

Read'

data Read'

A read alignment describes a linear alignment of a string of DNA to a reference sequence, in addition to metadata about the fragment (the molecule of DNA sequenced) and the read (the bases which were read by the sequencer). A read is equivalent to a line in a SAM file. A read belongs to exactly one read group and exactly one read group set. ### Generating a reference-aligned sequence string When interacting with mapped reads, it's often useful to produce a string representing the local alignment of the read to reference. The following pseudocode demonstrates one way of doing this: out = "" offset = 0 for c in read.alignment.cigar { switch c.operation { case "ALIGNMENT_MATCH", "SEQUENCE_MATCH", "SEQUENCE_MISMATCH": out += read.alignedSequence[offset:offset+c.operationLength] offset += c.operationLength break case "CLIP_SOFT", "INSERT": offset += c.operationLength break case "PAD": out += repeat("*", c.operationLength) break case "DELETE": out += repeat("-", c.operationLength) break case "SKIP": out += repeat(" ", c.operationLength) break case "CLIP_HARD": break } } return out ### Converting to SAM's CIGAR string The following pseudocode generates a SAM CIGAR string from the `cigar` field. Note that this is a lossy conversion (`cigar.referenceSequence` is lost). cigarMap = { "ALIGNMENT_MATCH": "M", "INSERT": "I", "DELETE": "D", "SKIP": "N", "CLIP_SOFT": "S", "CLIP_HARD": "H", "PAD": "P", "SEQUENCE_MATCH": "=", "SEQUENCE_MISMATCH": "X", } cigarStr = "" for c in read.alignment.cigar { cigarStr += c.operationLength + cigarMap[c.operation] } return cigarStr

See: read' smart constructor.

Instances

Eq Read'

Data Read'

Show Read'

Generic Read'

ToJSON Read'

FromJSON Read'

type Rep Read'

read' :: Read'

Creates a value of Read with the minimum fields required to make a request.

Use one of the following lenses to modify other fields as desired:

• rFragmentLength
• rDuplicateFragment
• rReadGroupSetId
• rNextMatePosition
• rFailedVendorQualityChecks
• rAlignment
• rFragmentName
• rNumberReads
• rId
• rSecondaryAlignment
• rReadGroupId
• rSupplementaryAlignment
• rAlignedSequence
• rProperPlacement
• rInfo
• rReadNumber
• rAlignedQuality

rFragmentLength :: Lens' Read' (Maybe Int32)

The observed length of the fragment, equivalent to TLEN in SAM.

rDuplicateFragment :: Lens' Read' (Maybe Bool)

The fragment is a PCR or optical duplicate (SAM flag 0x400)

rReadGroupSetId :: Lens' Read' (Maybe Text)

The ID of the read group set this read belongs to. (Every read must belong to exactly one read group set.)

rNextMatePosition :: Lens' Read' (Maybe Position)

The mapping of the primary alignment of the `(readNumber+1)%numberReads` read in the fragment. It replaces mate position and mate strand in SAM.

rFailedVendorQualityChecks :: Lens' Read' (Maybe Bool)

SAM flag 0x200

rAlignment :: Lens' Read' (Maybe LinearAlignment)

The linear alignment for this alignment record. This field will be null if the read is unmapped.

rFragmentName :: Lens' Read' (Maybe Text)

The fragment name. Equivalent to QNAME (query template name) in SAM.

rNumberReads :: Lens' Read' (Maybe Int32)

The number of reads in the fragment (extension to SAM flag 0x1).

rId :: Lens' Read' (Maybe Text)

The server-generated read ID, unique across all reads. This is different from the `fragmentName`.

rSecondaryAlignment :: Lens' Read' (Maybe Bool)

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.

rReadGroupId :: Lens' Read' (Maybe Text)

The ID of the read group this read belongs to. (Every read must belong to exactly one read group.)

rSupplementaryAlignment :: Lens' Read' (Maybe Bool)

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.

rAlignedSequence :: Lens' Read' (Maybe Text)

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.

rProperPlacement :: Lens' Read' (Maybe Bool)

The orientation and the distance between reads from the fragment are consistent with the sequencing protocol (SAM flag 0x2)

rInfo :: Lens' Read' (Maybe ReadInfo)

A map of additional read alignment information. This must be of the form map (string key mapping to a list of string values).

rReadNumber :: Lens' Read' (Maybe Int32)

The read number in sequencing. 0-based and less than numberReads. This field replaces SAM flag 0x40 and 0x80.

rAlignedQuality :: Lens' Read' [Int32]

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.

VariantCall

data VariantCall

A call represents the determination of genotype with respect to a particular variant. It may include associated information such as quality and phasing. For example, a call might assign a probability of 0.32 to the occurrence of a SNP named rs1234 in a call set with the name NA12345.

See: variantCall smart constructor.

Instances

Eq VariantCall

Data VariantCall

Show VariantCall

Generic VariantCall

ToJSON VariantCall

FromJSON VariantCall

type Rep VariantCall

variantCall :: VariantCall

Creates a value of VariantCall with the minimum fields required to make a request.

Use one of the following lenses to modify other fields as desired:

• vcGenotypeLikelihood
• vcCallSetName
• vcPhaseset
• vcCallSetId
• vcGenotype
• vcInfo

vcGenotypeLikelihood :: Lens' VariantCall [Double]

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`.

vcCallSetName :: Lens' VariantCall (Maybe Text)

The name of the call set this variant call belongs to.

vcPhaseset :: Lens' VariantCall (Maybe Text)

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 `*`.

vcCallSetId :: Lens' VariantCall (Maybe Text)

The ID of the call set this variant call belongs to.

vcGenotype :: Lens' VariantCall [Int32]

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.

vcInfo :: Lens' VariantCall (Maybe VariantCallInfo)

A map of additional variant call information. This must be of the form map (string key mapping to a list of string values).

ReadGroup

data ReadGroup

A read group is all the data that's processed the same way by the sequencer.

See: readGroup smart constructor.

Instances

Eq ReadGroup

Data ReadGroup

Show ReadGroup

Generic ReadGroup

ToJSON ReadGroup

FromJSON ReadGroup

type Rep ReadGroup

readGroup :: ReadGroup

Creates a value of ReadGroup with the minimum fields required to make a request.

Use one of the following lenses to modify other fields as desired:

• reaReferenceSetId
• reaPrograms
• reaExperiment
• reaName
• reaDataSetId
• reaId
• reaSampleId
• reaPredictedInsertSize
• reaDescription
• reaInfo

reaReferenceSetId :: Lens' ReadGroup (Maybe Text)

The reference set the reads in this read group are aligned to. Required if there are any read alignments.

reaPrograms :: Lens' ReadGroup [Program]

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.

reaExperiment :: Lens' ReadGroup (Maybe Experiment)

The experiment used to generate this read group.

reaName :: Lens' ReadGroup (Maybe Text)

The read group name. This corresponds to the 'RG ID field in the SAM spec.

reaDataSetId :: Lens' ReadGroup (Maybe Text)

The ID of the dataset this read group belongs to.

reaId :: Lens' ReadGroup (Maybe Text)

The server-generated read group ID, unique for all read groups. Note: This is different than the `'RG ID` field in the SAM spec. For that value, see the `name` field.

reaSampleId :: Lens' ReadGroup (Maybe Text)

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.

reaPredictedInsertSize :: Lens' ReadGroup (Maybe Int32)

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.

reaDescription :: Lens' ReadGroup (Maybe Text)

A free-form text description of this read group.

reaInfo :: Lens' ReadGroup (Maybe ReadGroupInfo)

A map of additional read group information. This must be of the form map (string key mapping to a list of string values).

Operation

data Operation

This resource represents a long-running operation that is the result of a network API call.

See: operation smart constructor.

Instances

Eq Operation

Data Operation

Show Operation

Generic Operation

ToJSON Operation

FromJSON Operation

type Rep Operation

operation :: Operation

Creates a value of Operation with the minimum fields required to make a request.

Use one of the following lenses to modify other fields as desired:

• oDone
• oError
• oResponse
• oName
• oMetadata

oDone :: Lens' Operation (Maybe Bool)

If the value is `false`, it means the operation is still in progress. If true, the operation is completed, and either `error` or `response` is available.

oError :: Lens' Operation (Maybe Status)

The error result of the operation in case of failure.

oResponse :: Lens' Operation (Maybe OperationResponse)

If importing ReadGroupSets, an ImportReadGroupSetsResponse is returned. If importing Variants, an ImportVariantsResponse is returned. For exports, an empty response is returned.

oName :: Lens' Operation (Maybe Text)

The server-assigned name, which is only unique within the same service that originally returns it. For example: `operations/CJHU7Oi_ChDrveSpBRjfuL-qzoWAgEw`

oMetadata :: Lens' Operation (Maybe OperationSchema)

An OperationMetadata object. This will always be returned with the Operation.

SearchReferenceSetsRequest

data SearchReferenceSetsRequest

Instances

Eq SearchReferenceSetsRequest

Data SearchReferenceSetsRequest

Show SearchReferenceSetsRequest

Generic SearchReferenceSetsRequest

ToJSON SearchReferenceSetsRequest

FromJSON SearchReferenceSetsRequest

type Rep SearchReferenceSetsRequest

searchReferenceSetsRequest :: SearchReferenceSetsRequest

Creates a value of SearchReferenceSetsRequest with the minimum fields required to make a request.

Use one of the following lenses to modify other fields as desired:

• srsrMD5checksums
• srsrAccessions
• srsrPageToken
• srsrAssemblyId
• srsrPageSize

srsrMD5checksums :: Lens' SearchReferenceSetsRequest [Text]

If present, return references for which the `md5checksum` matches. See `ReferenceSet.md5checksum` for details.

srsrAccessions :: Lens' SearchReferenceSetsRequest [Text]

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.

srsrPageToken :: Lens' SearchReferenceSetsRequest (Maybe Text)

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.

srsrAssemblyId :: Lens' SearchReferenceSetsRequest (Maybe Text)

If present, return reference sets for which a substring of their `assemblyId` matches this string (case insensitive).

srsrPageSize :: Lens' SearchReferenceSetsRequest (Maybe Int32)

Specifies the maximum number of results to return in a single page.

Empty

data Empty

A generic empty message that you can re-use to avoid defining duplicated empty messages in your APIs. A typical example is to use it as the request or the response type of an API method. For instance: service Foo { rpc Bar(google.protobuf.Empty) returns (google.protobuf.Empty); } The JSON representation for `Empty` is empty JSON object `{}`.

See: empty smart constructor.

Instances

Eq Empty

Data Empty

Show Empty

Generic Empty

ToJSON Empty

FromJSON Empty

type Rep Empty

empty :: Empty

Creates a value of Empty with the minimum fields required to make a request.

SearchReferencesResponse

data SearchReferencesResponse

Instances

Eq SearchReferencesResponse

Data SearchReferencesResponse

Show SearchReferencesResponse

Generic SearchReferencesResponse

ToJSON SearchReferencesResponse

FromJSON SearchReferencesResponse

type Rep SearchReferencesResponse

searchReferencesResponse :: SearchReferencesResponse

Creates a value of SearchReferencesResponse with the minimum fields required to make a request.

Use one of the following lenses to modify other fields as desired:

• srrNextPageToken
• srrReferences

srrNextPageToken :: Lens' SearchReferencesResponse (Maybe Text)

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.

srrReferences :: Lens' SearchReferencesResponse [Reference]

The matching references.

VariantSetMetadata

data VariantSetMetadata

Metadata describes a single piece of variant call metadata. These data include a top level key and either a single value string (value) or a list of key-value pairs (info.) Value and info are mutually exclusive.

See: variantSetMetadata smart constructor.

Instances

Eq VariantSetMetadata

Data VariantSetMetadata

Show VariantSetMetadata

Generic VariantSetMetadata

ToJSON VariantSetMetadata

FromJSON VariantSetMetadata

type Rep VariantSetMetadata

variantSetMetadata :: VariantSetMetadata

Creates a value of VariantSetMetadata with the minimum fields required to make a request.

Use one of the following lenses to modify other fields as desired:

• vsmValue
• vsmKey
• vsmId
• vsmType
• vsmNumber
• vsmDescription
• vsmInfo

vsmValue :: Lens' VariantSetMetadata (Maybe Text)

The value field for simple metadata

vsmKey :: Lens' VariantSetMetadata (Maybe Text)

The top-level key.

vsmId :: Lens' VariantSetMetadata (Maybe Text)

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.

vsmType :: Lens' VariantSetMetadata (Maybe Text)

The type of data. Possible types include: Integer, Float, Flag, Character, and String.

vsmNumber :: Lens' VariantSetMetadata (Maybe Text)

The number of values that can be included in a field described by this metadata.

vsmDescription :: Lens' VariantSetMetadata (Maybe Text)

A textual description of this metadata.

vsmInfo :: Lens' VariantSetMetadata (Maybe VariantSetMetadataInfo)

Remaining structured metadata key-value pairs. This must be of the form map (string key mapping to a list of string values).

CallSet

data CallSet

A call set is a collection of variant calls, typically for one sample. It belongs to a variant set.

See: callSet smart constructor.

Instances

Eq CallSet

Data CallSet

Show CallSet

Generic CallSet

ToJSON CallSet

FromJSON CallSet

type Rep CallSet

callSet :: CallSet

Creates a value of CallSet with the minimum fields required to make a request.

Use one of the following lenses to modify other fields as desired:

• csCreated
• csName
• csId
• csSampleId
• csVariantSetIds
• csInfo

csCreated :: Lens' CallSet (Maybe Int64)

The date this call set was created in milliseconds from the epoch.

csName :: Lens' CallSet (Maybe Text)

The call set name.

csId :: Lens' CallSet (Maybe Text)

The server-generated call set ID, unique across all call sets.

csSampleId :: Lens' CallSet (Maybe Text)

The sample ID this call set corresponds to.

csVariantSetIds :: Lens' CallSet [Text]

The IDs of the variant sets this call set belongs to. This field must have exactly length one, as a call set belongs to a single variant set. This field is repeated for compatibility with the GA4GH 0.5.1 API.

csInfo :: Lens' CallSet (Maybe CallSetInfo)

A map of additional call set information. This must be of the form map (string key mapping to a list of string values).

CoverageBucket

data CoverageBucket

A bucket over which read coverage has been precomputed. A bucket corresponds to a specific range of the reference sequence.

See: coverageBucket smart constructor.

Instances

Eq CoverageBucket

Data CoverageBucket

Show CoverageBucket

Generic CoverageBucket

ToJSON CoverageBucket

FromJSON CoverageBucket

type Rep CoverageBucket

coverageBucket :: CoverageBucket

Creates a value of CoverageBucket with the minimum fields required to make a request.

Use one of the following lenses to modify other fields as desired:

• cbRange
• cbMeanCoverage

cbRange :: Lens' CoverageBucket (Maybe Range)

The genomic coordinate range spanned by this bucket.

cbMeanCoverage :: Lens' CoverageBucket (Maybe Double)

The average number of reads which are aligned to each individual reference base in this bucket.

SearchReadGroupSetsRequest

data SearchReadGroupSetsRequest

The read group set search request.

See: searchReadGroupSetsRequest smart constructor.

Instances

Eq SearchReadGroupSetsRequest

Data SearchReadGroupSetsRequest

Show SearchReadGroupSetsRequest

Generic SearchReadGroupSetsRequest

ToJSON SearchReadGroupSetsRequest

FromJSON SearchReadGroupSetsRequest

type Rep SearchReadGroupSetsRequest

searchReadGroupSetsRequest :: SearchReadGroupSetsRequest

Creates a value of SearchReadGroupSetsRequest with the minimum fields required to make a request.

Use one of the following lenses to modify other fields as desired:

• srgsrDataSetIds
• srgsrName
• srgsrPageToken
• srgsrPageSize

srgsrDataSetIds :: Lens' SearchReadGroupSetsRequest [Text]

Restricts this query to read group sets within the given datasets. At least one ID must be provided.

srgsrName :: Lens' SearchReadGroupSetsRequest (Maybe Text)

Only return read group sets for which a substring of the name matches this string.

srgsrPageToken :: Lens' SearchReadGroupSetsRequest (Maybe Text)

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.

srgsrPageSize :: Lens' SearchReadGroupSetsRequest (Maybe Int32)

Specifies number of results to return in a single page. If unspecified, it will default to 256. The maximum value is 1024.

Reference

data Reference

A reference is a canonical assembled DNA sequence, intended to act as a reference coordinate space for other genomic annotations. A single reference might represent the human chromosome 1 or mitochandrial DNA, for instance. A reference belongs to one or more reference sets.

See: reference smart constructor.

Instances

Eq Reference

Data Reference

Show Reference

Generic Reference

ToJSON Reference

FromJSON Reference

type Rep Reference

reference :: Reference

Creates a value of Reference with the minimum fields required to make a request.

Use one of the following lenses to modify other fields as desired:

• refLength
• refSourceAccessions
• refMD5checksum
• refName
• refNcbiTaxonId
• refId
• refSourceURI

refLength :: Lens' Reference (Maybe Int64)

The length of this reference's sequence.

refSourceAccessions :: Lens' Reference [Text]

All known corresponding accession IDs in INSDC (GenBank/ENA/DDBJ) ideally with a version number, for example `GCF_000001405.26`.

refMD5checksum :: Lens' Reference (Maybe Text)

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.

refName :: Lens' Reference (Maybe Text)

The name of this reference, for example `22`.

refNcbiTaxonId :: Lens' Reference (Maybe Int32)

ID from http://www.ncbi.nlm.nih.gov/taxonomy (e.g. 9606->human) if not specified by the containing reference set.

refId :: Lens' Reference (Maybe Text)

The server-generated reference ID, unique across all references.

refSourceURI :: Lens' Reference (Maybe Text)

The URI from which the sequence was obtained. Specifies a FASTA format file/string with one name, sequence pair.

VariantCallInfo

data VariantCallInfo

A map of additional variant call information. This must be of the form map (string key mapping to a list of string values).

See: variantCallInfo smart constructor.

Instances

Eq VariantCallInfo

Data VariantCallInfo

Show VariantCallInfo

Generic VariantCallInfo

ToJSON VariantCallInfo

FromJSON VariantCallInfo

type Rep VariantCallInfo

variantCallInfo

Arguments

:: HashMap Text [JSONValue]

vciAddtional

-> VariantCallInfo

Creates a value of VariantCallInfo with the minimum fields required to make a request.

Use one of the following lenses to modify other fields as desired:

• vciAddtional

vciAddtional :: Lens' VariantCallInfo (HashMap Text [JSONValue])

ReadGroupInfo

data ReadGroupInfo

A map of additional read group information. This must be of the form map (string key mapping to a list of string values).

See: readGroupInfo smart constructor.

Instances

Eq ReadGroupInfo

Data ReadGroupInfo

Show ReadGroupInfo

Generic ReadGroupInfo

ToJSON ReadGroupInfo

FromJSON ReadGroupInfo

type Rep ReadGroupInfo

readGroupInfo

Arguments

:: HashMap Text [JSONValue]

rgiAddtional

-> ReadGroupInfo

Creates a value of ReadGroupInfo with the minimum fields required to make a request.

Use one of the following lenses to modify other fields as desired:

• rgiAddtional

rgiAddtional :: Lens' ReadGroupInfo (HashMap Text [JSONValue])

StatusDetailsItem

data StatusDetailsItem

Instances

Eq StatusDetailsItem

Data StatusDetailsItem

Show StatusDetailsItem

Generic StatusDetailsItem

ToJSON StatusDetailsItem

FromJSON StatusDetailsItem

type Rep StatusDetailsItem

statusDetailsItem

Arguments

:: HashMap Text JSONValue

sdiAddtional

-> StatusDetailsItem

Creates a value of StatusDetailsItem with the minimum fields required to make a request.

Use one of the following lenses to modify other fields as desired:

• sdiAddtional

sdiAddtional :: Lens' StatusDetailsItem (HashMap Text JSONValue)

Properties of the object. Contains field 'ype with type URL.

SearchCallSetsResponse

data SearchCallSetsResponse

The call set search response.

See: searchCallSetsResponse smart constructor.

Instances

Eq SearchCallSetsResponse

Data SearchCallSetsResponse

Show SearchCallSetsResponse

Generic SearchCallSetsResponse

ToJSON SearchCallSetsResponse

FromJSON SearchCallSetsResponse

type Rep SearchCallSetsResponse

searchCallSetsResponse :: SearchCallSetsResponse

Creates a value of SearchCallSetsResponse with the minimum fields required to make a request.

Use one of the following lenses to modify other fields as desired:

• scsrNextPageToken
• scsrCallSets

scsrNextPageToken :: Lens' SearchCallSetsResponse (Maybe Text)

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.

scsrCallSets :: Lens' SearchCallSetsResponse [CallSet]

The list of matching call sets.

SetIAMPolicyRequest

data SetIAMPolicyRequest

Request message for `SetIamPolicy` method.

See: setIAMPolicyRequest smart constructor.

Instances

Eq SetIAMPolicyRequest

Data SetIAMPolicyRequest

Show SetIAMPolicyRequest

Generic SetIAMPolicyRequest

ToJSON SetIAMPolicyRequest

FromJSON SetIAMPolicyRequest

type Rep SetIAMPolicyRequest

setIAMPolicyRequest :: SetIAMPolicyRequest

Creates a value of SetIAMPolicyRequest with the minimum fields required to make a request.

Use one of the following lenses to modify other fields as desired:

• siprPolicy

siprPolicy :: Lens' SetIAMPolicyRequest (Maybe Policy)

REQUIRED: The complete policy to be applied to the `resource`. The size of the policy is limited to a few 10s of KB. An empty policy is a valid policy but certain Cloud Platform services (such as Projects) might reject them.

SearchReadsRequest

data SearchReadsRequest

The read search request.

See: searchReadsRequest smart constructor.

Instances

Eq SearchReadsRequest

Data SearchReadsRequest

Show SearchReadsRequest

Generic SearchReadsRequest

ToJSON SearchReadsRequest

FromJSON SearchReadsRequest

type Rep SearchReadsRequest

searchReadsRequest :: SearchReadsRequest

Creates a value of SearchReadsRequest with the minimum fields required to make a request.

Use one of the following lenses to modify other fields as desired:

• srrStart
• srrReadGroupIds
• srrReferenceName
• srrEnd
• srrPageToken
• srrPageSize
• srrReadGroupSetIds

srrStart :: Lens' SearchReadsRequest (Maybe Int64)

The start position of the range on the reference, 0-based inclusive. If specified, `referenceName` must also be specified.

srrReadGroupIds :: Lens' SearchReadsRequest [Text]

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`.

srrReferenceName :: Lens' SearchReadsRequest (Maybe Text)

The reference sequence name, for example `chr1`, `1`, or `chrX`. If set to *, only unmapped reads are returned.

srrEnd :: Lens' SearchReadsRequest (Maybe Int64)

The end position of the range on the reference, 0-based exclusive. If specified, `referenceName` must also be specified.

srrPageToken :: Lens' SearchReadsRequest (Maybe Text)

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.

srrPageSize :: Lens' SearchReadsRequest (Maybe Int32)

Specifies number of results to return in a single page. If unspecified, it will default to 256. The maximum value is 2048.

srrReadGroupSetIds :: Lens' SearchReadsRequest [Text]

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`.

OperationMetadataRequest

data OperationMetadataRequest

The original request that started the operation. Note that this will be in current version of the API. If the operation was started with v1beta2 API and a GetOperation is performed on v1 API, a v1 request will be returned.

See: operationMetadataRequest smart constructor.

Instances

Eq OperationMetadataRequest

Data OperationMetadataRequest

Show OperationMetadataRequest

Generic OperationMetadataRequest

ToJSON OperationMetadataRequest

FromJSON OperationMetadataRequest

type Rep OperationMetadataRequest

operationMetadataRequest

Arguments

:: HashMap Text JSONValue

omrAddtional

-> OperationMetadataRequest

Creates a value of OperationMetadataRequest with the minimum fields required to make a request.

Use one of the following lenses to modify other fields as desired:

• omrAddtional

omrAddtional :: Lens' OperationMetadataRequest (HashMap Text JSONValue)

Properties of the object. Contains field 'ype with type URL.

VariantInfo

data VariantInfo

A map of additional variant information. This must be of the form map (string key mapping to a list of string values).

See: variantInfo smart constructor.

Instances

Eq VariantInfo

Data VariantInfo

Show VariantInfo

Generic VariantInfo

ToJSON VariantInfo

FromJSON VariantInfo

type Rep VariantInfo

variantInfo

Arguments

:: HashMap Text [JSONValue]

viAddtional

-> VariantInfo

Creates a value of VariantInfo with the minimum fields required to make a request.

Use one of the following lenses to modify other fields as desired:

• viAddtional

viAddtional :: Lens' VariantInfo (HashMap Text [JSONValue])

Experiment

data Experiment

Instances

Eq Experiment

Data Experiment

Show Experiment

Generic Experiment

ToJSON Experiment

FromJSON Experiment

type Rep Experiment

experiment :: Experiment

Creates a value of Experiment with the minimum fields required to make a request.

Use one of the following lenses to modify other fields as desired:

• eInstrumentModel
• ePlatformUnit
• eSequencingCenter
• eLibraryId

eInstrumentModel :: Lens' Experiment (Maybe Text)

The instrument model used as part of this experiment. This maps to sequencing technology in BAM.

ePlatformUnit :: Lens' Experiment (Maybe Text)

The platform unit used as part of this experiment e.g. flowcell-barcode.lane for Illumina or slide for SOLiD. Corresponds to the 'RG PU field in the SAM spec.

eSequencingCenter :: Lens' Experiment (Maybe Text)

The sequencing center used as part of this experiment.

eLibraryId :: Lens' Experiment (Maybe Text)

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.

SearchVariantSetsRequest

data SearchVariantSetsRequest

The search variant sets request.

See: searchVariantSetsRequest smart constructor.

Instances

Eq SearchVariantSetsRequest

Data SearchVariantSetsRequest

Show SearchVariantSetsRequest

Generic SearchVariantSetsRequest

ToJSON SearchVariantSetsRequest

FromJSON SearchVariantSetsRequest

type Rep SearchVariantSetsRequest

searchVariantSetsRequest :: SearchVariantSetsRequest

Creates a value of SearchVariantSetsRequest with the minimum fields required to make a request.

Use one of the following lenses to modify other fields as desired:

• svsrDataSetIds
• svsrPageToken
• svsrPageSize

svsrDataSetIds :: Lens' SearchVariantSetsRequest [Text]

Exactly one dataset ID must be provided here. Only variant sets which belong to this dataset will be returned.

svsrPageToken :: Lens' SearchVariantSetsRequest (Maybe Text)

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.

svsrPageSize :: Lens' SearchVariantSetsRequest (Maybe Int32)

The maximum number of variant sets to return in a request.

SearchVariantsResponse

data SearchVariantsResponse

The variant search response.

See: searchVariantsResponse smart constructor.

Instances

Eq SearchVariantsResponse

Data SearchVariantsResponse

Show SearchVariantsResponse

Generic SearchVariantsResponse

ToJSON SearchVariantsResponse

FromJSON SearchVariantsResponse

type Rep SearchVariantsResponse

searchVariantsResponse :: SearchVariantsResponse

Creates a value of SearchVariantsResponse with the minimum fields required to make a request.

Use one of the following lenses to modify other fields as desired:

• svrVariants
• svrNextPageToken

svrVariants :: Lens' SearchVariantsResponse [Variant]

The list of matching Variants.

svrNextPageToken :: Lens' SearchVariantsResponse (Maybe Text)

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.

SearchCallSetsRequest

data SearchCallSetsRequest

The call set search request.

See: searchCallSetsRequest smart constructor.

Instances

Eq SearchCallSetsRequest

Data SearchCallSetsRequest

Show SearchCallSetsRequest

Generic SearchCallSetsRequest

ToJSON SearchCallSetsRequest

FromJSON SearchCallSetsRequest

type Rep SearchCallSetsRequest

searchCallSetsRequest :: SearchCallSetsRequest

Creates a value of SearchCallSetsRequest with the minimum fields required to make a request.

Use one of the following lenses to modify other fields as desired:

• scsrName
• scsrPageToken
• scsrVariantSetIds
• scsrPageSize

scsrName :: Lens' SearchCallSetsRequest (Maybe Text)

Only return call sets for which a substring of the name matches this string.

scsrPageToken :: Lens' SearchCallSetsRequest (Maybe Text)

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.

scsrVariantSetIds :: Lens' SearchCallSetsRequest [Text]

Restrict the query to call sets within the given variant sets. At least one ID must be provided.

scsrPageSize :: Lens' SearchCallSetsRequest (Maybe Int32)

The maximum number of call sets to return. If unspecified, defaults to 1000.

SearchReadsResponse

data SearchReadsResponse

The read search response.

See: searchReadsResponse smart constructor.

Instances

Eq SearchReadsResponse

Data SearchReadsResponse

Show SearchReadsResponse

Generic SearchReadsResponse

ToJSON SearchReadsResponse

FromJSON SearchReadsResponse

type Rep SearchReadsResponse

searchReadsResponse :: SearchReadsResponse

Creates a value of SearchReadsResponse with the minimum fields required to make a request.

Use one of the following lenses to modify other fields as desired:

• sNextPageToken
• sAlignments

sNextPageToken :: Lens' SearchReadsResponse (Maybe Text)

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.

sAlignments :: Lens' SearchReadsResponse [Read']

The list of matching alignments sorted by mapped genomic coordinate, if any, ascending in position within the same reference. Unmapped reads, which have no position, are returned contiguously and are sorted in ascending lexicographic order by fragment name.

Program

data Program

Instances

Eq Program

Data Program

Show Program

Generic Program

ToJSON Program

FromJSON Program

type Rep Program

program :: Program

Creates a value of Program with the minimum fields required to make a request.

Use one of the following lenses to modify other fields as desired:

• pPrevProgramId
• pName
• pVersion
• pId
• pCommandLine

pPrevProgramId :: Lens' Program (Maybe Text)

The ID of the program run before this one.

pName :: Lens' Program (Maybe Text)

The name of the program.

pVersion :: Lens' Program (Maybe Text)

The version of the program run.

pId :: Lens' Program (Maybe Text)

The user specified locally unique ID of the program. Used along with `prevProgramId` to define an ordering between programs.

pCommandLine :: Lens' Program (Maybe Text)

The command line used to run this program.

SearchReferencesRequest

data SearchReferencesRequest

Instances

Eq SearchReferencesRequest

Data SearchReferencesRequest

Show SearchReferencesRequest

Generic SearchReferencesRequest

ToJSON SearchReferencesRequest

FromJSON SearchReferencesRequest

type Rep SearchReferencesRequest

searchReferencesRequest :: SearchReferencesRequest

Creates a value of SearchReferencesRequest with the minimum fields required to make a request.

Use one of the following lenses to modify other fields as desired:

• sReferenceSetId
• sMD5checksums
• sAccessions
• sPageToken
• sPageSize

sReferenceSetId :: Lens' SearchReferencesRequest (Maybe Text)

If present, return only references which belong to this reference set.

sMD5checksums :: Lens' SearchReferencesRequest [Text]

If present, return references for which the `md5checksum` matches. See `Reference.md5checksum` for construction details.

sAccessions :: Lens' SearchReferencesRequest [Text]

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.

sPageToken :: Lens' SearchReferencesRequest (Maybe Text)

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.

sPageSize :: Lens' SearchReferencesRequest (Maybe Int32)

Specifies the maximum number of results to return in a single page.

SearchReferenceSetsResponse

data SearchReferenceSetsResponse

Instances

Eq SearchReferenceSetsResponse

Data SearchReferenceSetsResponse

Show SearchReferenceSetsResponse

Generic SearchReferenceSetsResponse

ToJSON SearchReferenceSetsResponse

FromJSON SearchReferenceSetsResponse

type Rep SearchReferenceSetsResponse

searchReferenceSetsResponse :: SearchReferenceSetsResponse

Creates a value of SearchReferenceSetsResponse with the minimum fields required to make a request.

Use one of the following lenses to modify other fields as desired:

• srsrNextPageToken
• srsrReferenceSets

srsrNextPageToken :: Lens' SearchReferenceSetsResponse (Maybe Text)

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.

srsrReferenceSets :: Lens' SearchReferenceSetsResponse [ReferenceSet]

The matching references sets.

Range

data Range

A 0-based half-open genomic coordinate range for search requests.

See: range smart constructor.

Instances

Eq Range

Data Range

Show Range

Generic Range

ToJSON Range

FromJSON Range

type Rep Range

range :: Range

Creates a value of Range with the minimum fields required to make a request.

Use one of the following lenses to modify other fields as desired:

• rStart
• rReferenceName
• rEnd

rStart :: Lens' Range (Maybe Int64)

The start position of the range on the reference, 0-based inclusive.

rReferenceName :: Lens' Range (Maybe Text)

The reference sequence name, for example `chr1`, `1`, or `chrX`.

rEnd :: Lens' Range (Maybe Int64)

The end position of the range on the reference, 0-based exclusive.

ReadGroupSet

data ReadGroupSet

A read group set is a logical collection of read groups, which are collections of reads produced by a sequencer. A read group set typically models reads corresponding to one sample, sequenced one way, and aligned one way. * A read group set belongs to one dataset. * A read group belongs to one read group set. * A read belongs to one read group.

See: readGroupSet smart constructor.

Instances

Eq ReadGroupSet

Data ReadGroupSet

Show ReadGroupSet

Generic ReadGroupSet

ToJSON ReadGroupSet

FromJSON ReadGroupSet

type Rep ReadGroupSet

readGroupSet :: ReadGroupSet

Creates a value of ReadGroupSet with the minimum fields required to make a request.

Use one of the following lenses to modify other fields as desired:

• rgsReferenceSetId
• rgsName
• rgsDataSetId
• rgsId
• rgsInfo
• rgsReadGroups
• rgsFilename

rgsReferenceSetId :: Lens' ReadGroupSet (Maybe Text)

The reference set the reads in this read group set are aligned to.

rgsName :: Lens' ReadGroupSet (Maybe Text)

The read group set name. By default this will be initialized to the sample name of the sequenced data contained in this set.

rgsDataSetId :: Lens' ReadGroupSet (Maybe Text)

The dataset ID.

rgsId :: Lens' ReadGroupSet (Maybe Text)

The server-generated read group set ID, unique for all read group sets.

rgsInfo :: Lens' ReadGroupSet (Maybe ReadGroupSetInfo)

A map of additional read group set information.

rgsReadGroups :: Lens' ReadGroupSet [ReadGroup]

The read groups in this set. There are typically 1-10 read groups in a read group set.

rgsFilename :: Lens' ReadGroupSet (Maybe Text)

The filename of the original source file for this read group set, if any.

ExportReadGroupSetRequest

data ExportReadGroupSetRequest

The read group set export request.

See: exportReadGroupSetRequest smart constructor.

Instances

Eq ExportReadGroupSetRequest

Data ExportReadGroupSetRequest

Show ExportReadGroupSetRequest

Generic ExportReadGroupSetRequest

ToJSON ExportReadGroupSetRequest

FromJSON ExportReadGroupSetRequest

type Rep ExportReadGroupSetRequest

exportReadGroupSetRequest :: ExportReadGroupSetRequest

Creates a value of ExportReadGroupSetRequest with the minimum fields required to make a request.

Use one of the following lenses to modify other fields as desired:

• ergsrReferenceNames
• ergsrExportURI
• ergsrProjectId

ergsrReferenceNames :: Lens' ExportReadGroupSetRequest [Text]

The reference names to export. If this is not specified, all reference sequences, including unmapped reads, are exported. Use `*` to export only unmapped reads.

ergsrExportURI :: Lens' ExportReadGroupSetRequest (Maybe Text)

Required. A Google Cloud Storage URI for the exported BAM file. The currently authenticated user must have write access to the new file. An error will be returned if the URI already contains data.

ergsrProjectId :: Lens' ExportReadGroupSetRequest (Maybe Text)

Required. The Google Developers Console project ID that owns this export.

ImportVariantsResponse

data ImportVariantsResponse

The variant data import response.

See: importVariantsResponse smart constructor.

Instances

Eq ImportVariantsResponse

Data ImportVariantsResponse

Show ImportVariantsResponse

Generic ImportVariantsResponse

ToJSON ImportVariantsResponse

FromJSON ImportVariantsResponse

type Rep ImportVariantsResponse

importVariantsResponse :: ImportVariantsResponse

Creates a value of ImportVariantsResponse with the minimum fields required to make a request.

Use one of the following lenses to modify other fields as desired:

• ivrCallSetIds

ivrCallSetIds :: Lens' ImportVariantsResponse [Text]

IDs of the call sets that were created.

ListCoverageBucketsResponse

data ListCoverageBucketsResponse

Instances

Eq ListCoverageBucketsResponse

Data ListCoverageBucketsResponse

Show ListCoverageBucketsResponse

Generic ListCoverageBucketsResponse

ToJSON ListCoverageBucketsResponse

FromJSON ListCoverageBucketsResponse

type Rep ListCoverageBucketsResponse

listCoverageBucketsResponse :: ListCoverageBucketsResponse

Creates a value of ListCoverageBucketsResponse with the minimum fields required to make a request.

Use one of the following lenses to modify other fields as desired:

• lcbrNextPageToken
• lcbrBucketWidth
• lcbrCoverageBuckets

lcbrNextPageToken :: Lens' ListCoverageBucketsResponse (Maybe Text)

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.

lcbrBucketWidth :: Lens' ListCoverageBucketsResponse (Maybe Int64)

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`).

lcbrCoverageBuckets :: Lens' ListCoverageBucketsResponse [CoverageBucket]

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.

TestIAMPermissionsRequest

data TestIAMPermissionsRequest

Request message for `TestIamPermissions` method.

See: testIAMPermissionsRequest smart constructor.

Instances

Eq TestIAMPermissionsRequest

Data TestIAMPermissionsRequest

Show TestIAMPermissionsRequest

Generic TestIAMPermissionsRequest

ToJSON TestIAMPermissionsRequest

FromJSON TestIAMPermissionsRequest

type Rep TestIAMPermissionsRequest

testIAMPermissionsRequest :: TestIAMPermissionsRequest

Creates a value of TestIAMPermissionsRequest with the minimum fields required to make a request.

Use one of the following lenses to modify other fields as desired:

• tiprPermissions

tiprPermissions :: Lens' TestIAMPermissionsRequest [Text]

REQUIRED: The set of permissions to check for the 'resource'. Permissions with wildcards (such as '*' or 'storage.*') are not allowed. Allowed permissions are: * `genomics.datasets.create` * `genomics.datasets.delete` * `genomics.datasets.get` * `genomics.datasets.list` * `genomics.datasets.update` * `genomics.datasets.getIamPolicy` * `genomics.datasets.setIamPolicy`

ImportReadGroupSetsResponse

data ImportReadGroupSetsResponse

The read group set import response.

See: importReadGroupSetsResponse smart constructor.

Instances

Eq ImportReadGroupSetsResponse

Data ImportReadGroupSetsResponse

Show ImportReadGroupSetsResponse

Generic ImportReadGroupSetsResponse

ToJSON ImportReadGroupSetsResponse

FromJSON ImportReadGroupSetsResponse

type Rep ImportReadGroupSetsResponse

importReadGroupSetsResponse :: ImportReadGroupSetsResponse

Creates a value of ImportReadGroupSetsResponse with the minimum fields required to make a request.

Use one of the following lenses to modify other fields as desired:

• irgsrReadGroupSetIds

irgsrReadGroupSetIds :: Lens' ImportReadGroupSetsResponse [Text]

IDs of the read group sets that were created.

LinearAlignment

data LinearAlignment

A linear alignment can be represented by one CIGAR string. Describes the mapped position and local alignment of the read to the reference.

See: linearAlignment smart constructor.

Instances

Eq LinearAlignment

Data LinearAlignment

Show LinearAlignment

Generic LinearAlignment

ToJSON LinearAlignment

FromJSON LinearAlignment

type Rep LinearAlignment

linearAlignment :: LinearAlignment

Creates a value of LinearAlignment with the minimum fields required to make a request.

Use one of the following lenses to modify other fields as desired:

• laCigar
• laMAppingQuality
• laPosition

laCigar :: Lens' LinearAlignment [CigarUnit]

Represents the local alignment of this sequence (alignment matches, indels, etc) against the reference.

laMAppingQuality :: Lens' LinearAlignment (Maybe Int32)

The mapping quality of this alignment. Represents how likely the read maps to this position as opposed to other locations.

laPosition :: Lens' LinearAlignment (Maybe Position)

The position of this alignment.

VariantSet

data VariantSet

A variant set is a collection of call sets and variants. It contains summary statistics of those contents. A variant set belongs to a dataset.

See: variantSet smart constructor.

Instances

Eq VariantSet

Data VariantSet

Show VariantSet

Generic VariantSet

ToJSON VariantSet

FromJSON VariantSet

type Rep VariantSet

variantSet :: VariantSet

Creates a value of VariantSet with the minimum fields required to make a request.

Use one of the following lenses to modify other fields as desired:

• vsDataSetId
• vsReferenceBounds
• vsMetadata
• vsId

vsDataSetId :: Lens' VariantSet (Maybe Text)

The dataset to which this variant set belongs.

vsReferenceBounds :: Lens' VariantSet [ReferenceBound]

A list of all references used by the variants in a variant set with associated coordinate upper bounds for each one.

vsMetadata :: Lens' VariantSet [VariantSetMetadata]

The metadata associated with this variant set.

vsId :: Lens' VariantSet (Maybe Text)

The server-generated variant set ID, unique across all variant sets.

TestIAMPermissionsResponse

data TestIAMPermissionsResponse

Response message for `TestIamPermissions` method.

See: testIAMPermissionsResponse smart constructor.

Instances

Eq TestIAMPermissionsResponse

Data TestIAMPermissionsResponse

Show TestIAMPermissionsResponse

Generic TestIAMPermissionsResponse

ToJSON TestIAMPermissionsResponse

FromJSON TestIAMPermissionsResponse

type Rep TestIAMPermissionsResponse

testIAMPermissionsResponse :: TestIAMPermissionsResponse

Creates a value of TestIAMPermissionsResponse with the minimum fields required to make a request.

Use one of the following lenses to modify other fields as desired:

• tiamprPermissions

tiamprPermissions :: Lens' TestIAMPermissionsResponse [Text]

A subset of `TestPermissionsRequest.permissions` that the caller is allowed.

ListDataSetsResponse

data ListDataSetsResponse

The dataset list response.

See: listDataSetsResponse smart constructor.

Instances

Eq ListDataSetsResponse

Data ListDataSetsResponse

Show ListDataSetsResponse

Generic ListDataSetsResponse

ToJSON ListDataSetsResponse

FromJSON ListDataSetsResponse

type Rep ListDataSetsResponse

listDataSetsResponse :: ListDataSetsResponse

Creates a value of ListDataSetsResponse with the minimum fields required to make a request.

Use one of the following lenses to modify other fields as desired:

• ldsrNextPageToken
• ldsrDataSets

ldsrNextPageToken :: Lens' ListDataSetsResponse (Maybe Text)

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.

ldsrDataSets :: Lens' ListDataSetsResponse [DataSet]

The list of matching Datasets.

ImportReadGroupSetsRequest

data ImportReadGroupSetsRequest

The read group set import request.

See: importReadGroupSetsRequest smart constructor.

Instances

Eq ImportReadGroupSetsRequest

Data ImportReadGroupSetsRequest

Show ImportReadGroupSetsRequest

Generic ImportReadGroupSetsRequest

ToJSON ImportReadGroupSetsRequest

FromJSON ImportReadGroupSetsRequest

type Rep ImportReadGroupSetsRequest

importReadGroupSetsRequest :: ImportReadGroupSetsRequest

Creates a value of ImportReadGroupSetsRequest with the minimum fields required to make a request.

Use one of the following lenses to modify other fields as desired:

• irgsrReferenceSetId
• irgsrDataSetId
• irgsrSourceURIs
• irgsrPartitionStrategy

irgsrReferenceSetId :: Lens' ImportReadGroupSetsRequest (Maybe Text)

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.

irgsrDataSetId :: Lens' ImportReadGroupSetsRequest (Maybe Text)

Required. The ID of the dataset these read group sets will belong to. The caller must have WRITE permissions to this dataset.

irgsrSourceURIs :: Lens' ImportReadGroupSetsRequest [Text]

A list of URIs pointing at BAM files in Google Cloud Storage.

irgsrPartitionStrategy :: Lens' ImportReadGroupSetsRequest (Maybe Text)

The partition strategy describes how read groups are partitioned into read group sets.

ImportVariantsRequest

data ImportVariantsRequest

The variant data import request.

See: importVariantsRequest smart constructor.

Instances

Eq ImportVariantsRequest

Data ImportVariantsRequest

Show ImportVariantsRequest

Generic ImportVariantsRequest

ToJSON ImportVariantsRequest

FromJSON ImportVariantsRequest

type Rep ImportVariantsRequest

importVariantsRequest :: ImportVariantsRequest

Creates a value of ImportVariantsRequest with the minimum fields required to make a request.

Use one of the following lenses to modify other fields as desired:

• ivrVariantSetId
• ivrFormat
• ivrNormalizeReferenceNames
• ivrSourceURIs

ivrVariantSetId :: Lens' ImportVariantsRequest (Maybe Text)

Required. The variant set to which variant data should be imported.

ivrFormat :: Lens' ImportVariantsRequest (Maybe Text)

The format of the variant data being imported. If unspecified, defaults to to `VCF`.

ivrNormalizeReferenceNames :: Lens' ImportVariantsRequest (Maybe Bool)

Convert reference names to the canonical representation. hg19 haploytypes (those reference names containing "_hap") are not modified in any way. All other reference names are modified according to the following rules: The reference name is capitalized. The "chr" prefix is dropped for all autosomes and sex chromsomes. For example "chr17" becomes "17" and "chrX" becomes "X". All mitochondrial chromosomes ("chrM", "chrMT", etc) become "MT".

ivrSourceURIs :: Lens' ImportVariantsRequest [Text]

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.

CigarUnit

data CigarUnit

A single CIGAR operation.

See: cigarUnit smart constructor.

Instances

Eq CigarUnit

Data CigarUnit

Show CigarUnit

Generic CigarUnit

ToJSON CigarUnit

FromJSON CigarUnit

type Rep CigarUnit

cigarUnit :: CigarUnit

Creates a value of CigarUnit with the minimum fields required to make a request.

Use one of the following lenses to modify other fields as desired:

• cuOperation
• cuOperationLength
• cuReferenceSequence

cuOperation :: Lens' CigarUnit (Maybe Text)

cuOperationLength :: Lens' CigarUnit (Maybe Int64)

The number of genomic bases that the operation runs for. Required.

cuReferenceSequence :: Lens' CigarUnit (Maybe Text)

`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.

Policy

data Policy

Defines an Identity and Access Management (IAM) policy. It is used to specify access control policies for Cloud Platform resources. A `Policy` consists of a list of `bindings`. A `Binding` binds a list of `members` to a `role`, where the members can be user accounts, Google groups, Google domains, and service accounts. A `role` is a named list of permissions defined by IAM. **Example** { "bindings": [ { "role": "roles/owner", "members": [ "user:mike'example.com", "group:admins'example.com", "domain:google.com", "serviceAccount:my-other-app'appspot.gserviceaccount.com"] }, { "role": "roles/viewer", "members": ["user:sean'example.com"] } ] } For a description of IAM and its features, see the IAM developer's guide.

See: policy smart constructor.

Instances

Eq Policy

Data Policy

Show Policy

Generic Policy

ToJSON Policy

FromJSON Policy

type Rep Policy

policy :: Policy

Creates a value of Policy with the minimum fields required to make a request.

Use one of the following lenses to modify other fields as desired:

• polEtag
• polVersion
• polBindings

polEtag :: Lens' Policy (Maybe Word8)

Can be used to perform a read-modify-write.

polVersion :: Lens' Policy (Maybe Int32)

Version of the `Policy`. The default version is 0.

polBindings :: Lens' Policy [Binding]

Associates a list of `members` to a `role`. Multiple `bindings` must not be specified for the same `role`. `bindings` with no members will result in an error.

ExportVariantSetRequest

data ExportVariantSetRequest

The variant data export request.

See: exportVariantSetRequest smart constructor.

Instances

Eq ExportVariantSetRequest

Data ExportVariantSetRequest

Show ExportVariantSetRequest

Generic ExportVariantSetRequest

ToJSON ExportVariantSetRequest

FromJSON ExportVariantSetRequest

type Rep ExportVariantSetRequest

exportVariantSetRequest :: ExportVariantSetRequest

Creates a value of ExportVariantSetRequest with the minimum fields required to make a request.

Use one of the following lenses to modify other fields as desired:

• evsrBigQueryDataSet
• evsrBigQueryTable
• evsrFormat
• evsrCallSetIds
• evsrProjectId

evsrBigQueryDataSet :: Lens' ExportVariantSetRequest (Maybe Text)

Required. The BigQuery dataset to export data to. This dataset must already exist. Note that this is distinct from the Genomics concept of "dataset".

evsrBigQueryTable :: Lens' ExportVariantSetRequest (Maybe Text)

Required. The BigQuery table to export data to. If the table doesn't exist, it will be created. If it already exists, it will be overwritten.

evsrFormat :: Lens' ExportVariantSetRequest (Maybe Text)

The format for the exported data.

evsrCallSetIds :: Lens' ExportVariantSetRequest [Text]

If provided, only variant call information from the specified call sets will be exported. By default all variant calls are exported.

evsrProjectId :: Lens' ExportVariantSetRequest (Maybe Text)

Required. The Google Cloud project ID that owns the destination BigQuery dataset. The caller must have WRITE access to this project. This project will also own the resulting export job.

OperationMetadata

data OperationMetadata

Metadata describing an Operation.

See: operationMetadata smart constructor.

Instances

Eq OperationMetadata

Data OperationMetadata

Show OperationMetadata

Generic OperationMetadata

ToJSON OperationMetadata

FromJSON OperationMetadata

type Rep OperationMetadata

operationMetadata :: OperationMetadata

Creates a value of OperationMetadata with the minimum fields required to make a request.

Use one of the following lenses to modify other fields as desired:

• omEvents
• omProjectId
• omCreateTime
• omRequest

omEvents :: Lens' OperationMetadata [OperationEvent]

Optional event messages that were generated during the job's execution. This also contains any warnings that were generated during import or export.

omProjectId :: Lens' OperationMetadata (Maybe Text)

The Google Cloud Project in which the job is scoped.

omCreateTime :: Lens' OperationMetadata (Maybe Text)

The time at which the job was submitted to the Genomics service.

omRequest :: Lens' OperationMetadata (Maybe OperationMetadataRequest)

The original request that started the operation. Note that this will be in current version of the API. If the operation was started with v1beta2 API and a GetOperation is performed on v1 API, a v1 request will be returned.

SearchVariantSetsResponse

data SearchVariantSetsResponse

The search variant sets response.

See: searchVariantSetsResponse smart constructor.

Instances

Eq SearchVariantSetsResponse

Data SearchVariantSetsResponse

Show SearchVariantSetsResponse

Generic SearchVariantSetsResponse

ToJSON SearchVariantSetsResponse

FromJSON SearchVariantSetsResponse

type Rep SearchVariantSetsResponse

searchVariantSetsResponse :: SearchVariantSetsResponse

Creates a value of SearchVariantSetsResponse with the minimum fields required to make a request.

Use one of the following lenses to modify other fields as desired:

• svsrNextPageToken
• svsrVariantSets

svsrNextPageToken :: Lens' SearchVariantSetsResponse (Maybe Text)

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.

svsrVariantSets :: Lens' SearchVariantSetsResponse [VariantSet]

The variant sets belonging to the requested dataset.

SearchVariantsRequest

data SearchVariantsRequest

The variant search request.

See: searchVariantsRequest smart constructor.

Instances

Eq SearchVariantsRequest

Data SearchVariantsRequest

Show SearchVariantsRequest

Generic SearchVariantsRequest

ToJSON SearchVariantsRequest

FromJSON SearchVariantsRequest

type Rep SearchVariantsRequest

searchVariantsRequest :: SearchVariantsRequest

Creates a value of SearchVariantsRequest with the minimum fields required to make a request.

Use one of the following lenses to modify other fields as desired:

• svrStart
• svrCallSetIds
• svrReferenceName
• svrEnd
• svrMaxCalls
• svrPageToken
• svrVariantName
• svrVariantSetIds
• svrPageSize

svrStart :: Lens' SearchVariantsRequest (Maybe Int64)

The beginning of the window (0-based, inclusive) for which overlapping variants should be returned. If unspecified, defaults to 0.

svrCallSetIds :: Lens' SearchVariantsRequest [Text]

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.

svrReferenceName :: Lens' SearchVariantsRequest (Maybe Text)

Required. Only return variants in this reference sequence.

svrEnd :: Lens' SearchVariantsRequest (Maybe Int64)

The end of the window, 0-based exclusive. If unspecified or 0, defaults to the length of the reference.

svrMaxCalls :: Lens' SearchVariantsRequest (Maybe Int32)

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.

svrPageToken :: Lens' SearchVariantsRequest (Maybe Text)

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.

svrVariantName :: Lens' SearchVariantsRequest (Maybe Text)

Only return variants which have exactly this name.

svrVariantSetIds :: Lens' SearchVariantsRequest [Text]

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.

svrPageSize :: Lens' SearchVariantsRequest (Maybe Int32)

The maximum number of variants to return. If unspecified, defaults to 5000.

CallSetInfo

data CallSetInfo

A map of additional call set information. This must be of the form map (string key mapping to a list of string values).

See: callSetInfo smart constructor.

Instances

Eq CallSetInfo

Data CallSetInfo

Show CallSetInfo

Generic CallSetInfo

ToJSON CallSetInfo

FromJSON CallSetInfo

type Rep CallSetInfo

callSetInfo

Arguments

:: HashMap Text [JSONValue]

csiAddtional

-> CallSetInfo

Creates a value of CallSetInfo with the minimum fields required to make a request.

Use one of the following lenses to modify other fields as desired:

• csiAddtional

csiAddtional :: Lens' CallSetInfo (HashMap Text [JSONValue])

VariantSetMetadataInfo

data VariantSetMetadataInfo

Remaining structured metadata key-value pairs. This must be of the form map (string key mapping to a list of string values).

See: variantSetMetadataInfo smart constructor.

Instances

Eq VariantSetMetadataInfo

Data VariantSetMetadataInfo

Show VariantSetMetadataInfo

Generic VariantSetMetadataInfo

ToJSON VariantSetMetadataInfo

FromJSON VariantSetMetadataInfo

type Rep VariantSetMetadataInfo

variantSetMetadataInfo

Arguments

:: HashMap Text [JSONValue]

vsmiAddtional

-> VariantSetMetadataInfo

Creates a value of VariantSetMetadataInfo with the minimum fields required to make a request.

Use one of the following lenses to modify other fields as desired:

• vsmiAddtional

vsmiAddtional :: Lens' VariantSetMetadataInfo (HashMap Text [JSONValue])

OperationResponse

data OperationResponse

If importing ReadGroupSets, an ImportReadGroupSetsResponse is returned. If importing Variants, an ImportVariantsResponse is returned. For exports, an empty response is returned.

See: operationResponse smart constructor.

Instances

Eq OperationResponse

Data OperationResponse

Show OperationResponse

Generic OperationResponse

ToJSON OperationResponse

FromJSON OperationResponse

type Rep OperationResponse

operationResponse

Arguments

:: HashMap Text JSONValue

orAddtional

-> OperationResponse

Creates a value of OperationResponse with the minimum fields required to make a request.

Use one of the following lenses to modify other fields as desired:

• orAddtional

orAddtional :: Lens' OperationResponse (HashMap Text JSONValue)

Properties of the object. Contains field 'ype with type URL.

OperationEvent

data OperationEvent

An event that occurred during an Operation.

See: operationEvent smart constructor.

Instances

Eq OperationEvent

Data OperationEvent

Show OperationEvent

Generic OperationEvent

ToJSON OperationEvent

FromJSON OperationEvent

type Rep OperationEvent

operationEvent :: OperationEvent

Creates a value of OperationEvent with the minimum fields required to make a request.

Use one of the following lenses to modify other fields as desired:

• oeDescription

oeDescription :: Lens' OperationEvent (Maybe Text)

Required description of event.

ReferenceBound

data ReferenceBound

ReferenceBound records an upper bound for the starting coordinate of variants in a particular reference.

See: referenceBound smart constructor.

Instances

Eq ReferenceBound

Data ReferenceBound

Show ReferenceBound

Generic ReferenceBound

ToJSON ReferenceBound

FromJSON ReferenceBound

type Rep ReferenceBound

referenceBound :: ReferenceBound

Creates a value of ReferenceBound with the minimum fields required to make a request.

Use one of the following lenses to modify other fields as desired:

• rbUpperBound
• rbReferenceName

rbUpperBound :: Lens' ReferenceBound (Maybe Int64)

An upper bound (inclusive) on the starting coordinate of any variant in the reference sequence.

rbReferenceName :: Lens' ReferenceBound (Maybe Text)

The reference the bound is associate with.

UndeleteDataSetRequest

data UndeleteDataSetRequest

Instances

Eq UndeleteDataSetRequest

Data UndeleteDataSetRequest

Show UndeleteDataSetRequest

Generic UndeleteDataSetRequest

ToJSON UndeleteDataSetRequest

FromJSON UndeleteDataSetRequest

type Rep UndeleteDataSetRequest

undeleteDataSetRequest :: UndeleteDataSetRequest

Creates a value of UndeleteDataSetRequest with the minimum fields required to make a request.

Binding

data Binding

Associates `members` with a `role`.

See: binding smart constructor.

Instances

Eq Binding

Data Binding

Show Binding

Generic Binding

ToJSON Binding

FromJSON Binding

type Rep Binding

binding :: Binding

Creates a value of Binding with the minimum fields required to make a request.

Use one of the following lenses to modify other fields as desired:

• bMembers
• bRole

bMembers :: Lens' Binding [Text]

Specifies the identities requesting access for a Cloud Platform resource. `members` can have the following formats: * `allUsers`: A special identifier that represents anyone who is on the internet; with or without a Google account. * `allAuthenticatedUsers`: A special identifier that represents anyone who is authenticated with a Google account or a service account. * `user:{emailid}`: An email address that represents a specific Google account. For example, `alice'gmail.com` or `joe'example.com`. * `serviceAccount:{emailid}`: An email address that represents a service account. For example, `my-other-app'appspot.gserviceaccount.com`. * `group:{emailid}`: An email address that represents a Google group. For example, `admins'example.com`. * `domain:{domain}`: A Google Apps domain name that represents all the users of that domain. For example, `google.com` or `example.com`.

bRole :: Lens' Binding (Maybe Text)

Role that is assigned to `members`. For example, `roles/viewer`, `roles/editor`, or `roles/owner`. Required

Position

data Position

An abstraction for referring to a genomic position, in relation to some already known reference. For now, represents a genomic position as a reference name, a base number on that reference (0-based), and a determination of forward or reverse strand.

See: position smart constructor.

Instances

Eq Position

Data Position

Show Position

Generic Position

ToJSON Position

FromJSON Position

type Rep Position

position :: Position

Creates a value of Position with the minimum fields required to make a request.

Use one of the following lenses to modify other fields as desired:

• pReverseStrand
• pReferenceName
• pPosition

pReverseStrand :: Lens' Position (Maybe Bool)

Whether this position is on the reverse strand, as opposed to the forward strand.

pReferenceName :: Lens' Position (Maybe Text)

The name of the reference in whatever reference set is being used.

pPosition :: Lens' Position (Maybe Int64)

The 0-based offset from the start of the forward strand for that reference.

SearchReadGroupSetsResponse

data SearchReadGroupSetsResponse

The read group set search response.

See: searchReadGroupSetsResponse smart constructor.

Instances

Eq SearchReadGroupSetsResponse

Data SearchReadGroupSetsResponse

Show SearchReadGroupSetsResponse

Generic SearchReadGroupSetsResponse

ToJSON SearchReadGroupSetsResponse

FromJSON SearchReadGroupSetsResponse

type Rep SearchReadGroupSetsResponse

searchReadGroupSetsResponse :: SearchReadGroupSetsResponse

Creates a value of SearchReadGroupSetsResponse with the minimum fields required to make a request.

Use one of the following lenses to modify other fields as desired:

• srgsrNextPageToken
• srgsrReadGroupSets

srgsrNextPageToken :: Lens' SearchReadGroupSetsResponse (Maybe Text)

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.

srgsrReadGroupSets :: Lens' SearchReadGroupSetsResponse [ReadGroupSet]

The list of matching read group sets.

ReadGroupSetInfo

data ReadGroupSetInfo

A map of additional read group set information.

See: readGroupSetInfo smart constructor.

Instances

Eq ReadGroupSetInfo

Data ReadGroupSetInfo

Show ReadGroupSetInfo

Generic ReadGroupSetInfo

ToJSON ReadGroupSetInfo

FromJSON ReadGroupSetInfo

type Rep ReadGroupSetInfo

readGroupSetInfo

Arguments

:: HashMap Text [JSONValue]

rgsiAddtional

-> ReadGroupSetInfo

Creates a value of ReadGroupSetInfo with the minimum fields required to make a request.

Use one of the following lenses to modify other fields as desired:

• rgsiAddtional

rgsiAddtional :: Lens' ReadGroupSetInfo (HashMap Text [JSONValue])

ReferenceSet

data ReferenceSet

A reference set is a set of references which typically comprise a reference assembly for a species, such as `GRCh38` which is representative of the human genome. A reference set defines a common coordinate space for comparing reference-aligned experimental data. A reference set contains 1 or more references.

See: referenceSet smart constructor.

Instances

Eq ReferenceSet

Data ReferenceSet

Show ReferenceSet

Generic ReferenceSet

ToJSON ReferenceSet

FromJSON ReferenceSet

type Rep ReferenceSet

referenceSet :: ReferenceSet

Creates a value of ReferenceSet with the minimum fields required to make a request.

Use one of the following lenses to modify other fields as desired:

• rsSourceAccessions
• rsReferenceIds
• rsMD5checksum
• rsNcbiTaxonId
• rsId
• rsAssemblyId
• rsSourceURI
• rsDescription

rsSourceAccessions :: Lens' ReferenceSet [Text]

All known corresponding accession IDs in INSDC (GenBank/ENA/DDBJ) ideally with a version number, for example `NC_000001.11`.

rsReferenceIds :: Lens' ReferenceSet [Text]

The IDs of the reference objects that are part of this set. `Reference.md5checksum` must be unique within this set.

rsMD5checksum :: Lens' ReferenceSet (Maybe Text)

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.

rsNcbiTaxonId :: Lens' ReferenceSet (Maybe Int32)

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.

rsId :: Lens' ReferenceSet (Maybe Text)

The server-generated reference set ID, unique across all reference sets.

rsAssemblyId :: Lens' ReferenceSet (Maybe Text)

Public id of this reference set, such as `GRCh37`.

rsSourceURI :: Lens' ReferenceSet (Maybe Text)

The URI from which the references were obtained.

rsDescription :: Lens' ReferenceSet (Maybe Text)

Free text description of this reference set.