@@ -20,112 +20,8 @@ module Network.Google.Genomics.Types.Product where
2020import Network.Google.Genomics.Types.Sum
2121import Network.Google.Prelude
2222
23−--
24−-- /See:/ 'fastqMetadata' smart constructor.
25−data FastqMetadata = FastqMetadata
26− { _fmPlatformUnit :: !(Maybe Text)
27− , _fmReadGroupName :: !(Maybe Text)
28− , _fmLibraryName :: !(Maybe Text)
29− , _fmPlatformName :: !(Maybe Text)
30− , _fmSampleName :: !(Maybe Text)
31− } deriving (Eq,Show,Data,Typeable,Generic)
32−
33−-- | Creates a value of 'FastqMetadata' with the minimum fields required to make a request.
34−--
35−-- Use one of the following lenses to modify other fields as desired:
36−--
37−-- * 'fmPlatformUnit'
38−--
39−-- * 'fmReadGroupName'
40−--
41−-- * 'fmLibraryName'
42−--
43−-- * 'fmPlatformName'
44−--
45−-- * 'fmSampleName'
46−fastqMetadata
47− :: FastqMetadata
48−fastqMetadata =
49− FastqMetadata
50− { _fmPlatformUnit = Nothing
51− , _fmReadGroupName = Nothing
52− , _fmLibraryName = Nothing
53− , _fmPlatformName = Nothing
54− , _fmSampleName = Nothing
55− }
56−
57−-- | Optionally specifies the platform unit for alignment from FASTQ. For
58−-- example: flowcell-barcode.lane for Illumina or slide for SOLID.
59−fmPlatformUnit :: Lens' FastqMetadata (Maybe Text)
60−fmPlatformUnit
61− = lens _fmPlatformUnit
62− (\ s a -> s{_fmPlatformUnit = a})
63−
64−-- | Optionally specifies the read group name for alignment from FASTQ.
65−fmReadGroupName :: Lens' FastqMetadata (Maybe Text)
66−fmReadGroupName
67− = lens _fmReadGroupName
68− (\ s a -> s{_fmReadGroupName = a})
69−
70−-- | Optionally specifies the library name for alignment from FASTQ.
71−fmLibraryName :: Lens' FastqMetadata (Maybe Text)
72−fmLibraryName
73− = lens _fmLibraryName
74− (\ s a -> s{_fmLibraryName = a})
75−
76−-- | Optionally specifies the platform name for alignment from FASTQ. For
77−-- example: CAPILLARY, LS454, ILLUMINA, SOLID, HELICOS, IONTORRENT, PACBIO.
78−fmPlatformName :: Lens' FastqMetadata (Maybe Text)
79−fmPlatformName
80− = lens _fmPlatformName
81− (\ s a -> s{_fmPlatformName = a})
82−
83−-- | Optionally specifies the sample name for alignment from FASTQ.
84−fmSampleName :: Lens' FastqMetadata (Maybe Text)
85−fmSampleName
86− = lens _fmSampleName (\ s a -> s{_fmSampleName = a})
87−
88−instance FromJSON FastqMetadata where
89− parseJSON
90− = withObject "FastqMetadata"
91− (\ o ->
92− FastqMetadata <$>
93− (o .:? "platformUnit") <*> (o .:? "readGroupName")
94− <*> (o .:? "libraryName")
95− <*> (o .:? "platformName")
96− <*> (o .:? "sampleName"))
97−
98−instance ToJSON FastqMetadata where
99− toJSON FastqMetadata{..}
100− = object
101− (catMaybes
102− [("platformUnit" .=) <$> _fmPlatformUnit,
103− ("readGroupName" .=) <$> _fmReadGroupName,
104− ("libraryName" .=) <$> _fmLibraryName,
105− ("platformName" .=) <$> _fmPlatformName,
106− ("sampleName" .=) <$> _fmSampleName])
107−
108−-- | A string which maps to an array of values.
109−--
110−-- /See:/ 'callInfo' smart constructor.
111−data CallInfo =
112− CallInfo
113− deriving (Eq,Show,Data,Typeable,Generic)
114−
115−-- | Creates a value of 'CallInfo' with the minimum fields required to make a request.
116−--
117−callInfo
118− :: CallInfo
119−callInfo = CallInfo
120−
121−instance FromJSON CallInfo where
122− parseJSON
123− = withObject "CallInfo" (\ o -> pure CallInfo)
124−
125−instance ToJSON CallInfo where
126− toJSON = const emptyObject
127−
128−-- | A string which maps to an array of values.
23+-- | A map of additional read alignment information. This must be of the form
24+-- map (string key mapping to a list of string values).
12925--
13026-- /See:/ 'readInfo' smart constructor.
13127data ReadInfo =
@@ -145,127 +41,122 @@ instance FromJSON ReadInfo where
14541instance ToJSON ReadInfo where
14642 toJSON = const emptyObject
14743
148−--
149−-- /See:/ 'readGroupExperiment' smart constructor.
150−data ReadGroupExperiment = ReadGroupExperiment
151− { _rgeInstrumentModel :: !(Maybe Text)
152− , _rgePlatformUnit :: !(Maybe Text)
153− , _rgeSequencingCenter :: !(Maybe Text)
154− , _rgeLibraryId :: !(Maybe Text)
44+-- | The \`Status\` type defines a logical error model that is suitable for
45+-- different programming environments, including REST APIs and RPC APIs. It
46+-- is used by [gRPC](https:\/\/github.com\/grpc). The error model is
47+-- designed to be: - Simple to use and understand for most users - Flexible
48+-- enough to meet unexpected needs # Overview The \`Status\` message
49+-- contains three pieces of data: error code, error message, and error
50+-- details. The error code should be an enum value of google.rpc.Code, but
51+-- it may accept additional error codes if needed. The error message should
52+-- be a developer-facing English message that helps developers *understand*
53+-- and *resolve* the error. If a localized user-facing error message is
54+-- needed, put the localized message in the error details or localize it in
55+-- the client. The optional error details may contain arbitrary information
56+-- about the error. There is a predefined set of error detail types in the
57+-- package \`google.rpc\` which can be used for common error conditions. #
58+-- Language mapping The \`Status\` message is the logical representation of
59+-- the error model, but it is not necessarily the actual wire format. When
60+-- the \`Status\` message is exposed in different client libraries and
61+-- different wire protocols, it can be mapped differently. For example, it
62+-- will likely be mapped to some exceptions in Java, but more likely mapped
63+-- to some error codes in C. # Other uses The error model and the
64+-- \`Status\` message can be used in a variety of environments, either with
65+-- or without APIs, to provide a consistent developer experience across
66+-- different environments. Example uses of this error model include: -
67+-- Partial errors. If a service needs to return partial errors to the
68+-- client, it may embed the \`Status\` in the normal response to indicate
69+-- the partial errors. - Workflow errors. A typical workflow has multiple
70+-- steps. Each step may have a \`Status\` message for error reporting
71+-- purpose. - Batch operations. If a client uses batch request and batch
72+-- response, the \`Status\` message should be used directly inside batch
73+-- response, one for each error sub-response. - Asynchronous operations. If
74+-- an API call embeds asynchronous operation results in its response, the
75+-- status of those operations should be represented directly using the
76+-- \`Status\` message. - Logging. If some API errors are stored in logs,
77+-- the message \`Status\` could be used directly after any stripping needed
78+-- for security\/privacy reasons.
79+--
80+-- /See:/ 'status' smart constructor.
81+data Status = Status
82+ { _sDetails :: !(Maybe [StatusDetailsItem])
83+ , _sCode :: !(Maybe Int32)
84+ , _sMessage :: !(Maybe Text)
15585 } deriving (Eq,Show,Data,Typeable,Generic)
15686
157−-- | Creates a value of 'ReadGroupExperiment' with the minimum fields required to make a request.
87+-- | Creates a value of 'Status' with the minimum fields required to make a request.
15888--
15989-- Use one of the following lenses to modify other fields as desired:
16090--
161−-- * 'rgeInstrumentModel'
162−--
163−-- * 'rgePlatformUnit'
91+-- * 'sDetails'
16492--
165−-- * 'rgeSequencingCenter'
93+-- * 'sCode'
16694--
167−-- * 'rgeLibraryId'
168−readGroupExperiment
169− :: ReadGroupExperiment
170−readGroupExperiment =
171− ReadGroupExperiment
172− { _rgeInstrumentModel = Nothing
173− , _rgePlatformUnit = Nothing
174− , _rgeSequencingCenter = Nothing
175− , _rgeLibraryId = Nothing
95+-- * 'sMessage'
96+status
97+ :: Status
98+status =
99+ Status
100+ { _sDetails = Nothing
101+ , _sCode = Nothing
102+ , _sMessage = Nothing
176103 }
177104
178−-- | The instrument model used as part of this experiment. This maps to
179−-- sequencing technology in BAM.
180−rgeInstrumentModel :: Lens' ReadGroupExperiment (Maybe Text)
181−rgeInstrumentModel
182− = lens _rgeInstrumentModel
183− (\ s a -> s{_rgeInstrumentModel = a})
184−
185−-- | The platform unit used as part of this experiment e.g.
186−-- flowcell-barcode.lane for Illumina or slide for SOLiD. Corresponds to
187−-- the
188−rgePlatformUnit :: Lens' ReadGroupExperiment (Maybe Text)
189−rgePlatformUnit
190− = lens _rgePlatformUnit
191− (\ s a -> s{_rgePlatformUnit = a})
105+-- | A list of messages that carry the error details. There will be a common
106+-- set of message types for APIs to use.
107+sDetails :: Lens' Status [StatusDetailsItem]
108+sDetails
109+ = lens _sDetails (\ s a -> s{_sDetails = a}) .
110+ _Default
111+ . _Coerce
192112
193−-- | The sequencing center used as part of this experiment.
194−rgeSequencingCenter :: Lens' ReadGroupExperiment (Maybe Text)
195−rgeSequencingCenter
196− = lens _rgeSequencingCenter
197− (\ s a -> s{_rgeSequencingCenter = a})
113+-- | The status code, which should be an enum value of google.rpc.Code.
114+sCode :: Lens' Status (Maybe Int32)
115+sCode = lens _sCode (\ s a -> s{_sCode = a})
198116
199−-- | The library used as part of this experiment. Note: This is not an actual
200−-- ID within this repository, but rather an identifier for a library which
201−-- may be meaningful to some external system.
202−rgeLibraryId :: Lens' ReadGroupExperiment (Maybe Text)
203−rgeLibraryId
204− = lens _rgeLibraryId (\ s a -> s{_rgeLibraryId = a})
117+-- | A developer-facing error message, which should be in English. Any
118+-- user-facing error message should be localized and sent in the
119+-- google.rpc.Status.details field, or localized by the client.
120+sMessage :: Lens' Status (Maybe Text)
121+sMessage = lens _sMessage (\ s a -> s{_sMessage = a})
205122
206−instance FromJSON ReadGroupExperiment where
123+instance FromJSON Status where
207124 parseJSON
208− = withObject "ReadGroupExperiment"
125+ = withObject "Status"
209126 (\ o ->
210− ReadGroupExperiment <$>
211− (o .:? "instrumentModel") <*> (o .:? "platformUnit")
212− <*> (o .:? "sequencingCenter")
213− <*> (o .:? "libraryId"))
127+ Status <$>
128+ (o .:? "details" .!= mempty) <*> (o .:? "code") <*>
129+ (o .:? "message"))
214130
215−instance ToJSON ReadGroupExperiment where
216− toJSON ReadGroupExperiment{..}
131+instance ToJSON Status where
132+ toJSON Status{..}
217133 = object
218134 (catMaybes
219− [("instrumentModel" .=) <$> _rgeInstrumentModel,
220− ("platformUnit" .=) <$> _rgePlatformUnit,
221− ("sequencingCenter" .=) <$> _rgeSequencingCenter,
222− ("libraryId" .=) <$> _rgeLibraryId])
135+ [("details" .=) <$> _sDetails,
136+ ("code" .=) <$> _sCode,
137+ ("message" .=) <$> _sMessage])
223138
224−-- | Used to hold basic key value information.
139+-- | An OperationMetadata object. This will always be returned with the
140+-- Operation.
225141--
226−-- /See:/ 'keyValue' smart constructor.
227−data KeyValue = KeyValue
228− { _kvValue :: !(Maybe [Text])
229− , _kvKey :: !(Maybe Text)
230− } deriving (Eq,Show,Data,Typeable,Generic)
142+-- /See:/ 'operationSchema' smart constructor.
143+data OperationSchema =
144+ OperationSchema
145+ deriving (Eq,Show,Data,Typeable,Generic)
231146
232−-- | Creates a value of 'KeyValue' with the minimum fields required to make a request.
147+-- | Creates a value of 'OperationSchema' with the minimum fields required to make a request.
233148--
234−-- Use one of the following lenses to modify other fields as desired:
235−--
236−-- * 'kvValue'
237−--
238−-- * 'kvKey'
239−keyValue
240− :: KeyValue
241−keyValue =
242− KeyValue
243− { _kvValue = Nothing
244− , _kvKey = Nothing
245− }
149+operationSchema
150+ :: OperationSchema
151+operationSchema = OperationSchema
246152
247−-- | The string values.
248−kvValue :: Lens' KeyValue [Text]
249−kvValue
250− = lens _kvValue (\ s a -> s{_kvValue = a}) . _Default
251− . _Coerce
252−
253−-- | A string which maps to an array of values.
254−kvKey :: Lens' KeyValue (Maybe Text)
255−kvKey = lens _kvKey (\ s a -> s{_kvKey = a})
256−
257−instance FromJSON KeyValue where
153+instance FromJSON OperationSchema where
258154 parseJSON
259− = withObject "KeyValue"
260− (\ o ->
261− KeyValue <$>
262− (o .:? "value" .!= mempty) <*> (o .:? "key"))
155+ = withObject "OperationSchema"
156+ (\ o -> pure OperationSchema)
263157
264−instance ToJSON KeyValue where
265− toJSON KeyValue{..}
266− = object
267− (catMaybes
268− [("value" .=) <$> _kvValue, ("key" .=) <$> _kvKey])
158+instance ToJSON OperationSchema where
159+ toJSON = const emptyObject
269160
270161-- | A variant represents a change in DNA sequence relative to a reference
271162-- sequence. For example, a variant could represent a SNP or an insertion.
@@ -289,7 +180,7 @@ data Variant = Variant
289180 , _vQuality :: !(Maybe Double)
290181 , _vFilter :: !(Maybe [Text])
291182 , _vInfo :: !(Maybe VariantInfo)
292− , _vCalls :: !(Maybe [Call])
183+ , _vCalls :: !(Maybe [VariantCall])
293184 } deriving (Eq,Show,Data,Typeable,Generic)
294185
295186-- | Creates a value of 'Variant' with the minimum fields required to make a request.
@@ -363,7 +254,7 @@ vAlternateBases
363254 . _Default
364255 . _Coerce
365256
366−-- | The reference on which this variant occurs. (such as chr20 or X)
257+-- | The reference on which this variant occurs. (such as \`chr20\` or \`X\`)
367258vReferenceName :: Lens' Variant (Maybe Text)
368259vReferenceName
369260 = lens _vReferenceName
@@ -389,7 +280,7 @@ vReferenceBases
389280 = lens _vReferenceBases
390281 (\ s a -> s{_vReferenceBases = a})
391282
392−-- | The Google generated ID of the variant, immutable.
283+-- | The server-generated variant ID, unique across all variants.
393284vId :: Lens' Variant (Maybe Text)
394285vId = lens _vId (\ s a -> s{_vId = a})
395286
@@ -399,19 +290,20 @@ vQuality :: Lens' Variant (Maybe Double)
399290vQuality = lens _vQuality (\ s a -> s{_vQuality = a})
400291
401292-- | A list of filters (normally quality filters) this variant has failed.
402−-- PASS indicates this variant has passed all filters.
293+-- \`PASS\` indicates this variant has passed all filters.
403294vFilter :: Lens' Variant [Text]
404295vFilter
405296 = lens _vFilter (\ s a -> s{_vFilter = a}) . _Default
406297 . _Coerce
407298
408−-- | A string which maps to an array of values.
299+-- | A map of additional variant information. This must be of the form map
300+-- (string key mapping to a list of string values).
409301vInfo :: Lens' Variant (Maybe VariantInfo)
410302vInfo = lens _vInfo (\ s a -> s{_vInfo = a})
411303
412304-- | The variant calls for this particular variant. Each one represents the
413305-- determination of genotype with respect to this variant.
414−vCalls :: Lens' Variant [Call]
306+vCalls :: Lens' Variant [VariantCall]
415307vCalls
416308 = lens _vCalls (\ s a -> s{_vCalls = a}) . _Default .
417309 _Coerce
@@ -449,297 +341,6 @@ instance ToJSON Variant where
449341 ("filter" .=) <$> _vFilter, ("info" .=) <$> _vInfo,
450342 ("calls" .=) <$> _vCalls])
451343
452−-- | An annotation describes a region of reference genome. The value of an
453−-- annotation may be one of several canonical types, supplemented by
454−-- arbitrary info tags. A variant annotation is represented by one or more
455−-- of these canonical types. An annotation is not inherently associated
456−-- with a specific sample or individual (though a client could choose to
457−-- use annotations in this way). Example canonical annotation types are
458−-- \'Gene\' and \'Variant\'.
459−--
460−-- /See:/ 'annotation' smart constructor.
461−data Annotation = Annotation
462− { _aVariant :: !(Maybe VariantAnnotation)
463− , _aAnnotationSetId :: !(Maybe Text)
464− , _aName :: !(Maybe Text)
465− , _aId :: !(Maybe Text)
466− , _aType :: !(Maybe AnnotationType)
467− , _aTranscript :: !(Maybe Transcript)
468− , _aInfo :: !(Maybe AnnotationInfo)
469− , _aPosition :: !(Maybe RangePosition)
470− } deriving (Eq,Show,Data,Typeable,Generic)
471−
472−-- | Creates a value of 'Annotation' with the minimum fields required to make a request.
473−--
474−-- Use one of the following lenses to modify other fields as desired:
475−--
476−-- * 'aVariant'
477−--
478−-- * 'aAnnotationSetId'
479−--
480−-- * 'aName'
481−--
482−-- * 'aId'
483−--
484−-- * 'aType'
485−--
486−-- * 'aTranscript'
487−--
488−-- * 'aInfo'
489−--
490−-- * 'aPosition'
491−annotation
492− :: Annotation
493−annotation =
494− Annotation
495− { _aVariant = Nothing
496− , _aAnnotationSetId = Nothing
497− , _aName = Nothing
498− , _aId = Nothing
499− , _aType = Nothing
500− , _aTranscript = Nothing
501− , _aInfo = Nothing
502− , _aPosition = Nothing
503− }
504−
505−-- | A variant annotation, which describes the effect of a variant on the
506−-- genome, the coding sequence, and\/or higher level consequences at the
507−-- organism level e.g. pathogenicity. This field is only set for
508−-- annotations of type VARIANT.
509−aVariant :: Lens' Annotation (Maybe VariantAnnotation)
510−aVariant = lens _aVariant (\ s a -> s{_aVariant = a})
511−
512−-- | The ID of the containing annotation set.
513−aAnnotationSetId :: Lens' Annotation (Maybe Text)
514−aAnnotationSetId
515− = lens _aAnnotationSetId
516− (\ s a -> s{_aAnnotationSetId = a})
517−
518−-- | The display name of this annotation.
519−aName :: Lens' Annotation (Maybe Text)
520−aName = lens _aName (\ s a -> s{_aName = a})
521−
522−-- | The generated unique ID for this annotation.
523−aId :: Lens' Annotation (Maybe Text)
524−aId = lens _aId (\ s a -> s{_aId = a})
525−
526−-- | The data type for this annotation. Must match the containing annotation
527−-- set\'s type.
528−aType :: Lens' Annotation (Maybe AnnotationType)
529−aType = lens _aType (\ s a -> s{_aType = a})
530−
531−-- | A transcript value represents the assertion that a particular region of
532−-- the reference genome may be transcribed as RNA. An alternative splicing
533−-- pattern would be represented as a separate transcript object. This field
534−-- is only set for annotations of type TRANSCRIPT.
535−aTranscript :: Lens' Annotation (Maybe Transcript)
536−aTranscript
537− = lens _aTranscript (\ s a -> s{_aTranscript = a})
538−
539−-- | A string which maps to an array of values.
540−aInfo :: Lens' Annotation (Maybe AnnotationInfo)
541−aInfo = lens _aInfo (\ s a -> s{_aInfo = a})
542−
543−-- | The position of this annotation on the reference sequence.
544−aPosition :: Lens' Annotation (Maybe RangePosition)
545−aPosition
546− = lens _aPosition (\ s a -> s{_aPosition = a})
547−
548−instance FromJSON Annotation where
549− parseJSON
550− = withObject "Annotation"
551− (\ o ->
552− Annotation <$>
553− (o .:? "variant") <*> (o .:? "annotationSetId") <*>
554− (o .:? "name")
555− <*> (o .:? "id")
556− <*> (o .:? "type")
557− <*> (o .:? "transcript")
558− <*> (o .:? "info")
559− <*> (o .:? "position"))
560−
561−instance ToJSON Annotation where
562− toJSON Annotation{..}
563− = object
564− (catMaybes
565− [("variant" .=) <$> _aVariant,
566− ("annotationSetId" .=) <$> _aAnnotationSetId,
567− ("name" .=) <$> _aName, ("id" .=) <$> _aId,
568− ("type" .=) <$> _aType,
569− ("transcript" .=) <$> _aTranscript,
570− ("info" .=) <$> _aInfo,
571− ("position" .=) <$> _aPosition])
572−
573−-- | Describes an interleaved FASTQ file source for alignment.
574−--
575−-- /See:/ 'interleavedFastqSource' smart constructor.
576−data InterleavedFastqSource = InterleavedFastqSource
577− { _ifsMetadata :: !(Maybe FastqMetadata)
578− , _ifsSourceURIs :: !(Maybe [Text])
579− } deriving (Eq,Show,Data,Typeable,Generic)
580−
581−-- | Creates a value of 'InterleavedFastqSource' with the minimum fields required to make a request.
582−--
583−-- Use one of the following lenses to modify other fields as desired:
584−--
585−-- * 'ifsMetadata'
586−--
587−-- * 'ifsSourceURIs'
588−interleavedFastqSource
589− :: InterleavedFastqSource
590−interleavedFastqSource =
591− InterleavedFastqSource
592− { _ifsMetadata = Nothing
593− , _ifsSourceURIs = Nothing
594− }
595−
596−-- | Optionally specifies the metadata to be associated with the final
597−-- aligned read group set.
598−ifsMetadata :: Lens' InterleavedFastqSource (Maybe FastqMetadata)
599−ifsMetadata
600− = lens _ifsMetadata (\ s a -> s{_ifsMetadata = a})
601−
602−-- | A list of URIs pointing at interleaved FASTQ files in Google Cloud
603−-- Storage which will be aligned. The caller must have READ permissions for
604−-- these files.
605−ifsSourceURIs :: Lens' InterleavedFastqSource [Text]
606−ifsSourceURIs
607− = lens _ifsSourceURIs
608− (\ s a -> s{_ifsSourceURIs = a})
609− . _Default
610− . _Coerce
611−
612−instance FromJSON InterleavedFastqSource where
613− parseJSON
614− = withObject "InterleavedFastqSource"
615− (\ o ->
616− InterleavedFastqSource <$>
617− (o .:? "metadata") <*>
618− (o .:? "sourceUris" .!= mempty))
619−
620−instance ToJSON InterleavedFastqSource where
621− toJSON InterleavedFastqSource{..}
622− = object
623− (catMaybes
624− [("metadata" .=) <$> _ifsMetadata,
625− ("sourceUris" .=) <$> _ifsSourceURIs])
626−
627−-- | The read group set call request.
628−--
629−-- /See:/ 'callReadGroupSetsRequest' smart constructor.
630−data CallReadGroupSetsRequest = CallReadGroupSetsRequest
631− { _crgsrReadGroupSetId :: !(Maybe Text)
632− , _crgsrDatasetId :: !(Maybe Text)
633− , _crgsrSourceURIs :: !(Maybe [Text])
634− } deriving (Eq,Show,Data,Typeable,Generic)
635−
636−-- | Creates a value of 'CallReadGroupSetsRequest' with the minimum fields required to make a request.
637−--
638−-- Use one of the following lenses to modify other fields as desired:
639−--
640−-- * 'crgsrReadGroupSetId'
641−--
642−-- * 'crgsrDatasetId'
643−--
644−-- * 'crgsrSourceURIs'
645−callReadGroupSetsRequest
646− :: CallReadGroupSetsRequest
647−callReadGroupSetsRequest =
648− CallReadGroupSetsRequest
649− { _crgsrReadGroupSetId = Nothing
650− , _crgsrDatasetId = Nothing
651− , _crgsrSourceURIs = Nothing
652− }
653−
654−-- | The IDs of the read group sets which will be called. The caller must
655−-- have READ permissions for these read group sets. One of readGroupSetId
656−-- or sourceUris must be provided.
657−crgsrReadGroupSetId :: Lens' CallReadGroupSetsRequest (Maybe Text)
658−crgsrReadGroupSetId
659− = lens _crgsrReadGroupSetId
660− (\ s a -> s{_crgsrReadGroupSetId = a})
661−
662−-- | Required. The ID of the dataset the called variants will belong to. The
663−-- caller must have WRITE permissions to this dataset.
664−crgsrDatasetId :: Lens' CallReadGroupSetsRequest (Maybe Text)
665−crgsrDatasetId
666− = lens _crgsrDatasetId
667− (\ s a -> s{_crgsrDatasetId = a})
668−
669−-- | A list of URIs pointing at BAM files in Google Cloud Storage which will
670−-- be called. FASTQ files are not allowed. The caller must have READ
671−-- permissions for these files. One of readGroupSetId or sourceUris must be
672−-- provided.
673−crgsrSourceURIs :: Lens' CallReadGroupSetsRequest [Text]
674−crgsrSourceURIs
675− = lens _crgsrSourceURIs
676− (\ s a -> s{_crgsrSourceURIs = a})
677− . _Default
678− . _Coerce
679−
680−instance FromJSON CallReadGroupSetsRequest where
681− parseJSON
682− = withObject "CallReadGroupSetsRequest"
683− (\ o ->
684− CallReadGroupSetsRequest <$>
685− (o .:? "readGroupSetId") <*> (o .:? "datasetId") <*>
686− (o .:? "sourceUris" .!= mempty))
687−
688−instance ToJSON CallReadGroupSetsRequest where
689− toJSON CallReadGroupSetsRequest{..}
690− = object
691− (catMaybes
692− [("readGroupSetId" .=) <$> _crgsrReadGroupSetId,
693− ("datasetId" .=) <$> _crgsrDatasetId,
694− ("sourceUris" .=) <$> _crgsrSourceURIs])
695−
696−--
697−-- /See:/ 'batchAnnotationsResponseEntry' smart constructor.
698−data BatchAnnotationsResponseEntry = BatchAnnotationsResponseEntry
699− { _bareStatus :: !(Maybe BatchAnnotationsResponseEntryStatus)
700− , _bareAnnotation :: !(Maybe Annotation)
701− } deriving (Eq,Show,Data,Typeable,Generic)
702−
703−-- | Creates a value of 'BatchAnnotationsResponseEntry' with the minimum fields required to make a request.
704−--
705−-- Use one of the following lenses to modify other fields as desired:
706−--
707−-- * 'bareStatus'
708−--
709−-- * 'bareAnnotation'
710−batchAnnotationsResponseEntry
711− :: BatchAnnotationsResponseEntry
712−batchAnnotationsResponseEntry =
713− BatchAnnotationsResponseEntry
714− { _bareStatus = Nothing
715− , _bareAnnotation = Nothing
716− }
717−
718−-- | The resulting status for this annotation operation.
719−bareStatus :: Lens' BatchAnnotationsResponseEntry (Maybe BatchAnnotationsResponseEntryStatus)
720−bareStatus
721− = lens _bareStatus (\ s a -> s{_bareStatus = a})
722−
723−-- | The annotation, if any.
724−bareAnnotation :: Lens' BatchAnnotationsResponseEntry (Maybe Annotation)
725−bareAnnotation
726− = lens _bareAnnotation
727− (\ s a -> s{_bareAnnotation = a})
728−
729−instance FromJSON BatchAnnotationsResponseEntry where
730− parseJSON
731− = withObject "BatchAnnotationsResponseEntry"
732− (\ o ->
733− BatchAnnotationsResponseEntry <$>
734− (o .:? "status") <*> (o .:? "annotation"))
735−
736−instance ToJSON BatchAnnotationsResponseEntry where
737− toJSON BatchAnnotationsResponseEntry{..}
738− = object
739− (catMaybes
740− [("status" .=) <$> _bareStatus,
741− ("annotation" .=) <$> _bareAnnotation])
742−
743344--
744345-- /See:/ 'listBasesResponse' smart constructor.
745346data ListBasesResponse = ListBasesResponse
@@ -775,9 +376,9 @@ lbrNextPageToken
775376 = lens _lbrNextPageToken
776377 (\ s a -> s{_lbrNextPageToken = a})
777378
778−-- | The offset position (0-based) of the given sequence from the start of
779−-- this Reference. This value will differ for each page in a paginated
780−-- request.
379+-- | The offset position (0-based) of the given \`sequence\` from the start
380+-- of this \`Reference\`. This value will differ for each page in a
381+-- paginated request.
781382lbrOffset :: Lens' ListBasesResponse (Maybe Int64)
782383lbrOffset
783384 = lens _lbrOffset (\ s a -> s{_lbrOffset = a})
@@ -803,64 +404,146 @@ instance ToJSON ListBasesResponse where
803404 ("offset" .=) <$> _lbrOffset,
804405 ("sequence" .=) <$> _lbrSequence])
805406
407+-- | The response message for Operations.ListOperations.
408+--
409+-- /See:/ 'listOperationsResponse' smart constructor.
410+data ListOperationsResponse = ListOperationsResponse
411+ { _lorNextPageToken :: !(Maybe Text)
412+ , _lorOperations :: !(Maybe [Operation])
413+ } deriving (Eq,Show,Data,Typeable,Generic)
414+
415+-- | Creates a value of 'ListOperationsResponse' with the minimum fields required to make a request.
416+--
417+-- Use one of the following lenses to modify other fields as desired:
418+--
419+-- * 'lorNextPageToken'
420+--
421+-- * 'lorOperations'
422+listOperationsResponse
423+ :: ListOperationsResponse
424+listOperationsResponse =
425+ ListOperationsResponse
426+ { _lorNextPageToken = Nothing
427+ , _lorOperations = Nothing
428+ }
429+
430+-- | The standard List next-page token.
431+lorNextPageToken :: Lens' ListOperationsResponse (Maybe Text)
432+lorNextPageToken
433+ = lens _lorNextPageToken
434+ (\ s a -> s{_lorNextPageToken = a})
435+
436+-- | A list of operations that matches the specified filter in the request.
437+lorOperations :: Lens' ListOperationsResponse [Operation]
438+lorOperations
439+ = lens _lorOperations
440+ (\ s a -> s{_lorOperations = a})
441+ . _Default
442+ . _Coerce
443+
444+instance FromJSON ListOperationsResponse where
445+ parseJSON
446+ = withObject "ListOperationsResponse"
447+ (\ o ->
448+ ListOperationsResponse <$>
449+ (o .:? "nextPageToken") <*>
450+ (o .:? "operations" .!= mempty))
451+
452+instance ToJSON ListOperationsResponse where
453+ toJSON ListOperationsResponse{..}
454+ = object
455+ (catMaybes
456+ [("nextPageToken" .=) <$> _lorNextPageToken,
457+ ("operations" .=) <$> _lorOperations])
458+
459+-- | Request message for \`GetIamPolicy\` method.
460+--
461+-- /See:/ 'getIAMPolicyRequest' smart constructor.
462+data GetIAMPolicyRequest =
463+ GetIAMPolicyRequest
464+ deriving (Eq,Show,Data,Typeable,Generic)
465+
466+-- | Creates a value of 'GetIAMPolicyRequest' with the minimum fields required to make a request.
467+--
468+getIAMPolicyRequest
469+ :: GetIAMPolicyRequest
470+getIAMPolicyRequest = GetIAMPolicyRequest
471+
472+instance FromJSON GetIAMPolicyRequest where
473+ parseJSON
474+ = withObject "GetIAMPolicyRequest"
475+ (\ o -> pure GetIAMPolicyRequest)
476+
477+instance ToJSON GetIAMPolicyRequest where
478+ toJSON = const emptyObject
479+
480+-- | The request message for Operations.CancelOperation.
481+--
482+-- /See:/ 'cancelOperationRequest' smart constructor.
483+data CancelOperationRequest =
484+ CancelOperationRequest
485+ deriving (Eq,Show,Data,Typeable,Generic)
486+
487+-- | Creates a value of 'CancelOperationRequest' with the minimum fields required to make a request.
488+--
489+cancelOperationRequest
490+ :: CancelOperationRequest
491+cancelOperationRequest = CancelOperationRequest
492+
493+instance FromJSON CancelOperationRequest where
494+ parseJSON
495+ = withObject "CancelOperationRequest"
496+ (\ o -> pure CancelOperationRequest)
497+
498+instance ToJSON CancelOperationRequest where
499+ toJSON = const emptyObject
500+
806501-- | A Dataset is a collection of genomic data.
807502--
808503-- /See:/ 'dataset' smart constructor.
809504data Dataset = Dataset
810− { _dIsPublic :: !(Maybe Bool)
811− , _dProjectNumber :: !(Maybe Int64)
812− , _dName :: !(Maybe Text)
813− , _dId :: !(Maybe Text)
814− , _dCreateTime :: !(Maybe Int64)
505+ { _dName :: !(Maybe Text)
506+ , _dId :: !(Maybe Text)
507+ , _dProjectId :: !(Maybe Text)
508+ , _dCreateTime :: !(Maybe Text)
815509 } deriving (Eq,Show,Data,Typeable,Generic)
816510
817511-- | Creates a value of 'Dataset' with the minimum fields required to make a request.
818512--
819513-- Use one of the following lenses to modify other fields as desired:
820514--
821−-- * 'dIsPublic'
822−--
823−-- * 'dProjectNumber'
824−--
825515-- * 'dName'
826516--
827517-- * 'dId'
828518--
519+-- * 'dProjectId'
520+--
829521-- * 'dCreateTime'
830522dataset
831523 :: Dataset
832524dataset =
833525 Dataset
834− { _dIsPublic = Nothing
835− , _dProjectNumber = Nothing
836− , _dName = Nothing
526+ { _dName = Nothing
837527 , _dId = Nothing
528+ , _dProjectId = Nothing
838529 , _dCreateTime = Nothing
839530 }
840531
841−-- | Flag indicating whether or not a dataset is publicly viewable. If a
842−-- dataset is not public, it inherits viewing permissions from its project.
843−dIsPublic :: Lens' Dataset (Maybe Bool)
844−dIsPublic
845− = lens _dIsPublic (\ s a -> s{_dIsPublic = a})
846−
847−-- | The Google Developers Console project number that this dataset belongs
848−-- to.
849−dProjectNumber :: Lens' Dataset (Maybe Int64)
850−dProjectNumber
851− = lens _dProjectNumber
852− (\ s a -> s{_dProjectNumber = a})
853−
854532-- | The dataset name.
855533dName :: Lens' Dataset (Maybe Text)
856534dName = lens _dName (\ s a -> s{_dName = a})
857535
858−-- | The Google generated ID of the dataset, immutable.
536+-- | The server-generated dataset ID, unique across all datasets.
859537dId :: Lens' Dataset (Maybe Text)
860538dId = lens _dId (\ s a -> s{_dId = a})
861539
540+-- | The Google Developers Console project ID that this dataset belongs to.
541+dProjectId :: Lens' Dataset (Maybe Text)
542+dProjectId
543+ = lens _dProjectId (\ s a -> s{_dProjectId = a})
544+
862545-- | The time this dataset was created, in seconds from the epoch.
863−dCreateTime :: Lens' Dataset (Maybe Int64)
546+dCreateTime :: Lens' Dataset (Maybe Text)
864547dCreateTime
865548 = lens _dCreateTime (\ s a -> s{_dCreateTime = a})
866549
@@ -869,25 +552,23 @@ instance FromJSON Dataset where
869552 = withObject "Dataset"
870553 (\ o ->
871554 Dataset <$>
872− (o .:? "isPublic") <*> (o .:? "projectNumber") <*>
873− (o .:? "name")
874− <*> (o .:? "id")
555+ (o .:? "name") <*> (o .:? "id") <*>
556+ (o .:? "projectId")
875557 <*> (o .:? "createTime"))
876558
877559instance ToJSON Dataset where
878560 toJSON Dataset{..}
879561 = object
880562 (catMaybes
881− [("isPublic" .=) <$> _dIsPublic,
882− ("projectNumber" .=) <$> _dProjectNumber,
883− ("name" .=) <$> _dName, ("id" .=) <$> _dId,
563+ [("name" .=) <$> _dName, ("id" .=) <$> _dId,
564+ ("projectId" .=) <$> _dProjectId,
884565 ("createTime" .=) <$> _dCreateTime])
885566
886567-- | A read alignment describes a linear alignment of a string of DNA to a
887568-- reference sequence, in addition to metadata about the fragment (the
888569-- molecule of DNA sequenced) and the read (the bases which were read by
889570-- the sequencer). A read is equivalent to a line in a SAM file. A read
890−-- belongs to exactly one read group and exactly one read group set.
571+-- belongs to exactly one read group and exactly one read group set. ###
891572-- Generating a reference-aligned sequence string When interacting with
892573-- mapped reads, it\'s often useful to produce a string representing the
893574-- local alignment of the read to reference. The following pseudocode
@@ -899,10 +580,10 @@ instance ToJSON Dataset where
899580-- c.operationLength break case \"PAD\": out += repeat(\"*\",
900581-- c.operationLength) break case \"DELETE\": out += repeat(\"-\",
901582-- c.operationLength) break case \"SKIP\": out += repeat(\" \",
902−-- c.operationLength) break case \"CLIP_HARD\": break } } return out
583+-- c.operationLength) break case \"CLIP_HARD\": break } } return out ###
903584-- Converting to SAM\'s CIGAR string The following pseudocode generates a
904−-- SAM CIGAR string from the cigar field. Note that this is a lossy
905−-- conversion (cigar.referenceSequence is lost). cigarMap = {
585+-- SAM CIGAR string from the \`cigar\` field. Note that this is a lossy
586+-- conversion (\`cigar.referenceSequence\` is lost). cigarMap = {
906587-- \"ALIGNMENT_MATCH\": \"M\", \"INSERT\": \"I\", \"DELETE\": \"D\",
907588-- \"SKIP\": \"N\", \"CLIP_SOFT\": \"S\", \"CLIP_HARD\": \"H\", \"PAD\":
908589-- \"P\", \"SEQUENCE_MATCH\": \"=\", \"SEQUENCE_MISMATCH\": \"X\", }
@@ -1009,10 +690,9 @@ rReadGroupSetId
1009690 = lens _rReadGroupSetId
1010691 (\ s a -> s{_rReadGroupSetId = a})
1011692
1012−-- | The position of the primary alignment of the (readNumber+1)%numberReads
1013−-- read in the fragment. It replaces mate position and mate strand in SAM.
1014−-- This field will be unset if that read is unmapped or if the fragment
1015−-- only has a single read.
693+-- | The mapping of the primary alignment of the
694+-- \`(readNumber+1)%numberReads\` read in the fragment. It replaces mate
695+-- position and mate strand in SAM.
1016696rNextMatePosition :: Lens' Read' (Maybe Position)
1017697rNextMatePosition
1018698 = lens _rNextMatePosition
@@ -1024,7 +704,7 @@ rFailedVendorQualityChecks
1024704 = lens _rFailedVendorQualityChecks
1025705 (\ s a -> s{_rFailedVendorQualityChecks = a})
1026706
1027−-- | The linear alignment for this alignment record. This field will be unset
707+-- | The linear alignment for this alignment record. This field will be null
1028708-- if the read is unmapped.
1029709rAlignment :: Lens' Read' (Maybe LinearAlignment)
1030710rAlignment
@@ -1041,8 +721,8 @@ rNumberReads :: Lens' Read' (Maybe Int32)
1041721rNumberReads
1042722 = lens _rNumberReads (\ s a -> s{_rNumberReads = a})
1043723
1044−-- | The unique ID for this read. This is a generated unique ID, not to be
1045−-- confused with fragmentName.
724+-- | The server-generated read ID, unique across all reads. This is different
725+-- from the \`fragmentName\`.
1046726rId :: Lens' Read' (Maybe Text)
1047727rId = lens _rId (\ s a -> s{_rId = a})
1048728
@@ -1050,8 +730,8 @@ rId = lens _rId (\ s a -> s{_rId = a})
1050730-- secondary alignment represents an alternative to the primary alignment
1051731-- for this read. Aligners may return secondary alignments if a read can
1052732-- map ambiguously to multiple coordinates in the genome. By convention,
1053−-- each read has one and only one alignment where both secondaryAlignment
1054−-- and supplementaryAlignment are false.
733+-- each read has one and only one alignment where both
734+-- \`secondaryAlignment\` and \`supplementaryAlignment\` are false.
1055735rSecondaryAlignment :: Lens' Read' (Maybe Bool)
1056736rSecondaryAlignment
1057737 = lens _rSecondaryAlignment
@@ -1071,21 +751,21 @@ rReadGroupId
1071751-- alignment; the remaining linear alignments will be designated as
1072752-- supplementary alignments. These alignments may have different mapping
1073753-- quality scores. In each linear alignment in a chimeric alignment, the
1074−-- read will be hard clipped. The alignedSequence and alignedQuality fields
1075−-- in the alignment record will only represent the bases for its respective
1076−-- linear alignment.
754+-- read will be hard clipped. The \`alignedSequence\` and
755+-- \`alignedQuality\` fields in the alignment record will only represent
756+-- the bases for its respective linear alignment.
1077757rSupplementaryAlignment :: Lens' Read' (Maybe Bool)
1078758rSupplementaryAlignment
1079759 = lens _rSupplementaryAlignment
1080760 (\ s a -> s{_rSupplementaryAlignment = a})
1081761
1082762-- | The bases of the read sequence contained in this alignment record,
1083−-- without CIGAR operations applied. alignedSequence and alignedQuality may
1084−-- be shorter than the full read sequence and quality. This will occur if
1085−-- the alignment is part of a chimeric alignment, or if the read was
1086−-- trimmed. When this occurs, the CIGAR for this read will begin\/end with
1087−-- a hard clip operator that will indicate the length of the excised
1088−-- sequence.
763+-- *without CIGAR operations applied*. \`alignedSequence\` and
764+-- \`alignedQuality\` may be shorter than the full read sequence and
765+-- quality. This will occur if the alignment is part of a chimeric
766+-- alignment, or if the read was trimmed. When this occurs, the CIGAR for
767+-- this read will begin\/end with a hard clip operator that will indicate
768+-- the length of the excised sequence.
1089769rAlignedSequence :: Lens' Read' (Maybe Text)
1090770rAlignedSequence
1091771 = lens _rAlignedSequence
@@ -1098,7 +778,8 @@ rProperPlacement
1098778 = lens _rProperPlacement
1099779 (\ s a -> s{_rProperPlacement = a})
1100780
1101−-- | A string which maps to an array of values.
781+-- | A map of additional read alignment information. This must be of the form
782+-- map (string key mapping to a list of string values).
1102783rInfo :: Lens' Read' (Maybe ReadInfo)
1103784rInfo = lens _rInfo (\ s a -> s{_rInfo = a})
1104785
@@ -1109,8 +790,8 @@ rReadNumber
1109790 = lens _rReadNumber (\ s a -> s{_rReadNumber = a})
1110791
1111792-- | The quality of the read sequence contained in this alignment record.
1112−-- alignedSequence and alignedQuality may be shorter than the full read
1113−-- sequence and quality. This will occur if the alignment is part of a
793+-- \`alignedSequence\` and \`alignedQuality\` may be shorter than the full
794+-- read sequence and quality. This will occur if the alignment is part of a
1114795-- chimeric alignment, or if the read was trimmed. When this occurs, the
1115796-- CIGAR for this read will begin\/end with a hard clip operator that will
1116797-- indicate the length of the excised sequence.
@@ -1168,112 +849,47 @@ instance ToJSON Read' where
1168849 ("readNumber" .=) <$> _rReadNumber,
1169850 ("alignedQuality" .=) <$> _rAlignedQuality])
1170851
1171−--
1172−-- /See:/ 'transcriptExon' smart constructor.
1173−data TranscriptExon = TranscriptExon
1174− { _teStart :: !(Maybe Int64)
1175− , _teEnd :: !(Maybe Int64)
1176− , _teFrame :: !(Maybe Int32Value)
1177− } deriving (Eq,Show,Data,Typeable,Generic)
1178−
1179−-- | Creates a value of 'TranscriptExon' with the minimum fields required to make a request.
1180−--
1181−-- Use one of the following lenses to modify other fields as desired:
1182−--
1183−-- * 'teStart'
1184−--
1185−-- * 'teEnd'
1186−--
1187−-- * 'teFrame'
1188−transcriptExon
1189− :: TranscriptExon
1190−transcriptExon =
1191− TranscriptExon
1192− { _teStart = Nothing
1193− , _teEnd = Nothing
1194− , _teFrame = Nothing
1195− }
1196−
1197−-- | The start position of the exon on this annotation\'s reference sequence,
1198−-- 0-based inclusive. Note that this is relative to the reference start,
1199−-- and not the containing annotation start.
1200−teStart :: Lens' TranscriptExon (Maybe Int64)
1201−teStart = lens _teStart (\ s a -> s{_teStart = a})
1202−
1203−-- | The end position of the exon on this annotation\'s reference sequence,
1204−-- 0-based exclusive. Note that this is relative to the reference start,
1205−-- and not the containing annotation start.
1206−teEnd :: Lens' TranscriptExon (Maybe Int64)
1207−teEnd = lens _teEnd (\ s a -> s{_teEnd = a})
1208−
1209−-- | The frame of this exon. Contains a value of 0, 1, or 2, which indicates
1210−-- the offset of the first coding base of the exon within the reading frame
1211−-- of the coding DNA sequence, if any. This field is dependent on the
1212−-- strandedness of this annotation (see Annotation.position.reverseStrand).
1213−-- For forward stranded annotations, this offset is relative to the
1214−-- exon.start. For reverse strand annotations, this offset is relative to
1215−-- the exon.end-1. Unset if this exon does not intersect the coding
1216−-- sequence. Upon creation of a transcript, the frame must be populated for
1217−-- all or none of the coding exons.
1218−teFrame :: Lens' TranscriptExon (Maybe Int32Value)
1219−teFrame = lens _teFrame (\ s a -> s{_teFrame = a})
1220−
1221−instance FromJSON TranscriptExon where
1222− parseJSON
1223− = withObject "TranscriptExon"
1224− (\ o ->
1225− TranscriptExon <$>
1226− (o .:? "start") <*> (o .:? "end") <*>
1227− (o .:? "frame"))
1228−
1229−instance ToJSON TranscriptExon where
1230− toJSON TranscriptExon{..}
1231− = object
1232− (catMaybes
1233− [("start" .=) <$> _teStart, ("end" .=) <$> _teEnd,
1234− ("frame" .=) <$> _teFrame])
1235−
1236852-- | A call represents the determination of genotype with respect to a
1237853-- particular variant. It may include associated information such as
1238854-- quality and phasing. For example, a call might assign a probability of
1239855-- 0.32 to the occurrence of a SNP named rs1234 in a call set with the name
1240856-- NA12345.
1241857--
1242−-- /See:/ 'call' smart constructor.
1243−data Call = Call
1244− { _cGenotypeLikelihood :: !(Maybe [Double])
1245− , _cCallSetName :: !(Maybe Text)
1246− , _cPhaseset :: !(Maybe Text)
1247− , _cCallSetId :: !(Maybe Text)
1248− , _cGenotype :: !(Maybe [Int32])
1249− , _cInfo :: !(Maybe CallInfo)
858+-- /See:/ 'variantCall' smart constructor.
859+data VariantCall = VariantCall
860+ { _vcGenotypeLikelihood :: !(Maybe [Double])
861+ , _vcCallSetName :: !(Maybe Text)
862+ , _vcPhaseset :: !(Maybe Text)
863+ , _vcCallSetId :: !(Maybe Text)
864+ , _vcGenotype :: !(Maybe [Int32])
865+ , _vcInfo :: !(Maybe VariantCallInfo)
1250866 } deriving (Eq,Show,Data,Typeable,Generic)
1251867
1252−-- | Creates a value of 'Call' with the minimum fields required to make a request.
868+-- | Creates a value of 'VariantCall' with the minimum fields required to make a request.
1253869--
1254870-- Use one of the following lenses to modify other fields as desired:
1255871--
1256−-- * 'cGenotypeLikelihood'
872+-- * 'vcGenotypeLikelihood'
1257873--
1258−-- * 'cCallSetName'
874+-- * 'vcCallSetName'
1259875--
1260−-- * 'cPhaseset'
876+-- * 'vcPhaseset'
1261877--
1262−-- * 'cCallSetId'
878+-- * 'vcCallSetId'
1263879--
1264−-- * 'cGenotype'
880+-- * 'vcGenotype'
1265881--
1266−-- * 'cInfo'
1267−call
1268− :: Call
1269−call =
1270− Call
1271− { _cGenotypeLikelihood = Nothing
1272− , _cCallSetName = Nothing
1273− , _cPhaseset = Nothing
1274− , _cCallSetId = Nothing
1275− , _cGenotype = Nothing
1276− , _cInfo = Nothing
882+-- * 'vcInfo'
883+variantCall
884+ :: VariantCall
885+variantCall =
886+ VariantCall
887+ { _vcGenotypeLikelihood = Nothing
888+ , _vcCallSetName = Nothing
889+ , _vcPhaseset = Nothing
890+ , _vcCallSetId = Nothing
891+ , _vcGenotype = Nothing
892+ , _vcInfo = Nothing
1277893 }
1278894
1279895-- | The genotype likelihoods for this variant call. Each array entry
@@ -1281,57 +897,60 @@ call =
1281897-- ordering is defined by the GL tag in the VCF spec. If Phred-scaled
1282898-- genotype likelihood scores (PL) are available and log10(P) genotype
1283899-- likelihood scores (GL) are not, PL scores are converted to GL scores. If
1284−-- both are available, PL scores are stored in info.
1285−cGenotypeLikelihood :: Lens' Call [Double]
1286−cGenotypeLikelihood
1287− = lens _cGenotypeLikelihood
1288− (\ s a -> s{_cGenotypeLikelihood = a})
900+-- both are available, PL scores are stored in \`info\`.
901+vcGenotypeLikelihood :: Lens' VariantCall [Double]
902+vcGenotypeLikelihood
903+ = lens _vcGenotypeLikelihood
904+ (\ s a -> s{_vcGenotypeLikelihood = a})
1289905 . _Default
1290906 . _Coerce
1291907
1292908-- | The name of the call set this variant call belongs to.
1293−cCallSetName :: Lens' Call (Maybe Text)
1294−cCallSetName
1295− = lens _cCallSetName (\ s a -> s{_cCallSetName = a})
909+vcCallSetName :: Lens' VariantCall (Maybe Text)
910+vcCallSetName
911+ = lens _vcCallSetName
912+ (\ s a -> s{_vcCallSetName = a})
1296913
1297914-- | If this field is present, this variant call\'s genotype ordering implies
1298915-- the phase of the bases and is consistent with any other variant calls in
1299916-- the same reference sequence which have the same phaseset value. When
1300917-- importing data from VCF, if the genotype data was phased but no phase
1301−-- set was specified this field will be set to *.
1302−cPhaseset :: Lens' Call (Maybe Text)
1303−cPhaseset
1304− = lens _cPhaseset (\ s a -> s{_cPhaseset = a})
918+-- set was specified this field will be set to \`*\`.
919+vcPhaseset :: Lens' VariantCall (Maybe Text)
920+vcPhaseset
921+ = lens _vcPhaseset (\ s a -> s{_vcPhaseset = a})
1305922
1306923-- | The ID of the call set this variant call belongs to.
1307−cCallSetId :: Lens' Call (Maybe Text)
1308−cCallSetId
1309− = lens _cCallSetId (\ s a -> s{_cCallSetId = a})
924+vcCallSetId :: Lens' VariantCall (Maybe Text)
925+vcCallSetId
926+ = lens _vcCallSetId (\ s a -> s{_vcCallSetId = a})
1310927
1311928-- | The genotype of this variant call. Each value represents either the
1312−-- value of the referenceBases field or a 1-based index into
1313−-- alternateBases. If a variant had a referenceBases value of T and an
1314−-- alternateBases value of [\"A\", \"C\"], and the genotype was [2, 1],
1315−-- that would mean the call represented the heterozygous value CA for this
1316−-- variant. If the genotype was instead [0, 1], the represented value would
1317−-- be TA. Ordering of the genotype values is important if the phaseset is
1318−-- present. If a genotype is not called (that is, a . is present in the GT
1319−-- string) -1 is returned.
1320−cGenotype :: Lens' Call [Int32]
1321−cGenotype
1322− = lens _cGenotype (\ s a -> s{_cGenotype = a}) .
929+-- value of the \`referenceBases\` field or a 1-based index into
930+-- \`alternateBases\`. If a variant had a \`referenceBases\` value of \`T\`
931+-- and an \`alternateBases\` value of \`[\"A\", \"C\"]\`, and the
932+-- \`genotype\` was \`[2, 1]\`, that would mean the call represented the
933+-- heterozygous value \`CA\` for this variant. If the \`genotype\` was
934+-- instead \`[0, 1]\`, the represented value would be \`TA\`. Ordering of
935+-- the genotype values is important if the \`phaseset\` is present. If a
936+-- genotype is not called (that is, a \`.\` is present in the GT string) -1
937+-- is returned.
938+vcGenotype :: Lens' VariantCall [Int32]
939+vcGenotype
940+ = lens _vcGenotype (\ s a -> s{_vcGenotype = a}) .
1323941 _Default
1324942 . _Coerce
1325943
1326−-- | A string which maps to an array of values.
1327−cInfo :: Lens' Call (Maybe CallInfo)
1328−cInfo = lens _cInfo (\ s a -> s{_cInfo = a})
944+-- | A map of additional variant call information. This must be of the form
945+-- map (string key mapping to a list of string values).
946+vcInfo :: Lens' VariantCall (Maybe VariantCallInfo)
947+vcInfo = lens _vcInfo (\ s a -> s{_vcInfo = a})
1329948
1330−instance FromJSON Call where
949+instance FromJSON VariantCall where
1331950 parseJSON
1332− = withObject "Call"
951+ = withObject "VariantCall"
1333952 (\ o ->
1334− Call <$>
953+ VariantCall <$>
1335954 (o .:? "genotypeLikelihood" .!= mempty) <*>
1336955 (o .:? "callSetName")
1337956 <*> (o .:? "phaseset")
@@ -1339,168 +958,16 @@ instance FromJSON Call where
1339958 <*> (o .:? "genotype" .!= mempty)
1340959 <*> (o .:? "info"))
1341960
1342−instance ToJSON Call where
1343− toJSON Call{..}
1344− = object
1345− (catMaybes
1346− [("genotypeLikelihood" .=) <$> _cGenotypeLikelihood,
1347− ("callSetName" .=) <$> _cCallSetName,
1348− ("phaseset" .=) <$> _cPhaseset,
1349− ("callSetId" .=) <$> _cCallSetId,
1350− ("genotype" .=) <$> _cGenotype,
1351− ("info" .=) <$> _cInfo])
1352−
1353−-- | A 0-based half-open genomic coordinate range for search requests.
1354−--
1355−-- /See:/ 'queryRange' smart constructor.
1356−data QueryRange = QueryRange
1357− { _qrStart :: !(Maybe Int64)
1358− , _qrReferenceId :: !(Maybe Text)
1359− , _qrReferenceName :: !(Maybe Text)
1360− , _qrEnd :: !(Maybe Int64)
1361− } deriving (Eq,Show,Data,Typeable,Generic)
1362−
1363−-- | Creates a value of 'QueryRange' with the minimum fields required to make a request.
1364−--
1365−-- Use one of the following lenses to modify other fields as desired:
1366−--
1367−-- * 'qrStart'
1368−--
1369−-- * 'qrReferenceId'
1370−--
1371−-- * 'qrReferenceName'
1372−--
1373−-- * 'qrEnd'
1374−queryRange
1375− :: QueryRange
1376−queryRange =
1377− QueryRange
1378− { _qrStart = Nothing
1379− , _qrReferenceId = Nothing
1380− , _qrReferenceName = Nothing
1381− , _qrEnd = Nothing
1382− }
1383−
1384−-- | The start position of the range on the reference, 0-based inclusive. If
1385−-- specified, referenceId or referenceName must also be specified. Defaults
1386−-- to 0.
1387−qrStart :: Lens' QueryRange (Maybe Int64)
1388−qrStart = lens _qrStart (\ s a -> s{_qrStart = a})
1389−
1390−-- | The ID of the reference to query. At most one of referenceId and
1391−-- referenceName should be specified.
1392−qrReferenceId :: Lens' QueryRange (Maybe Text)
1393−qrReferenceId
1394− = lens _qrReferenceId
1395− (\ s a -> s{_qrReferenceId = a})
1396−
1397−-- | The name of the reference to query, within the reference set associated
1398−-- with this query. At most one of referenceId and referenceName pshould be
1399−-- specified.
1400−qrReferenceName :: Lens' QueryRange (Maybe Text)
1401−qrReferenceName
1402− = lens _qrReferenceName
1403− (\ s a -> s{_qrReferenceName = a})
1404−
1405−-- | The end position of the range on the reference, 0-based exclusive. If
1406−-- specified, referenceId or referenceName must also be specified. If unset
1407−-- or 0, defaults to the length of the reference.
1408−qrEnd :: Lens' QueryRange (Maybe Int64)
1409−qrEnd = lens _qrEnd (\ s a -> s{_qrEnd = a})
1410−
1411−instance FromJSON QueryRange where
1412− parseJSON
1413− = withObject "QueryRange"
1414− (\ o ->
1415− QueryRange <$>
1416− (o .:? "start") <*> (o .:? "referenceId") <*>
1417− (o .:? "referenceName")
1418− <*> (o .:? "end"))
1419−
1420−instance ToJSON QueryRange where
1421− toJSON QueryRange{..}
961+instance ToJSON VariantCall where
962+ toJSON VariantCall{..}
1422963 = object
1423964 (catMaybes
1424− [("start" .=) <$> _qrStart,
1425− ("referenceId" .=) <$> _qrReferenceId,
1426− ("referenceName" .=) <$> _qrReferenceName,
1427− ("end" .=) <$> _qrEnd])
1428−
1429−--
1430−-- /See:/ 'batchCreateAnnotationsRequest' smart constructor.
1431−newtype BatchCreateAnnotationsRequest = BatchCreateAnnotationsRequest
1432− { _bcarAnnotations :: Maybe [Annotation]
1433− } deriving (Eq,Show,Data,Typeable,Generic)
1434−
1435−-- | Creates a value of 'BatchCreateAnnotationsRequest' with the minimum fields required to make a request.
1436−--
1437−-- Use one of the following lenses to modify other fields as desired:
1438−--
1439−-- * 'bcarAnnotations'
1440−batchCreateAnnotationsRequest
1441− :: BatchCreateAnnotationsRequest
1442−batchCreateAnnotationsRequest =
1443− BatchCreateAnnotationsRequest
1444− { _bcarAnnotations = Nothing
1445− }
1446−
1447−-- | The annotations to be created. At most 4096 can be specified in a single
1448−-- request.
1449−bcarAnnotations :: Lens' BatchCreateAnnotationsRequest [Annotation]
1450−bcarAnnotations
1451− = lens _bcarAnnotations
1452− (\ s a -> s{_bcarAnnotations = a})
1453− . _Default
1454− . _Coerce
1455−
1456−instance FromJSON BatchCreateAnnotationsRequest where
1457− parseJSON
1458− = withObject "BatchCreateAnnotationsRequest"
1459− (\ o ->
1460− BatchCreateAnnotationsRequest <$>
1461− (o .:? "annotations" .!= mempty))
1462−
1463−instance ToJSON BatchCreateAnnotationsRequest where
1464− toJSON BatchCreateAnnotationsRequest{..}
1465− = object
1466− (catMaybes [("annotations" .=) <$> _bcarAnnotations])
1467−
1468−--
1469−-- /See:/ 'mergeVariantsRequest' smart constructor.
1470−newtype MergeVariantsRequest = MergeVariantsRequest
1471− { _mvrVariants :: Maybe [Variant]
1472− } deriving (Eq,Show,Data,Typeable,Generic)
1473−
1474−-- | Creates a value of 'MergeVariantsRequest' with the minimum fields required to make a request.
1475−--
1476−-- Use one of the following lenses to modify other fields as desired:
1477−--
1478−-- * 'mvrVariants'
1479−mergeVariantsRequest
1480− :: MergeVariantsRequest
1481−mergeVariantsRequest =
1482− MergeVariantsRequest
1483− { _mvrVariants = Nothing
1484− }
1485−
1486−-- | The variants to be merged with existing variants.
1487−mvrVariants :: Lens' MergeVariantsRequest [Variant]
1488−mvrVariants
1489− = lens _mvrVariants (\ s a -> s{_mvrVariants = a}) .
1490− _Default
1491− . _Coerce
1492−
1493−instance FromJSON MergeVariantsRequest where
1494− parseJSON
1495− = withObject "MergeVariantsRequest"
1496− (\ o ->
1497− MergeVariantsRequest <$>
1498− (o .:? "variants" .!= mempty))
1499−
1500−instance ToJSON MergeVariantsRequest where
1501− toJSON MergeVariantsRequest{..}
1502− = object
1503− (catMaybes [("variants" .=) <$> _mvrVariants])
965+ [("genotypeLikelihood" .=) <$> _vcGenotypeLikelihood,
966+ ("callSetName" .=) <$> _vcCallSetName,
967+ ("phaseset" .=) <$> _vcPhaseset,
968+ ("callSetId" .=) <$> _vcCallSetId,
969+ ("genotype" .=) <$> _vcGenotype,
970+ ("info" .=) <$> _vcInfo])
1504971
1505972-- | A read group is all the data that\'s processed the same way by the
1506973-- sequencer.
@@ -1508,8 +975,8 @@ instance ToJSON MergeVariantsRequest where
1508975-- /See:/ 'readGroup' smart constructor.
1509976data ReadGroup = ReadGroup
1510977 { _rgReferenceSetId :: !(Maybe Text)
1511− , _rgPrograms :: !(Maybe [ReadGroupProgram])
1512− , _rgExperiment :: !(Maybe ReadGroupExperiment)
978+ , _rgPrograms :: !(Maybe [Program])
979+ , _rgExperiment :: !(Maybe Experiment)
1513980 , _rgName :: !(Maybe Text)
1514981 , _rgDatasetId :: !(Maybe Text)
1515982 , _rgId :: !(Maybe Text)
@@ -1569,14 +1036,14 @@ rgReferenceSetId
15691036-- identical for all read groups within a read group set. For this reason,
15701037-- only the first read group in a returned set will have this field
15711038-- populated.
1572−rgPrograms :: Lens' ReadGroup [ReadGroupProgram]
1039+rgPrograms :: Lens' ReadGroup [Program]
15731040rgPrograms
15741041 = lens _rgPrograms (\ s a -> s{_rgPrograms = a}) .
15751042 _Default
15761043 . _Coerce
15771044
15781045-- | The experiment used to generate this read group.
1579−rgExperiment :: Lens' ReadGroup (Maybe ReadGroupExperiment)
1046+rgExperiment :: Lens' ReadGroup (Maybe Experiment)
15801047rgExperiment
15811048 = lens _rgExperiment (\ s a -> s{_rgExperiment = a})
15821049
@@ -1590,8 +1057,9 @@ rgDatasetId :: Lens' ReadGroup (Maybe Text)
15901057rgDatasetId
15911058 = lens _rgDatasetId (\ s a -> s{_rgDatasetId = a})
15921059
1593−-- | The generated unique read group ID. Note: This is different than the
1594−-- \'RG ID field in the SAM spec. For that value, see the name field.
1060+-- | The server-generated read group ID, unique for all read groups. Note:
1061+-- This is different than the \`\'RG ID\` field in the SAM spec. For that
1062+-- value, see the \`name\` field.
15951063rgId :: Lens' ReadGroup (Maybe Text)
15961064rgId = lens _rgId (\ s a -> s{_rgId = a})
15971065
@@ -1616,7 +1084,8 @@ rgDescription
16161084 = lens _rgDescription
16171085 (\ s a -> s{_rgDescription = a})
16181086
1619−-- | A string which maps to an array of values.
1087+-- | A map of additional read group information. This must be of the form map
1088+-- (string key mapping to a list of string values).
16201089rgInfo :: Lens' ReadGroup (Maybe ReadGroupInfo)
16211090rgInfo = lens _rgInfo (\ s a -> s{_rgInfo = a})
16221091
@@ -1651,24 +1120,107 @@ instance ToJSON ReadGroup where
16511120 ("description" .=) <$> _rgDescription,
16521121 ("info" .=) <$> _rgInfo])
16531122
1654−-- |
1123+-- | This resource represents a long-running operation that is the result of
1124+-- a network API call.
16551125--
1656−-- /See:/ 'searchReferenceSetsRequest' smart constructor.
1657−data SearchReferenceSetsRequest = SearchReferenceSetsRequest
1658− { _srsrMD5checksums :: !(Maybe [Text])
1659− , _srsrAccessions :: !(Maybe [Text])
1660− , _srsrPageToken :: !(Maybe Text)
1661− , _srsrAssemblyId :: !(Maybe Text)
1662− , _srsrPageSize :: !(Maybe Int32)
1126+-- /See:/ 'operation' smart constructor.
1127+data Operation = Operation
1128+ { _oDone :: !(Maybe Bool)
1129+ , _oError :: !(Maybe Status)
1130+ , _oResponse :: !(Maybe OperationResponse)
1131+ , _oName :: !(Maybe Text)
1132+ , _oMetadata :: !(Maybe OperationSchema)
16631133 } deriving (Eq,Show,Data,Typeable,Generic)
16641134
1665−-- | Creates a value of 'SearchReferenceSetsRequest' with the minimum fields required to make a request.
1135+-- | Creates a value of 'Operation' with the minimum fields required to make a request.
16661136--
16671137-- Use one of the following lenses to modify other fields as desired:
16681138--
1669−-- * 'srsrMD5checksums'
1139+-- * 'oDone'
16701140--
1671−-- * 'srsrAccessions'
1141+-- * 'oError'
1142+--
1143+-- * 'oResponse'
1144+--
1145+-- * 'oName'
1146+--
1147+-- * 'oMetadata'
1148+operation
1149+ :: Operation
1150+operation =
1151+ Operation
1152+ { _oDone = Nothing
1153+ , _oError = Nothing
1154+ , _oResponse = Nothing
1155+ , _oName = Nothing
1156+ , _oMetadata = Nothing
1157+ }
1158+
1159+-- | If the value is \`false\`, it means the operation is still in progress.
1160+-- If true, the operation is completed, and either \`error\` or
1161+-- \`response\` is available.
1162+oDone :: Lens' Operation (Maybe Bool)
1163+oDone = lens _oDone (\ s a -> s{_oDone = a})
1164+
1165+-- | The error result of the operation in case of failure.
1166+oError :: Lens' Operation (Maybe Status)
1167+oError = lens _oError (\ s a -> s{_oError = a})
1168+
1169+-- | If importing ReadGroupSets, an ImportReadGroupSetsResponse is returned.
1170+-- If importing Variants, an ImportVariantsResponse is returned. For
1171+-- exports, an empty response is returned.
1172+oResponse :: Lens' Operation (Maybe OperationResponse)
1173+oResponse
1174+ = lens _oResponse (\ s a -> s{_oResponse = a})
1175+
1176+-- | The server-assigned name, which is only unique within the same service
1177+-- that originally returns it. For example:
1178+-- \`operations\/CJHU7Oi_ChDrveSpBRjfuL-qzoWAgEw\`
1179+oName :: Lens' Operation (Maybe Text)
1180+oName = lens _oName (\ s a -> s{_oName = a})
1181+
1182+-- | An OperationMetadata object. This will always be returned with the
1183+-- Operation.
1184+oMetadata :: Lens' Operation (Maybe OperationSchema)
1185+oMetadata
1186+ = lens _oMetadata (\ s a -> s{_oMetadata = a})
1187+
1188+instance FromJSON Operation where
1189+ parseJSON
1190+ = withObject "Operation"
1191+ (\ o ->
1192+ Operation <$>
1193+ (o .:? "done") <*> (o .:? "error") <*>
1194+ (o .:? "response")
1195+ <*> (o .:? "name")
1196+ <*> (o .:? "metadata"))
1197+
1198+instance ToJSON Operation where
1199+ toJSON Operation{..}
1200+ = object
1201+ (catMaybes
1202+ [("done" .=) <$> _oDone, ("error" .=) <$> _oError,
1203+ ("response" .=) <$> _oResponse,
1204+ ("name" .=) <$> _oName,
1205+ ("metadata" .=) <$> _oMetadata])
1206+
1207+--
1208+-- /See:/ 'searchReferenceSetsRequest' smart constructor.
1209+data SearchReferenceSetsRequest = SearchReferenceSetsRequest
1210+ { _srsrMD5checksums :: !(Maybe [Text])
1211+ , _srsrAccessions :: !(Maybe [Text])
1212+ , _srsrPageToken :: !(Maybe Text)
1213+ , _srsrAssemblyId :: !(Maybe Text)
1214+ , _srsrPageSize :: !(Maybe Int32)
1215+ } deriving (Eq,Show,Data,Typeable,Generic)
1216+
1217+-- | Creates a value of 'SearchReferenceSetsRequest' with the minimum fields required to make a request.
1218+--
1219+-- Use one of the following lenses to modify other fields as desired:
1220+--
1221+-- * 'srsrMD5checksums'
1222+--
1223+-- * 'srsrAccessions'
16721224--
16731225-- * 'srsrPageToken'
16741226--
@@ -1686,8 +1238,8 @@ searchReferenceSetsRequest =
16861238 , _srsrPageSize = Nothing
16871239 }
16881240
1689−-- | If present, return references for which the md5checksum matches. See
1690−-- ReferenceSet.md5checksum for details.
1241+-- | If present, return references for which the \`md5checksum\` matches. See
1242+-- \`ReferenceSet.md5checksum\` for details.
16911243srsrMD5checksums :: Lens' SearchReferenceSetsRequest [Text]
16921244srsrMD5checksums
16931245 = lens _srsrMD5checksums
@@ -1697,9 +1249,9 @@ srsrMD5checksums
16971249
16981250-- | If present, return references for which the accession matches any of
16991251-- these strings. Best to give a version number, for example
1700−-- GCF_000001405.26. If only the main accession number is given then all
1701−-- records with that main accession will be returned, whichever version.
1702−-- Note that different versions will have different sequences.
1252+-- \`GCF_000001405.26\`. If only the main accession number is given then
1253+-- all records with that main accession will be returned, whichever
1254+-- version. Note that different versions will have different sequences.
17031255srsrAccessions :: Lens' SearchReferenceSetsRequest [Text]
17041256srsrAccessions
17051257 = lens _srsrAccessions
@@ -1709,14 +1261,14 @@ srsrAccessions
17091261
17101262-- | The continuation token, which is used to page through large result sets.
17111263-- To get the next page of results, set this parameter to the value of
1712−-- nextPageToken from the previous response.
1264+-- \`nextPageToken\` from the previous response.
17131265srsrPageToken :: Lens' SearchReferenceSetsRequest (Maybe Text)
17141266srsrPageToken
17151267 = lens _srsrPageToken
17161268 (\ s a -> s{_srsrPageToken = a})
17171269
17181270-- | If present, return reference sets for which a substring of their
1719−-- assemblyId matches this string (case insensitive).
1271+-- \`assemblyId\` matches this string (case insensitive).
17201272srsrAssemblyId :: Lens' SearchReferenceSetsRequest (Maybe Text)
17211273srsrAssemblyId
17221274 = lens _srsrAssemblyId
@@ -1748,6 +1300,29 @@ instance ToJSON SearchReferenceSetsRequest where
17481300 ("assemblyId" .=) <$> _srsrAssemblyId,
17491301 ("pageSize" .=) <$> _srsrPageSize])
17501302
1303+-- | A generic empty message that you can re-use to avoid defining duplicated
1304+-- empty messages in your APIs. A typical example is to use it as the
1305+-- request or the response type of an API method. For instance: service Foo
1306+-- { rpc Bar(google.protobuf.Empty) returns (google.protobuf.Empty); } The
1307+-- JSON representation for \`Empty\` is empty JSON object \`{}\`.
1308+--
1309+-- /See:/ 'empty' smart constructor.
1310+data Empty =
1311+ Empty
1312+ deriving (Eq,Show,Data,Typeable,Generic)
1313+
1314+-- | Creates a value of 'Empty' with the minimum fields required to make a request.
1315+--
1316+empty
1317+ :: Empty
1318+empty = Empty
1319+
1320+instance FromJSON Empty where
1321+ parseJSON = withObject "Empty" (\ o -> pure Empty)
1322+
1323+instance ToJSON Empty where
1324+ toJSON = const emptyObject
1325+
17511326--
17521327-- /See:/ 'searchReferencesResponse' smart constructor.
17531328data SearchReferencesResponse = SearchReferencesResponse
@@ -1802,6 +1377,108 @@ instance ToJSON SearchReferencesResponse where
18021377 [("nextPageToken" .=) <$> _srrNextPageToken,
18031378 ("references" .=) <$> _srrReferences])
18041379
1380+-- | Metadata describes a single piece of variant call metadata. These data
1381+-- include a top level key and either a single value string (value) or a
1382+-- list of key-value pairs (info.) Value and info are mutually exclusive.
1383+--
1384+-- /See:/ 'variantSetMetadata' smart constructor.
1385+data VariantSetMetadata = VariantSetMetadata
1386+ { _vsmValue :: !(Maybe Text)
1387+ , _vsmKey :: !(Maybe Text)
1388+ , _vsmId :: !(Maybe Text)
1389+ , _vsmType :: !(Maybe Text)
1390+ , _vsmNumber :: !(Maybe Text)
1391+ , _vsmDescription :: !(Maybe Text)
1392+ , _vsmInfo :: !(Maybe VariantSetMetadataInfo)
1393+ } deriving (Eq,Show,Data,Typeable,Generic)
1394+
1395+-- | Creates a value of 'VariantSetMetadata' with the minimum fields required to make a request.
1396+--
1397+-- Use one of the following lenses to modify other fields as desired:
1398+--
1399+-- * 'vsmValue'
1400+--
1401+-- * 'vsmKey'
1402+--
1403+-- * 'vsmId'
1404+--
1405+-- * 'vsmType'
1406+--
1407+-- * 'vsmNumber'
1408+--
1409+-- * 'vsmDescription'
1410+--
1411+-- * 'vsmInfo'
1412+variantSetMetadata
1413+ :: VariantSetMetadata
1414+variantSetMetadata =
1415+ VariantSetMetadata
1416+ { _vsmValue = Nothing
1417+ , _vsmKey = Nothing
1418+ , _vsmId = Nothing
1419+ , _vsmType = Nothing
1420+ , _vsmNumber = Nothing
1421+ , _vsmDescription = Nothing
1422+ , _vsmInfo = Nothing
1423+ }
1424+
1425+-- | The value field for simple metadata
1426+vsmValue :: Lens' VariantSetMetadata (Maybe Text)
1427+vsmValue = lens _vsmValue (\ s a -> s{_vsmValue = a})
1428+
1429+-- | The top-level key.
1430+vsmKey :: Lens' VariantSetMetadata (Maybe Text)
1431+vsmKey = lens _vsmKey (\ s a -> s{_vsmKey = a})
1432+
1433+-- | User-provided ID field, not enforced by this API. Two or more pieces of
1434+-- structured metadata with identical id and key fields are considered
1435+-- equivalent.
1436+vsmId :: Lens' VariantSetMetadata (Maybe Text)
1437+vsmId = lens _vsmId (\ s a -> s{_vsmId = a})
1438+
1439+-- | The type of data. Possible types include: Integer, Float, Flag,
1440+-- Character, and String.
1441+vsmType :: Lens' VariantSetMetadata (Maybe Text)
1442+vsmType = lens _vsmType (\ s a -> s{_vsmType = a})
1443+
1444+-- | The number of values that can be included in a field described by this
1445+-- metadata.
1446+vsmNumber :: Lens' VariantSetMetadata (Maybe Text)
1447+vsmNumber
1448+ = lens _vsmNumber (\ s a -> s{_vsmNumber = a})
1449+
1450+-- | A textual description of this metadata.
1451+vsmDescription :: Lens' VariantSetMetadata (Maybe Text)
1452+vsmDescription
1453+ = lens _vsmDescription
1454+ (\ s a -> s{_vsmDescription = a})
1455+
1456+-- | Remaining structured metadata key-value pairs. This must be of the form
1457+-- map (string key mapping to a list of string values).
1458+vsmInfo :: Lens' VariantSetMetadata (Maybe VariantSetMetadataInfo)
1459+vsmInfo = lens _vsmInfo (\ s a -> s{_vsmInfo = a})
1460+
1461+instance FromJSON VariantSetMetadata where
1462+ parseJSON
1463+ = withObject "VariantSetMetadata"
1464+ (\ o ->
1465+ VariantSetMetadata <$>
1466+ (o .:? "value") <*> (o .:? "key") <*> (o .:? "id")
1467+ <*> (o .:? "type")
1468+ <*> (o .:? "number")
1469+ <*> (o .:? "description")
1470+ <*> (o .:? "info"))
1471+
1472+instance ToJSON VariantSetMetadata where
1473+ toJSON VariantSetMetadata{..}
1474+ = object
1475+ (catMaybes
1476+ [("value" .=) <$> _vsmValue, ("key" .=) <$> _vsmKey,
1477+ ("id" .=) <$> _vsmId, ("type" .=) <$> _vsmType,
1478+ ("number" .=) <$> _vsmNumber,
1479+ ("description" .=) <$> _vsmDescription,
1480+ ("info" .=) <$> _vsmInfo])
1481+
18051482-- | A call set is a collection of variant calls, typically for one sample.
18061483-- It belongs to a variant set.
18071484--
@@ -1851,7 +1528,7 @@ csCreated
18511528csName :: Lens' CallSet (Maybe Text)
18521529csName = lens _csName (\ s a -> s{_csName = a})
18531530
1854−-- | The Google generated ID of the call set, immutable.
1531+-- | The server-generated call set ID, unique across all call sets.
18551532csId :: Lens' CallSet (Maybe Text)
18561533csId = lens _csId (\ s a -> s{_csId = a})
18571534
@@ -1860,7 +1537,10 @@ csSampleId :: Lens' CallSet (Maybe Text)
18601537csSampleId
18611538 = lens _csSampleId (\ s a -> s{_csSampleId = a})
18621539
1863−-- | The IDs of the variant sets this call set belongs to.
1540+-- | The IDs of the variant sets this call set belongs to. This field must
1541+-- have exactly length one, as a call set belongs to a single variant set.
1542+-- This field is repeated for compatibility with the [GA4GH 0.5.1
1543+-- API](https:\/\/github.com\/ga4gh\/schemas\/blob\/v0.5.1\/src\/main\/resources\/avro\/variants.avdl#L76).
18641544csVariantSetIds :: Lens' CallSet [Text]
18651545csVariantSetIds
18661546 = lens _csVariantSetIds
@@ -1868,7 +1548,8 @@ csVariantSetIds
18681548 . _Default
18691549 . _Coerce
18701550
1871−-- | A string which maps to an array of values.
1551+-- | A map of additional call set information. This must be of the form map
1552+-- (string key mapping to a list of string values).
18721553csInfo :: Lens' CallSet (Maybe CallSetInfo)
18731554csInfo = lens _csInfo (\ s a -> s{_csInfo = a})
18741555
@@ -1941,120 +1622,6 @@ instance ToJSON CoverageBucket where
19411622 [("range" .=) <$> _cbRange,
19421623 ("meanCoverage" .=) <$> _cbMeanCoverage])
19431624
1944−-- | A Variant annotation.
1945−--
1946−-- /See:/ 'variantAnnotation' smart constructor.
1947−data VariantAnnotation = VariantAnnotation
1948− { _vaEffect :: !(Maybe VariantAnnotationEffect)
1949− , _vaClinicalSignificance :: !(Maybe VariantAnnotationClinicalSignificance)
1950− , _vaAlternateBases :: !(Maybe Text)
1951− , _vaGeneId :: !(Maybe Text)
1952− , _vaConditions :: !(Maybe [VariantAnnotationCondition])
1953− , _vaType :: !(Maybe VariantAnnotationType)
1954− , _vaTranscriptIds :: !(Maybe [Text])
1955− } deriving (Eq,Show,Data,Typeable,Generic)
1956−
1957−-- | Creates a value of 'VariantAnnotation' with the minimum fields required to make a request.
1958−--
1959−-- Use one of the following lenses to modify other fields as desired:
1960−--
1961−-- * 'vaEffect'
1962−--
1963−-- * 'vaClinicalSignificance'
1964−--
1965−-- * 'vaAlternateBases'
1966−--
1967−-- * 'vaGeneId'
1968−--
1969−-- * 'vaConditions'
1970−--
1971−-- * 'vaType'
1972−--
1973−-- * 'vaTranscriptIds'
1974−variantAnnotation
1975− :: VariantAnnotation
1976−variantAnnotation =
1977− VariantAnnotation
1978− { _vaEffect = Nothing
1979− , _vaClinicalSignificance = Nothing
1980− , _vaAlternateBases = Nothing
1981− , _vaGeneId = Nothing
1982− , _vaConditions = Nothing
1983− , _vaType = Nothing
1984− , _vaTranscriptIds = Nothing
1985− }
1986−
1987−-- | Effect of the variant on the coding sequence.
1988−vaEffect :: Lens' VariantAnnotation (Maybe VariantAnnotationEffect)
1989−vaEffect = lens _vaEffect (\ s a -> s{_vaEffect = a})
1990−
1991−-- | Describes the clinical significance of a variant. It is adapted from the
1992−-- ClinVar controlled vocabulary for clinical significance described at:
1993−-- http:\/\/www.ncbi.nlm.nih.gov\/clinvar\/docs\/clinsig\/
1994−vaClinicalSignificance :: Lens' VariantAnnotation (Maybe VariantAnnotationClinicalSignificance)
1995−vaClinicalSignificance
1996− = lens _vaClinicalSignificance
1997− (\ s a -> s{_vaClinicalSignificance = a})
1998−
1999−-- | The alternate allele for this variant. If multiple alternate alleles
2000−-- exist at this location, create a separate variant for each one, as they
2001−-- may represent distinct conditions.
2002−vaAlternateBases :: Lens' VariantAnnotation (Maybe Text)
2003−vaAlternateBases
2004− = lens _vaAlternateBases
2005− (\ s a -> s{_vaAlternateBases = a})
2006−
2007−-- | Google annotation ID of the gene affected by this variant. This should
2008−-- be provided when the variant is created.
2009−vaGeneId :: Lens' VariantAnnotation (Maybe Text)
2010−vaGeneId = lens _vaGeneId (\ s a -> s{_vaGeneId = a})
2011−
2012−-- | The set of conditions associated with this variant. A condition
2013−-- describes the way a variant influences human health.
2014−vaConditions :: Lens' VariantAnnotation [VariantAnnotationCondition]
2015−vaConditions
2016− = lens _vaConditions (\ s a -> s{_vaConditions = a})
2017− . _Default
2018− . _Coerce
2019−
2020−-- | Type has been adapted from ClinVar\'s list of variant types.
2021−vaType :: Lens' VariantAnnotation (Maybe VariantAnnotationType)
2022−vaType = lens _vaType (\ s a -> s{_vaType = a})
2023−
2024−-- | Google annotation IDs of the transcripts affected by this variant. These
2025−-- should be provided when the variant is created.
2026−vaTranscriptIds :: Lens' VariantAnnotation [Text]
2027−vaTranscriptIds
2028− = lens _vaTranscriptIds
2029− (\ s a -> s{_vaTranscriptIds = a})
2030− . _Default
2031− . _Coerce
2032−
2033−instance FromJSON VariantAnnotation where
2034− parseJSON
2035− = withObject "VariantAnnotation"
2036− (\ o ->
2037− VariantAnnotation <$>
2038− (o .:? "effect") <*> (o .:? "clinicalSignificance")
2039− <*> (o .:? "alternateBases")
2040− <*> (o .:? "geneId")
2041− <*> (o .:? "conditions" .!= mempty)
2042− <*> (o .:? "type")
2043− <*> (o .:? "transcriptIds" .!= mempty))
2044−
2045−instance ToJSON VariantAnnotation where
2046− toJSON VariantAnnotation{..}
2047− = object
2048− (catMaybes
2049− [("effect" .=) <$> _vaEffect,
2050− ("clinicalSignificance" .=) <$>
2051− _vaClinicalSignificance,
2052− ("alternateBases" .=) <$> _vaAlternateBases,
2053− ("geneId" .=) <$> _vaGeneId,
2054− ("conditions" .=) <$> _vaConditions,
2055− ("type" .=) <$> _vaType,
2056− ("transcriptIds" .=) <$> _vaTranscriptIds])
2057−
20581625-- | The read group set search request.
20591626--
20601627-- /See:/ 'searchReadGroupSetsRequest' smart constructor.
@@ -2103,7 +1670,7 @@ srgsrName
21031670
21041671-- | The continuation token, which is used to page through large result sets.
21051672-- To get the next page of results, set this parameter to the value of
2106−-- nextPageToken from the previous response.
1673+-- \`nextPageToken\` from the previous response.
21071674srgsrPageToken :: Lens' SearchReadGroupSetsRequest (Maybe Text)
21081675srgsrPageToken
21091676 = lens _srgsrPageToken
@@ -2134,55 +1701,6 @@ instance ToJSON SearchReadGroupSetsRequest where
21341701 ("pageToken" .=) <$> _srgsrPageToken,
21351702 ("pageSize" .=) <$> _srgsrPageSize])
21361703
2137−-- |
2138−--
2139−-- /See:/ 'batchAnnotationsResponseEntryStatus' smart constructor.
2140−data BatchAnnotationsResponseEntryStatus = BatchAnnotationsResponseEntryStatus
2141− { _baresCode :: !(Maybe Int32)
2142− , _baresMessage :: !(Maybe Text)
2143− } deriving (Eq,Show,Data,Typeable,Generic)
2144−
2145−-- | Creates a value of 'BatchAnnotationsResponseEntryStatus' with the minimum fields required to make a request.
2146−--
2147−-- Use one of the following lenses to modify other fields as desired:
2148−--
2149−-- * 'baresCode'
2150−--
2151−-- * 'baresMessage'
2152−batchAnnotationsResponseEntryStatus
2153− :: BatchAnnotationsResponseEntryStatus
2154−batchAnnotationsResponseEntryStatus =
2155− BatchAnnotationsResponseEntryStatus
2156− { _baresCode = Nothing
2157− , _baresMessage = Nothing
2158− }
2159−
2160−-- | The HTTP status code for this operation.
2161−baresCode :: Lens' BatchAnnotationsResponseEntryStatus (Maybe Int32)
2162−baresCode
2163− = lens _baresCode (\ s a -> s{_baresCode = a})
2164−
2165−-- | Error message for this status, if any.
2166−baresMessage :: Lens' BatchAnnotationsResponseEntryStatus (Maybe Text)
2167−baresMessage
2168− = lens _baresMessage (\ s a -> s{_baresMessage = a})
2169−
2170−instance FromJSON BatchAnnotationsResponseEntryStatus
2171− where
2172− parseJSON
2173− = withObject "BatchAnnotationsResponseEntryStatus"
2174− (\ o ->
2175− BatchAnnotationsResponseEntryStatus <$>
2176− (o .:? "code") <*> (o .:? "message"))
2177−
2178−instance ToJSON BatchAnnotationsResponseEntryStatus
2179− where
2180− toJSON BatchAnnotationsResponseEntryStatus{..}
2181− = object
2182− (catMaybes
2183− [("code" .=) <$> _baresCode,
2184− ("message" .=) <$> _baresMessage])
2185−
21861704-- | A reference is a canonical assembled DNA sequence, intended to act as a
21871705-- reference coordinate space for other genomic annotations. A single
21881706-- reference might represent the human chromosome 1 or mitochandrial DNA,
@@ -2235,7 +1753,7 @@ refLength
22351753 = lens _refLength (\ s a -> s{_refLength = a})
22361754
22371755-- | All known corresponding accession IDs in INSDC (GenBank\/ENA\/DDBJ)
2238−-- ideally with a version number, for example GCF_000001405.26.
1756+-- ideally with a version number, for example \`GCF_000001405.26\`.
22391757refSourceAccessions :: Lens' Reference [Text]
22401758refSourceAccessions
22411759 = lens _refSourceAccessions
@@ -2251,7 +1769,7 @@ refMD5checksum
22511769 = lens _refMD5checksum
22521770 (\ s a -> s{_refMD5checksum = a})
22531771
2254−-- | The name of this reference, for example 22.
1772+-- | The name of this reference, for example \`22\`.
22551773refName :: Lens' Reference (Maybe Text)
22561774refName = lens _refName (\ s a -> s{_refName = a})
22571775
@@ -2262,7 +1780,7 @@ refNcbiTaxonId
22621780 = lens _refNcbiTaxonId
22631781 (\ s a -> s{_refNcbiTaxonId = a})
22641782
2265−-- | The Google generated immutable ID of the reference.
1783+-- | The server-generated reference ID, unique across all references.
22661784refId :: Lens' Reference (Maybe Text)
22671785refId = lens _refId (\ s a -> s{_refId = a})
22681786
@@ -2283,7 +1801,7 @@ instance FromJSON Reference where
22831801 <*> (o .:? "name")
22841802 <*> (o .:? "ncbiTaxonId")
22851803 <*> (o .:? "id")
2286− <*> (o .:? "sourceURI"))
1804+ <*> (o .:? "sourceUri"))
22871805
22881806instance ToJSON Reference where
22891807 toJSON Reference{..}
@@ -2295,46 +1813,32 @@ instance ToJSON Reference where
22951813 ("name" .=) <$> _refName,
22961814 ("ncbiTaxonId" .=) <$> _refNcbiTaxonId,
22971815 ("id" .=) <$> _refId,
2298− ("sourceURI" .=) <$> _refSourceURI])
1816+ ("sourceUri" .=) <$> _refSourceURI])
22991817
1818+-- | A map of additional variant call information. This must be of the form
1819+-- map (string key mapping to a list of string values).
23001820--
2301−-- /See:/ 'batchAnnotationsResponse' smart constructor.
2302−newtype BatchAnnotationsResponse = BatchAnnotationsResponse
2303− { _barEntries :: Maybe [BatchAnnotationsResponseEntry]
2304− } deriving (Eq,Show,Data,Typeable,Generic)
1821+-- /See:/ 'variantCallInfo' smart constructor.
1822+data VariantCallInfo =
1823+ VariantCallInfo
1824+ deriving (Eq,Show,Data,Typeable,Generic)
23051825
2306−-- | Creates a value of 'BatchAnnotationsResponse' with the minimum fields required to make a request.
2307−--
2308−-- Use one of the following lenses to modify other fields as desired:
1826+-- | Creates a value of 'VariantCallInfo' with the minimum fields required to make a request.
23091827--
2310−-- * 'barEntries'
2311−batchAnnotationsResponse
2312− :: BatchAnnotationsResponse
2313−batchAnnotationsResponse =
2314− BatchAnnotationsResponse
2315− { _barEntries = Nothing
2316− }
1828+variantCallInfo
1829+ :: VariantCallInfo
1830+variantCallInfo = VariantCallInfo
23171831
2318−-- | The resulting per-annotation entries, ordered consistently with the
2319−-- original request.
2320−barEntries :: Lens' BatchAnnotationsResponse [BatchAnnotationsResponseEntry]
2321−barEntries
2322− = lens _barEntries (\ s a -> s{_barEntries = a}) .
2323− _Default
2324− . _Coerce
2325−
2326−instance FromJSON BatchAnnotationsResponse where
1832+instance FromJSON VariantCallInfo where
23271833 parseJSON
2328− = withObject "BatchAnnotationsResponse"
2329− (\ o ->
2330− BatchAnnotationsResponse <$>
2331− (o .:? "entries" .!= mempty))
1834+ = withObject "VariantCallInfo"
1835+ (\ o -> pure VariantCallInfo)
23321836
2333−instance ToJSON BatchAnnotationsResponse where
2334− toJSON BatchAnnotationsResponse{..}
2335− = object (catMaybes [("entries" .=) <$> _barEntries])
1837+instance ToJSON VariantCallInfo where
1838+ toJSON = const emptyObject
23361839
2337−-- | A string which maps to an array of values.
1840+-- | A map of additional read group information. This must be of the form map
1841+-- (string key mapping to a list of string values).
23381842--
23391843-- /See:/ 'readGroupInfo' smart constructor.
23401844data ReadGroupInfo =
@@ -2355,108 +1859,25 @@ instance FromJSON ReadGroupInfo where
23551859instance ToJSON ReadGroupInfo where
23561860 toJSON = const emptyObject
23571861
2358−-- | The jobs search request.
23591862--
2360−-- /See:/ 'searchJobsRequest' smart constructor.
2361−data SearchJobsRequest = SearchJobsRequest
2362− { _sjrCreatedAfter :: !(Maybe Int64)
2363− , _sjrStatus :: !(Maybe [SearchJobsRequestStatusItem])
2364− , _sjrProjectNumber :: !(Maybe Int64)
2365− , _sjrPageToken :: !(Maybe Text)
2366− , _sjrPageSize :: !(Maybe Int32)
2367− , _sjrCreatedBefore :: !(Maybe Int64)
2368− } deriving (Eq,Show,Data,Typeable,Generic)
1863+-- /See:/ 'statusDetailsItem' smart constructor.
1864+data StatusDetailsItem =
1865+ StatusDetailsItem
1866+ deriving (Eq,Show,Data,Typeable,Generic)
23691867
2370−-- | Creates a value of 'SearchJobsRequest' with the minimum fields required to make a request.
2371−--
2372−-- Use one of the following lenses to modify other fields as desired:
2373−--
2374−-- * 'sjrCreatedAfter'
2375−--
2376−-- * 'sjrStatus'
2377−--
2378−-- * 'sjrProjectNumber'
1868+-- | Creates a value of 'StatusDetailsItem' with the minimum fields required to make a request.
23791869--
2380−-- * 'sjrPageToken'
2381−--
2382−-- * 'sjrPageSize'
2383−--
2384−-- * 'sjrCreatedBefore'
2385−searchJobsRequest
2386− :: SearchJobsRequest
2387−searchJobsRequest =
2388− SearchJobsRequest
2389− { _sjrCreatedAfter = Nothing
2390− , _sjrStatus = Nothing
2391− , _sjrProjectNumber = Nothing
2392− , _sjrPageToken = Nothing
2393− , _sjrPageSize = Nothing
2394− , _sjrCreatedBefore = Nothing
2395− }
2396−
2397−-- | If specified, only jobs created on or after this date, given in
2398−-- milliseconds since Unix epoch, will be returned.
2399−sjrCreatedAfter :: Lens' SearchJobsRequest (Maybe Int64)
2400−sjrCreatedAfter
2401− = lens _sjrCreatedAfter
2402− (\ s a -> s{_sjrCreatedAfter = a})
2403−
2404−-- | Only return jobs which have a matching status.
2405−sjrStatus :: Lens' SearchJobsRequest [SearchJobsRequestStatusItem]
2406−sjrStatus
2407− = lens _sjrStatus (\ s a -> s{_sjrStatus = a}) .
2408− _Default
2409− . _Coerce
1870+statusDetailsItem
1871+ :: StatusDetailsItem
1872+statusDetailsItem = StatusDetailsItem
24101873
2411−-- | Required. Only return jobs which belong to this Google Developers
2412−-- Console project.
2413−sjrProjectNumber :: Lens' SearchJobsRequest (Maybe Int64)
2414−sjrProjectNumber
2415− = lens _sjrProjectNumber
2416− (\ s a -> s{_sjrProjectNumber = a})
2417−
2418−-- | The continuation token which is used to page through large result sets.
2419−-- To get the next page of results, set this parameter to the value of the
2420−-- nextPageToken from the previous response.
2421−sjrPageToken :: Lens' SearchJobsRequest (Maybe Text)
2422−sjrPageToken
2423− = lens _sjrPageToken (\ s a -> s{_sjrPageToken = a})
2424−
2425−-- | Specifies the number of results to return in a single page. Defaults to
2426−-- 128. The maximum value is 256.
2427−sjrPageSize :: Lens' SearchJobsRequest (Maybe Int32)
2428−sjrPageSize
2429− = lens _sjrPageSize (\ s a -> s{_sjrPageSize = a})
2430−
2431−-- | If specified, only jobs created prior to this date, given in
2432−-- milliseconds since Unix epoch, will be returned.
2433−sjrCreatedBefore :: Lens' SearchJobsRequest (Maybe Int64)
2434−sjrCreatedBefore
2435− = lens _sjrCreatedBefore
2436− (\ s a -> s{_sjrCreatedBefore = a})
2437−
2438−instance FromJSON SearchJobsRequest where
1874+instance FromJSON StatusDetailsItem where
24391875 parseJSON
2440− = withObject "SearchJobsRequest"
2441− (\ o ->
2442− SearchJobsRequest <$>
2443− (o .:? "createdAfter") <*>
2444− (o .:? "status" .!= mempty)
2445− <*> (o .:? "projectNumber")
2446− <*> (o .:? "pageToken")
2447− <*> (o .:? "pageSize")
2448− <*> (o .:? "createdBefore"))
1876+ = withObject "StatusDetailsItem"
1877+ (\ o -> pure StatusDetailsItem)
24491878
2450−instance ToJSON SearchJobsRequest where
2451− toJSON SearchJobsRequest{..}
2452− = object
2453− (catMaybes
2454− [("createdAfter" .=) <$> _sjrCreatedAfter,
2455− ("status" .=) <$> _sjrStatus,
2456− ("projectNumber" .=) <$> _sjrProjectNumber,
2457− ("pageToken" .=) <$> _sjrPageToken,
2458− ("pageSize" .=) <$> _sjrPageSize,
2459− ("createdBefore" .=) <$> _sjrCreatedBefore])
1879+instance ToJSON StatusDetailsItem where
1880+ toJSON = const emptyObject
24601881
24611882-- | The call set search response.
24621883--
@@ -2512,180 +1933,41 @@ instance ToJSON SearchCallSetsResponse where
25121933 [("nextPageToken" .=) <$> _scsrNextPageToken,
25131934 ("callSets" .=) <$> _scsrCallSets])
25141935
2515−-- | The job creation request.
2516−--
2517−-- /See:/ 'experimentalCreateJobRequest' smart constructor.
2518−data ExperimentalCreateJobRequest = ExperimentalCreateJobRequest
2519− { _ecjrGcsOutputPath :: !(Maybe Text)
2520− , _ecjrProjectNumber :: !(Maybe Int64)
2521− , _ecjrAlign :: !(Maybe Bool)
2522− , _ecjrSourceURIs :: !(Maybe [Text])
2523− , _ecjrPairedSourceURIs :: !(Maybe [Text])
2524− , _ecjrCallVariants :: !(Maybe Bool)
2525− } deriving (Eq,Show,Data,Typeable,Generic)
2526−
2527−-- | Creates a value of 'ExperimentalCreateJobRequest' with the minimum fields required to make a request.
2528−--
2529−-- Use one of the following lenses to modify other fields as desired:
2530−--
2531−-- * 'ecjrGcsOutputPath'
2532−--
2533−-- * 'ecjrProjectNumber'
2534−--
2535−-- * 'ecjrAlign'
1936+-- | Request message for \`SetIamPolicy\` method.
25361937--
2537−-- * 'ecjrSourceURIs'
2538−--
2539−-- * 'ecjrPairedSourceURIs'
2540−--
2541−-- * 'ecjrCallVariants'
2542−experimentalCreateJobRequest
2543− :: ExperimentalCreateJobRequest
2544−experimentalCreateJobRequest =
2545− ExperimentalCreateJobRequest
2546− { _ecjrGcsOutputPath = Nothing
2547− , _ecjrProjectNumber = Nothing
2548− , _ecjrAlign = Nothing
2549− , _ecjrSourceURIs = Nothing
2550− , _ecjrPairedSourceURIs = Nothing
2551− , _ecjrCallVariants = Nothing
2552− }
2553−
2554−-- | Specifies where to copy the results of certain pipelines. This should be
2555−-- in the form of gs:\/\/bucket\/path.
2556−ecjrGcsOutputPath :: Lens' ExperimentalCreateJobRequest (Maybe Text)
2557−ecjrGcsOutputPath
2558− = lens _ecjrGcsOutputPath
2559− (\ s a -> s{_ecjrGcsOutputPath = a})
2560−
2561−-- | Required. The Google Cloud Project ID with which to associate the
2562−-- request.
2563−ecjrProjectNumber :: Lens' ExperimentalCreateJobRequest (Maybe Int64)
2564−ecjrProjectNumber
2565− = lens _ecjrProjectNumber
2566− (\ s a -> s{_ecjrProjectNumber = a})
2567−
2568−-- | Specifies whether or not to run the alignment pipeline. Either align or
2569−-- callVariants must be set.
2570−ecjrAlign :: Lens' ExperimentalCreateJobRequest (Maybe Bool)
2571−ecjrAlign
2572− = lens _ecjrAlign (\ s a -> s{_ecjrAlign = a})
2573−
2574−-- | A list of Google Cloud Storage URIs of data files to operate upon. These
2575−-- can be .bam, interleaved .fastq, or paired .fastq. If specifying paired
2576−-- .fastq files, the first of each pair of files should be listed here, and
2577−-- the second of each pair should be listed in pairedSourceUris.
2578−ecjrSourceURIs :: Lens' ExperimentalCreateJobRequest [Text]
2579−ecjrSourceURIs
2580− = lens _ecjrSourceURIs
2581− (\ s a -> s{_ecjrSourceURIs = a})
2582− . _Default
2583− . _Coerce
2584−
2585−-- | A list of Google Cloud Storage URIs of paired end .fastq files to
2586−-- operate upon. If specified, this represents the second file of each
2587−-- paired .fastq file. The first file of each pair should be specified in
2588−-- sourceUris.
2589−ecjrPairedSourceURIs :: Lens' ExperimentalCreateJobRequest [Text]
2590−ecjrPairedSourceURIs
2591− = lens _ecjrPairedSourceURIs
2592− (\ s a -> s{_ecjrPairedSourceURIs = a})
2593− . _Default
2594− . _Coerce
2595−
2596−-- | Specifies whether or not to run the variant calling pipeline. Either
2597−-- align or callVariants must be set.
2598−ecjrCallVariants :: Lens' ExperimentalCreateJobRequest (Maybe Bool)
2599−ecjrCallVariants
2600− = lens _ecjrCallVariants
2601− (\ s a -> s{_ecjrCallVariants = a})
2602−
2603−instance FromJSON ExperimentalCreateJobRequest where
2604− parseJSON
2605− = withObject "ExperimentalCreateJobRequest"
2606− (\ o ->
2607− ExperimentalCreateJobRequest <$>
2608− (o .:? "gcsOutputPath") <*> (o .:? "projectNumber")
2609− <*> (o .:? "align")
2610− <*> (o .:? "sourceUris" .!= mempty)
2611− <*> (o .:? "pairedSourceUris" .!= mempty)
2612− <*> (o .:? "callVariants"))
2613−
2614−instance ToJSON ExperimentalCreateJobRequest where
2615− toJSON ExperimentalCreateJobRequest{..}
2616− = object
2617− (catMaybes
2618− [("gcsOutputPath" .=) <$> _ecjrGcsOutputPath,
2619− ("projectNumber" .=) <$> _ecjrProjectNumber,
2620− ("align" .=) <$> _ecjrAlign,
2621− ("sourceUris" .=) <$> _ecjrSourceURIs,
2622− ("pairedSourceUris" .=) <$> _ecjrPairedSourceURIs,
2623− ("callVariants" .=) <$> _ecjrCallVariants])
2624−
2625−-- | A summary representation of the service request that spawned the job.
2626−--
2627−-- /See:/ 'jobRequest' smart constructor.
2628−data JobRequest = JobRequest
2629− { _jrDestination :: !(Maybe [Text])
2630− , _jrSource :: !(Maybe [Text])
2631− , _jrType :: !(Maybe JobRequestType)
1938+-- /See:/ 'setIAMPolicyRequest' smart constructor.
1939+newtype SetIAMPolicyRequest = SetIAMPolicyRequest
1940+ { _siprPolicy :: Maybe Policy
26321941 } deriving (Eq,Show,Data,Typeable,Generic)
26331942
2634−-- | Creates a value of 'JobRequest' with the minimum fields required to make a request.
1943+-- | Creates a value of 'SetIAMPolicyRequest' with the minimum fields required to make a request.
26351944--
26361945-- Use one of the following lenses to modify other fields as desired:
26371946--
2638−-- * 'jrDestination'
2639−--
2640−-- * 'jrSource'
2641−--
2642−-- * 'jrType'
2643−jobRequest
2644− :: JobRequest
2645−jobRequest =
2646− JobRequest
2647− { _jrDestination = Nothing
2648− , _jrSource = Nothing
2649− , _jrType = Nothing
1947+-- * 'siprPolicy'
1948+setIAMPolicyRequest
1949+ :: SetIAMPolicyRequest
1950+setIAMPolicyRequest =
1951+ SetIAMPolicyRequest
1952+ { _siprPolicy = Nothing
26501953 }
26511954
2652−-- | The data destination of the request, for example, a Google BigQuery
2653−-- Table or Dataset ID.
2654−jrDestination :: Lens' JobRequest [Text]
2655−jrDestination
2656− = lens _jrDestination
2657− (\ s a -> s{_jrDestination = a})
2658− . _Default
2659− . _Coerce
2660−
2661−-- | The data source of the request, for example, a Google Cloud Storage
2662−-- object path or Readset ID.
2663−jrSource :: Lens' JobRequest [Text]
2664−jrSource
2665− = lens _jrSource (\ s a -> s{_jrSource = a}) .
2666− _Default
2667− . _Coerce
1955+-- | REQUIRED: The complete policy to be applied to the \`resource\`. The
1956+-- size of the policy is limited to a few 10s of KB. An empty policy is a
1957+-- valid policy but certain Cloud Platform services (such as Projects)
1958+-- might reject them.
1959+siprPolicy :: Lens' SetIAMPolicyRequest (Maybe Policy)
1960+siprPolicy
1961+ = lens _siprPolicy (\ s a -> s{_siprPolicy = a})
26681962
2669−-- | The original request type.
2670−jrType :: Lens' JobRequest (Maybe JobRequestType)
2671−jrType = lens _jrType (\ s a -> s{_jrType = a})
2672−
2673−instance FromJSON JobRequest where
1963+instance FromJSON SetIAMPolicyRequest where
26741964 parseJSON
2675− = withObject "JobRequest"
2676− (\ o ->
2677− JobRequest <$>
2678− (o .:? "destination" .!= mempty) <*>
2679− (o .:? "source" .!= mempty)
2680− <*> (o .:? "type"))
1965+ = withObject "SetIAMPolicyRequest"
1966+ (\ o -> SetIAMPolicyRequest <$> (o .:? "policy"))
26811967
2682−instance ToJSON JobRequest where
2683− toJSON JobRequest{..}
2684− = object
2685− (catMaybes
2686− [("destination" .=) <$> _jrDestination,
2687− ("source" .=) <$> _jrSource,
2688− ("type" .=) <$> _jrType])
1968+instance ToJSON SetIAMPolicyRequest where
1969+ toJSON SetIAMPolicyRequest{..}
1970+ = object (catMaybes [("policy" .=) <$> _siprPolicy])
26891971
26901972-- | The read search request.
26911973--
@@ -2731,13 +2013,13 @@ searchReadsRequest =
27312013 }
27322014
27332015-- | The start position of the range on the reference, 0-based inclusive. If
2734−-- specified, referenceName must also be specified.
2016+-- specified, \`referenceName\` must also be specified.
27352017srrStart :: Lens' SearchReadsRequest (Maybe Int64)
27362018srrStart = lens _srrStart (\ s a -> s{_srrStart = a})
27372019
27382020-- | The IDs of the read groups within which to search for reads. All
27392021-- specified read groups must belong to the same read group sets. Must
2740−-- specify one of readGroupSetIds or readGroupIds.
2022+-- specify one of \`readGroupSetIds\` or \`readGroupIds\`.
27412023srrReadGroupIds :: Lens' SearchReadsRequest [Text]
27422024srrReadGroupIds
27432025 = lens _srrReadGroupIds
@@ -2745,21 +2027,21 @@ srrReadGroupIds
27452027 . _Default
27462028 . _Coerce
27472029
2748−-- | The reference sequence name, for example chr1, 1, or chrX. If set to *,
2749−-- only unmapped reads are returned.
2030+-- | The reference sequence name, for example \`chr1\`, \`1\`, or \`chrX\`.
2031+-- If set to *, only unmapped reads are returned.
27502032srrReferenceName :: Lens' SearchReadsRequest (Maybe Text)
27512033srrReferenceName
27522034 = lens _srrReferenceName
27532035 (\ s a -> s{_srrReferenceName = a})
27542036
27552037-- | The end position of the range on the reference, 0-based exclusive. If
2756−-- specified, referenceName must also be specified.
2038+-- specified, \`referenceName\` must also be specified.
27572039srrEnd :: Lens' SearchReadsRequest (Maybe Int64)
27582040srrEnd = lens _srrEnd (\ s a -> s{_srrEnd = a})
27592041
27602042-- | The continuation token, which is used to page through large result sets.
27612043-- To get the next page of results, set this parameter to the value of
2762−-- nextPageToken from the previous response.
2044+-- \`nextPageToken\` from the previous response.
27632045srrPageToken :: Lens' SearchReadsRequest (Maybe Text)
27642046srrPageToken
27652047 = lens _srrPageToken (\ s a -> s{_srrPageToken = a})
@@ -2773,7 +2055,7 @@ srrPageSize
27732055-- | The IDs of the read groups sets within which to search for reads. All
27742056-- specified read group sets must be aligned against a common set of
27752057-- reference sequences; this defines the genomic coordinates for the query.
2776−-- Must specify one of readGroupSetIds or readGroupIds.
2058+-- Must specify one of \`readGroupSetIds\` or \`readGroupIds\`.
27772059srrReadGroupSetIds :: Lens' SearchReadsRequest [Text]
27782060srrReadGroupSetIds
27792061 = lens _srrReadGroupSetIds
@@ -2805,7 +2087,32 @@ instance ToJSON SearchReadsRequest where
28052087 ("pageSize" .=) <$> _srrPageSize,
28062088 ("readGroupSetIds" .=) <$> _srrReadGroupSetIds])
28072089
2808−-- | A string which maps to an array of values.
2090+-- | The original request that started the operation. Note that this will be
2091+-- in current version of the API. If the operation was started with v1beta2
2092+-- API and a GetOperation is performed on v1 API, a v1 request will be
2093+-- returned.
2094+--
2095+-- /See:/ 'operationMetadataRequest' smart constructor.
2096+data OperationMetadataRequest =
2097+ OperationMetadataRequest
2098+ deriving (Eq,Show,Data,Typeable,Generic)
2099+
2100+-- | Creates a value of 'OperationMetadataRequest' with the minimum fields required to make a request.
2101+--
2102+operationMetadataRequest
2103+ :: OperationMetadataRequest
2104+operationMetadataRequest = OperationMetadataRequest
2105+
2106+instance FromJSON OperationMetadataRequest where
2107+ parseJSON
2108+ = withObject "OperationMetadataRequest"
2109+ (\ o -> pure OperationMetadataRequest)
2110+
2111+instance ToJSON OperationMetadataRequest where
2112+ toJSON = const emptyObject
2113+
2114+-- | A map of additional variant information. This must be of the form map
2115+-- (string key mapping to a list of string values).
28092116--
28102117-- /See:/ 'variantInfo' smart constructor.
28112118data VariantInfo =
@@ -2825,6 +2132,82 @@ instance FromJSON VariantInfo where
28252132instance ToJSON VariantInfo where
28262133 toJSON = const emptyObject
28272134
2135+--
2136+-- /See:/ 'experiment' smart constructor.
2137+data Experiment = Experiment
2138+ { _eInstrumentModel :: !(Maybe Text)
2139+ , _ePlatformUnit :: !(Maybe Text)
2140+ , _eSequencingCenter :: !(Maybe Text)
2141+ , _eLibraryId :: !(Maybe Text)
2142+ } deriving (Eq,Show,Data,Typeable,Generic)
2143+
2144+-- | Creates a value of 'Experiment' with the minimum fields required to make a request.
2145+--
2146+-- Use one of the following lenses to modify other fields as desired:
2147+--
2148+-- * 'eInstrumentModel'
2149+--
2150+-- * 'ePlatformUnit'
2151+--
2152+-- * 'eSequencingCenter'
2153+--
2154+-- * 'eLibraryId'
2155+experiment
2156+ :: Experiment
2157+experiment =
2158+ Experiment
2159+ { _eInstrumentModel = Nothing
2160+ , _ePlatformUnit = Nothing
2161+ , _eSequencingCenter = Nothing
2162+ , _eLibraryId = Nothing
2163+ }
2164+
2165+-- | The instrument model used as part of this experiment. This maps to
2166+-- sequencing technology in BAM.
2167+eInstrumentModel :: Lens' Experiment (Maybe Text)
2168+eInstrumentModel
2169+ = lens _eInstrumentModel
2170+ (\ s a -> s{_eInstrumentModel = a})
2171+
2172+-- | The platform unit used as part of this experiment e.g.
2173+-- flowcell-barcode.lane for Illumina or slide for SOLiD. Corresponds to
2174+-- the \'RG PU field in the SAM spec.
2175+ePlatformUnit :: Lens' Experiment (Maybe Text)
2176+ePlatformUnit
2177+ = lens _ePlatformUnit
2178+ (\ s a -> s{_ePlatformUnit = a})
2179+
2180+-- | The sequencing center used as part of this experiment.
2181+eSequencingCenter :: Lens' Experiment (Maybe Text)
2182+eSequencingCenter
2183+ = lens _eSequencingCenter
2184+ (\ s a -> s{_eSequencingCenter = a})
2185+
2186+-- | The library used as part of this experiment. Note: This is not an actual
2187+-- ID within this repository, but rather an identifier for a library which
2188+-- may be meaningful to some external system.
2189+eLibraryId :: Lens' Experiment (Maybe Text)
2190+eLibraryId
2191+ = lens _eLibraryId (\ s a -> s{_eLibraryId = a})
2192+
2193+instance FromJSON Experiment where
2194+ parseJSON
2195+ = withObject "Experiment"
2196+ (\ o ->
2197+ Experiment <$>
2198+ (o .:? "instrumentModel") <*> (o .:? "platformUnit")
2199+ <*> (o .:? "sequencingCenter")
2200+ <*> (o .:? "libraryId"))
2201+
2202+instance ToJSON Experiment where
2203+ toJSON Experiment{..}
2204+ = object
2205+ (catMaybes
2206+ [("instrumentModel" .=) <$> _eInstrumentModel,
2207+ ("platformUnit" .=) <$> _ePlatformUnit,
2208+ ("sequencingCenter" .=) <$> _eSequencingCenter,
2209+ ("libraryId" .=) <$> _eLibraryId])
2210+
28282211-- | The search variant sets request.
28292212--
28302213-- /See:/ 'searchVariantSetsRequest' smart constructor.
@@ -2863,7 +2246,7 @@ svsrDatasetIds
28632246
28642247-- | The continuation token, which is used to page through large result sets.
28652248-- To get the next page of results, set this parameter to the value of
2866−-- nextPageToken from the previous response.
2249+-- \`nextPageToken\` from the previous response.
28672250svsrPageToken :: Lens' SearchVariantSetsRequest (Maybe Text)
28682251svsrPageToken
28692252 = lens _svsrPageToken
@@ -2891,409 +2274,35 @@ instance ToJSON SearchVariantSetsRequest where
28912274 ("pageToken" .=) <$> _svsrPageToken,
28922275 ("pageSize" .=) <$> _svsrPageSize])
28932276
2277+-- | The variant search response.
28942278--
2895−-- /See:/ 'readGroupProgram' smart constructor.
2896−data ReadGroupProgram = ReadGroupProgram
2897− { _rgpPrevProgramId :: !(Maybe Text)
2898− , _rgpName :: !(Maybe Text)
2899− , _rgpVersion :: !(Maybe Text)
2900− , _rgpId :: !(Maybe Text)
2901− , _rgpCommandLine :: !(Maybe Text)
2279+-- /See:/ 'searchVariantsResponse' smart constructor.
2280+data SearchVariantsResponse = SearchVariantsResponse
2281+ { _svrVariants :: !(Maybe [Variant])
2282+ , _svrNextPageToken :: !(Maybe Text)
29022283 } deriving (Eq,Show,Data,Typeable,Generic)
29032284
2904−-- | Creates a value of 'ReadGroupProgram' with the minimum fields required to make a request.
2285+-- | Creates a value of 'SearchVariantsResponse' with the minimum fields required to make a request.
29052286--
29062287-- Use one of the following lenses to modify other fields as desired:
29072288--
2908−-- * 'rgpPrevProgramId'
2909−--
2910−-- * 'rgpName'
2911−--
2912−-- * 'rgpVersion'
2913−--
2914−-- * 'rgpId'
2289+-- * 'svrVariants'
29152290--
2916−-- * 'rgpCommandLine'
2917−readGroupProgram
2918− :: ReadGroupProgram
2919−readGroupProgram =
2920− ReadGroupProgram
2921− { _rgpPrevProgramId = Nothing
2922− , _rgpName = Nothing
2923− , _rgpVersion = Nothing
2924− , _rgpId = Nothing
2925− , _rgpCommandLine = Nothing
2291+-- * 'svrNextPageToken'
2292+searchVariantsResponse
2293+ :: SearchVariantsResponse
2294+searchVariantsResponse =
2295+ SearchVariantsResponse
2296+ { _svrVariants = Nothing
2297+ , _svrNextPageToken = Nothing
29262298 }
29272299
2928−-- | The ID of the program run before this one.
2929−rgpPrevProgramId :: Lens' ReadGroupProgram (Maybe Text)
2930−rgpPrevProgramId
2931− = lens _rgpPrevProgramId
2932− (\ s a -> s{_rgpPrevProgramId = a})
2933−
2934−-- | The name of the program.
2935−rgpName :: Lens' ReadGroupProgram (Maybe Text)
2936−rgpName = lens _rgpName (\ s a -> s{_rgpName = a})
2937−
2938−-- | The version of the program run.
2939−rgpVersion :: Lens' ReadGroupProgram (Maybe Text)
2940−rgpVersion
2941− = lens _rgpVersion (\ s a -> s{_rgpVersion = a})
2942−
2943−-- | The user specified locally unique ID of the program. Used along with
2944−-- prevProgramId to define an ordering between programs.
2945−rgpId :: Lens' ReadGroupProgram (Maybe Text)
2946−rgpId = lens _rgpId (\ s a -> s{_rgpId = a})
2947−
2948−-- | The command line used to run this program.
2949−rgpCommandLine :: Lens' ReadGroupProgram (Maybe Text)
2950−rgpCommandLine
2951− = lens _rgpCommandLine
2952− (\ s a -> s{_rgpCommandLine = a})
2953−
2954−instance FromJSON ReadGroupProgram where
2955− parseJSON
2956− = withObject "ReadGroupProgram"
2957− (\ o ->
2958− ReadGroupProgram <$>
2959− (o .:? "prevProgramId") <*> (o .:? "name") <*>
2960− (o .:? "version")
2961− <*> (o .:? "id")
2962− <*> (o .:? "commandLine"))
2963−
2964−instance ToJSON ReadGroupProgram where
2965− toJSON ReadGroupProgram{..}
2966− = object
2967− (catMaybes
2968− [("prevProgramId" .=) <$> _rgpPrevProgramId,
2969− ("name" .=) <$> _rgpName,
2970− ("version" .=) <$> _rgpVersion, ("id" .=) <$> _rgpId,
2971− ("commandLine" .=) <$> _rgpCommandLine])
2972−
2973−-- | Wrapper message for \`int32\`. The JSON representation for
2974−-- \`Int32Value\` is JSON number.
2975−--
2976−-- /See:/ 'int32Value' smart constructor.
2977−newtype Int32Value = Int32Value
2978− { _ivValue :: Maybe Int32
2979− } deriving (Eq,Show,Data,Typeable,Generic)
2980−
2981−-- | Creates a value of 'Int32Value' with the minimum fields required to make a request.
2982−--
2983−-- Use one of the following lenses to modify other fields as desired:
2984−--
2985−-- * 'ivValue'
2986−int32Value
2987− :: Int32Value
2988−int32Value =
2989− Int32Value
2990− { _ivValue = Nothing
2991− }
2992−
2993−-- | The int32 value.
2994−ivValue :: Lens' Int32Value (Maybe Int32)
2995−ivValue = lens _ivValue (\ s a -> s{_ivValue = a})
2996−
2997−instance FromJSON Int32Value where
2998− parseJSON
2999− = withObject "Int32Value"
3000− (\ o -> Int32Value <$> (o .:? "value"))
3001−
3002−instance ToJSON Int32Value where
3003− toJSON Int32Value{..}
3004− = object (catMaybes [("value" .=) <$> _ivValue])
3005−
3006−-- | A string which maps to an array of values.
3007−--
3008−-- /See:/ 'annotationInfo' smart constructor.
3009−data AnnotationInfo =
3010− AnnotationInfo
3011− deriving (Eq,Show,Data,Typeable,Generic)
3012−
3013−-- | Creates a value of 'AnnotationInfo' with the minimum fields required to make a request.
3014−--
3015−annotationInfo
3016− :: AnnotationInfo
3017−annotationInfo = AnnotationInfo
3018−
3019−instance FromJSON AnnotationInfo where
3020− parseJSON
3021− = withObject "AnnotationInfo"
3022− (\ o -> pure AnnotationInfo)
3023−
3024−instance ToJSON AnnotationInfo where
3025− toJSON = const emptyObject
3026−
3027−-- | The read group set export request.
3028−--
3029−-- /See:/ 'exportReadGroupSetsRequest' smart constructor.
3030−data ExportReadGroupSetsRequest = ExportReadGroupSetsRequest
3031− { _ergsrReferenceNames :: !(Maybe [Text])
3032− , _ergsrProjectNumber :: !(Maybe Int64)
3033− , _ergsrExportURI :: !(Maybe Text)
3034− , _ergsrReadGroupSetIds :: !(Maybe [Text])
3035− } deriving (Eq,Show,Data,Typeable,Generic)
3036−
3037−-- | Creates a value of 'ExportReadGroupSetsRequest' with the minimum fields required to make a request.
3038−--
3039−-- Use one of the following lenses to modify other fields as desired:
3040−--
3041−-- * 'ergsrReferenceNames'
3042−--
3043−-- * 'ergsrProjectNumber'
3044−--
3045−-- * 'ergsrExportURI'
3046−--
3047−-- * 'ergsrReadGroupSetIds'
3048−exportReadGroupSetsRequest
3049− :: ExportReadGroupSetsRequest
3050−exportReadGroupSetsRequest =
3051− ExportReadGroupSetsRequest
3052− { _ergsrReferenceNames = Nothing
3053− , _ergsrProjectNumber = Nothing
3054− , _ergsrExportURI = Nothing
3055− , _ergsrReadGroupSetIds = Nothing
3056− }
3057−
3058−-- | The reference names to export. If this is not specified, all reference
3059−-- sequences, including unmapped reads, are exported. Use * to export only
3060−-- unmapped reads.
3061−ergsrReferenceNames :: Lens' ExportReadGroupSetsRequest [Text]
3062−ergsrReferenceNames
3063− = lens _ergsrReferenceNames
3064− (\ s a -> s{_ergsrReferenceNames = a})
3065− . _Default
3066− . _Coerce
3067−
3068−-- | Required. The Google Developers Console project number that owns this
3069−-- export.
3070−ergsrProjectNumber :: Lens' ExportReadGroupSetsRequest (Maybe Int64)
3071−ergsrProjectNumber
3072− = lens _ergsrProjectNumber
3073− (\ s a -> s{_ergsrProjectNumber = a})
3074−
3075−-- | Required. A Google Cloud Storage URI for the exported BAM file. The
3076−-- currently authenticated user must have write access to the new file. An
3077−-- error will be returned if the URI already contains data.
3078−ergsrExportURI :: Lens' ExportReadGroupSetsRequest (Maybe Text)
3079−ergsrExportURI
3080− = lens _ergsrExportURI
3081− (\ s a -> s{_ergsrExportURI = a})
3082−
3083−-- | Required. The IDs of the read group sets to export.
3084−ergsrReadGroupSetIds :: Lens' ExportReadGroupSetsRequest [Text]
3085−ergsrReadGroupSetIds
3086− = lens _ergsrReadGroupSetIds
3087− (\ s a -> s{_ergsrReadGroupSetIds = a})
3088− . _Default
3089− . _Coerce
3090−
3091−instance FromJSON ExportReadGroupSetsRequest where
3092− parseJSON
3093− = withObject "ExportReadGroupSetsRequest"
3094− (\ o ->
3095− ExportReadGroupSetsRequest <$>
3096− (o .:? "referenceNames" .!= mempty) <*>
3097− (o .:? "projectNumber")
3098− <*> (o .:? "exportUri")
3099− <*> (o .:? "readGroupSetIds" .!= mempty))
3100−
3101−instance ToJSON ExportReadGroupSetsRequest where
3102− toJSON ExportReadGroupSetsRequest{..}
3103− = object
3104− (catMaybes
3105− [("referenceNames" .=) <$> _ergsrReferenceNames,
3106− ("projectNumber" .=) <$> _ergsrProjectNumber,
3107− ("exportUri" .=) <$> _ergsrExportURI,
3108− ("readGroupSetIds" .=) <$> _ergsrReadGroupSetIds])
3109−
3110−--
3111−-- /See:/ 'searchAnnotationsResponse' smart constructor.
3112−data SearchAnnotationsResponse = SearchAnnotationsResponse
3113− { _sarAnnotations :: !(Maybe [Annotation])
3114− , _sarNextPageToken :: !(Maybe Text)
3115− } deriving (Eq,Show,Data,Typeable,Generic)
3116−
3117−-- | Creates a value of 'SearchAnnotationsResponse' with the minimum fields required to make a request.
3118−--
3119−-- Use one of the following lenses to modify other fields as desired:
3120−--
3121−-- * 'sarAnnotations'
3122−--
3123−-- * 'sarNextPageToken'
3124−searchAnnotationsResponse
3125− :: SearchAnnotationsResponse
3126−searchAnnotationsResponse =
3127− SearchAnnotationsResponse
3128− { _sarAnnotations = Nothing
3129− , _sarNextPageToken = Nothing
3130− }
3131−
3132−-- | The matching annotations.
3133−sarAnnotations :: Lens' SearchAnnotationsResponse [Annotation]
3134−sarAnnotations
3135− = lens _sarAnnotations
3136− (\ s a -> s{_sarAnnotations = a})
3137− . _Default
3138− . _Coerce
3139−
3140−-- | The continuation token, which is used to page through large result sets.
3141−-- Provide this value in a subsequent request to return the next page of
3142−-- results. This field will be empty if there aren\'t any additional
3143−-- results.
3144−sarNextPageToken :: Lens' SearchAnnotationsResponse (Maybe Text)
3145−sarNextPageToken
3146− = lens _sarNextPageToken
3147− (\ s a -> s{_sarNextPageToken = a})
3148−
3149−instance FromJSON SearchAnnotationsResponse where
3150− parseJSON
3151− = withObject "SearchAnnotationsResponse"
3152− (\ o ->
3153− SearchAnnotationsResponse <$>
3154− (o .:? "annotations" .!= mempty) <*>
3155− (o .:? "nextPageToken"))
3156−
3157−instance ToJSON SearchAnnotationsResponse where
3158− toJSON SearchAnnotationsResponse{..}
3159− = object
3160− (catMaybes
3161− [("annotations" .=) <$> _sarAnnotations,
3162− ("nextPageToken" .=) <$> _sarNextPageToken])
3163−
3164−--
3165−-- /See:/ 'searchAnnotationSetsRequest' smart constructor.
3166−data SearchAnnotationSetsRequest = SearchAnnotationSetsRequest
3167− { _sasrReferenceSetId :: !(Maybe Text)
3168− , _sasrTypes :: !(Maybe [SearchAnnotationSetsRequestTypesItem])
3169− , _sasrDatasetIds :: !(Maybe [Text])
3170− , _sasrName :: !(Maybe Text)
3171− , _sasrPageToken :: !(Maybe Text)
3172− , _sasrPageSize :: !(Maybe Int32)
3173− } deriving (Eq,Show,Data,Typeable,Generic)
3174−
3175−-- | Creates a value of 'SearchAnnotationSetsRequest' with the minimum fields required to make a request.
3176−--
3177−-- Use one of the following lenses to modify other fields as desired:
3178−--
3179−-- * 'sasrReferenceSetId'
3180−--
3181−-- * 'sasrTypes'
3182−--
3183−-- * 'sasrDatasetIds'
3184−--
3185−-- * 'sasrName'
3186−--
3187−-- * 'sasrPageToken'
3188−--
3189−-- * 'sasrPageSize'
3190−searchAnnotationSetsRequest
3191− :: SearchAnnotationSetsRequest
3192−searchAnnotationSetsRequest =
3193− SearchAnnotationSetsRequest
3194− { _sasrReferenceSetId = Nothing
3195− , _sasrTypes = Nothing
3196− , _sasrDatasetIds = Nothing
3197− , _sasrName = Nothing
3198− , _sasrPageToken = Nothing
3199− , _sasrPageSize = Nothing
3200− }
3201−
3202−-- | If specified, only annotation sets associated with the given reference
3203−-- set are returned.
3204−sasrReferenceSetId :: Lens' SearchAnnotationSetsRequest (Maybe Text)
3205−sasrReferenceSetId
3206− = lens _sasrReferenceSetId
3207− (\ s a -> s{_sasrReferenceSetId = a})
3208−
3209−-- | If specified, only annotation sets that have any of these types are
3210−-- returned.
3211−sasrTypes :: Lens' SearchAnnotationSetsRequest [SearchAnnotationSetsRequestTypesItem]
3212−sasrTypes
3213− = lens _sasrTypes (\ s a -> s{_sasrTypes = a}) .
3214− _Default
3215− . _Coerce
3216−
3217−-- | The dataset IDs to search within. Caller must have READ access to these
3218−-- datasets.
3219−sasrDatasetIds :: Lens' SearchAnnotationSetsRequest [Text]
3220−sasrDatasetIds
3221− = lens _sasrDatasetIds
3222− (\ s a -> s{_sasrDatasetIds = a})
3223− . _Default
3224− . _Coerce
3225−
3226−-- | Only return annotations sets for which a substring of the name matches
3227−-- this string (case insensitive).
3228−sasrName :: Lens' SearchAnnotationSetsRequest (Maybe Text)
3229−sasrName = lens _sasrName (\ s a -> s{_sasrName = a})
3230−
3231−-- | The continuation token, which is used to page through large result sets.
3232−-- To get the next page of results, set this parameter to the value of
3233−-- nextPageToken from the previous response.
3234−sasrPageToken :: Lens' SearchAnnotationSetsRequest (Maybe Text)
3235−sasrPageToken
3236− = lens _sasrPageToken
3237− (\ s a -> s{_sasrPageToken = a})
3238−
3239−-- | Specifies number of results to return in a single page. If unspecified,
3240−-- it will default to 128. The maximum value is 1024.
3241−sasrPageSize :: Lens' SearchAnnotationSetsRequest (Maybe Int32)
3242−sasrPageSize
3243− = lens _sasrPageSize (\ s a -> s{_sasrPageSize = a})
3244−
3245−instance FromJSON SearchAnnotationSetsRequest where
3246− parseJSON
3247− = withObject "SearchAnnotationSetsRequest"
3248− (\ o ->
3249− SearchAnnotationSetsRequest <$>
3250− (o .:? "referenceSetId") <*>
3251− (o .:? "types" .!= mempty)
3252− <*> (o .:? "datasetIds" .!= mempty)
3253− <*> (o .:? "name")
3254− <*> (o .:? "pageToken")
3255− <*> (o .:? "pageSize"))
3256−
3257−instance ToJSON SearchAnnotationSetsRequest where
3258− toJSON SearchAnnotationSetsRequest{..}
3259− = object
3260− (catMaybes
3261− [("referenceSetId" .=) <$> _sasrReferenceSetId,
3262− ("types" .=) <$> _sasrTypes,
3263− ("datasetIds" .=) <$> _sasrDatasetIds,
3264− ("name" .=) <$> _sasrName,
3265− ("pageToken" .=) <$> _sasrPageToken,
3266− ("pageSize" .=) <$> _sasrPageSize])
3267−
3268−-- | The variant search response.
3269−--
3270−-- /See:/ 'searchVariantsResponse' smart constructor.
3271−data SearchVariantsResponse = SearchVariantsResponse
3272− { _svrVariants :: !(Maybe [Variant])
3273− , _svrNextPageToken :: !(Maybe Text)
3274− } deriving (Eq,Show,Data,Typeable,Generic)
3275−
3276−-- | Creates a value of 'SearchVariantsResponse' with the minimum fields required to make a request.
3277−--
3278−-- Use one of the following lenses to modify other fields as desired:
3279−--
3280−-- * 'svrVariants'
3281−--
3282−-- * 'svrNextPageToken'
3283−searchVariantsResponse
3284− :: SearchVariantsResponse
3285−searchVariantsResponse =
3286− SearchVariantsResponse
3287− { _svrVariants = Nothing
3288− , _svrNextPageToken = Nothing
3289− }
3290−
3291−-- | The list of matching Variants.
3292−svrVariants :: Lens' SearchVariantsResponse [Variant]
3293−svrVariants
3294− = lens _svrVariants (\ s a -> s{_svrVariants = a}) .
3295− _Default
3296− . _Coerce
2300+-- | The list of matching Variants.
2301+svrVariants :: Lens' SearchVariantsResponse [Variant]
2302+svrVariants
2303+ = lens _svrVariants (\ s a -> s{_svrVariants = a}) .
2304+ _Default
2305+ . _Coerce
32972306
32982307-- | The continuation token, which is used to page through large result sets.
32992308-- Provide this value in a subsequent request to return the next page of
@@ -3319,40 +2328,6 @@ instance ToJSON SearchVariantsResponse where
33192328 [("variants" .=) <$> _svrVariants,
33202329 ("nextPageToken" .=) <$> _svrNextPageToken])
33212330
3322−-- | The job creation response.
3323−--
3324−-- /See:/ 'experimentalCreateJobResponse' smart constructor.
3325−newtype ExperimentalCreateJobResponse = ExperimentalCreateJobResponse
3326− { _ecjrJobId :: Maybe Text
3327− } deriving (Eq,Show,Data,Typeable,Generic)
3328−
3329−-- | Creates a value of 'ExperimentalCreateJobResponse' with the minimum fields required to make a request.
3330−--
3331−-- Use one of the following lenses to modify other fields as desired:
3332−--
3333−-- * 'ecjrJobId'
3334−experimentalCreateJobResponse
3335− :: ExperimentalCreateJobResponse
3336−experimentalCreateJobResponse =
3337− ExperimentalCreateJobResponse
3338− { _ecjrJobId = Nothing
3339− }
3340−
3341−-- | A job ID that can be used to get status information.
3342−ecjrJobId :: Lens' ExperimentalCreateJobResponse (Maybe Text)
3343−ecjrJobId
3344− = lens _ecjrJobId (\ s a -> s{_ecjrJobId = a})
3345−
3346−instance FromJSON ExperimentalCreateJobResponse where
3347− parseJSON
3348− = withObject "ExperimentalCreateJobResponse"
3349− (\ o ->
3350− ExperimentalCreateJobResponse <$> (o .:? "jobId"))
3351−
3352−instance ToJSON ExperimentalCreateJobResponse where
3353− toJSON ExperimentalCreateJobResponse{..}
3354− = object (catMaybes [("jobId" .=) <$> _ecjrJobId])
3355−
33562331-- | The call set search request.
33572332--
33582333-- /See:/ 'searchCallSetsRequest' smart constructor.
@@ -3391,7 +2366,7 @@ scsrName = lens _scsrName (\ s a -> s{_scsrName = a})
33912366
33922367-- | The continuation token, which is used to page through large result sets.
33932368-- To get the next page of results, set this parameter to the value of
3394−-- nextPageToken from the previous response.
2369+-- \`nextPageToken\` from the previous response.
33952370scsrPageToken :: Lens' SearchCallSetsRequest (Maybe Text)
33962371scsrPageToken
33972372 = lens _scsrPageToken
@@ -3487,83 +2462,83 @@ instance ToJSON SearchReadsResponse where
34872462 [("nextPageToken" .=) <$> _sNextPageToken,
34882463 ("alignments" .=) <$> _sAlignments])
34892464
3490−-- | Describes a paired-end FASTQ file source for alignment.
34912465--
3492−-- /See:/ 'pairedFastqSource' smart constructor.
3493−data PairedFastqSource = PairedFastqSource
3494− { _pfsFirstSourceURIs :: !(Maybe [Text])
3495− , _pfsMetadata :: !(Maybe FastqMetadata)
3496− , _pfsSecondSourceURIs :: !(Maybe [Text])
2466+-- /See:/ 'program' smart constructor.
2467+data Program = Program
2468+ { _pPrevProgramId :: !(Maybe Text)
2469+ , _pName :: !(Maybe Text)
2470+ , _pVersion :: !(Maybe Text)
2471+ , _pId :: !(Maybe Text)
2472+ , _pCommandLine :: !(Maybe Text)
34972473 } deriving (Eq,Show,Data,Typeable,Generic)
34982474
3499−-- | Creates a value of 'PairedFastqSource' with the minimum fields required to make a request.
2475+-- | Creates a value of 'Program' with the minimum fields required to make a request.
35002476--
35012477-- Use one of the following lenses to modify other fields as desired:
35022478--
3503−-- * 'pfsFirstSourceURIs'
2479+-- * 'pPrevProgramId'
35042480--
3505−-- * 'pfsMetadata'
2481+-- * 'pName'
35062482--
3507−-- * 'pfsSecondSourceURIs'
3508−pairedFastqSource
3509− :: PairedFastqSource
3510−pairedFastqSource =
3511− PairedFastqSource
3512− { _pfsFirstSourceURIs = Nothing
3513− , _pfsMetadata = Nothing
3514− , _pfsSecondSourceURIs = Nothing
2483+-- * 'pVersion'
2484+--
2485+-- * 'pId'
2486+--
2487+-- * 'pCommandLine'
2488+program
2489+ :: Program
2490+program =
2491+ Program
2492+ { _pPrevProgramId = Nothing
2493+ , _pName = Nothing
2494+ , _pVersion = Nothing
2495+ , _pId = Nothing
2496+ , _pCommandLine = Nothing
35152497 }
35162498
3517−-- | A list of URIs pointing at paired end FASTQ files in Google Cloud
3518−-- Storage which will be aligned. The first of each paired file should be
3519−-- specified here, in an order that matches the second of each paired file
3520−-- specified in secondSourceUris. For example: firstSourceUris:
3521−-- [file1_1.fq, file2_1.fq], secondSourceUris: [file1_2.fq, file2_2.fq].
3522−-- The caller must have READ permissions for these files.
3523−pfsFirstSourceURIs :: Lens' PairedFastqSource [Text]
3524−pfsFirstSourceURIs
3525− = lens _pfsFirstSourceURIs
3526− (\ s a -> s{_pfsFirstSourceURIs = a})
3527− . _Default
3528− . _Coerce
2499+-- | The ID of the program run before this one.
2500+pPrevProgramId :: Lens' Program (Maybe Text)
2501+pPrevProgramId
2502+ = lens _pPrevProgramId
2503+ (\ s a -> s{_pPrevProgramId = a})
35292504
3530−-- | Optionally specifies the metadata to be associated with the final
3531−-- aligned read group set.
3532−pfsMetadata :: Lens' PairedFastqSource (Maybe FastqMetadata)
3533−pfsMetadata
3534− = lens _pfsMetadata (\ s a -> s{_pfsMetadata = a})
3535−
3536−-- | A list of URIs pointing at paired end FASTQ files in Google Cloud
3537−-- Storage which will be aligned. The second of each paired file should be
3538−-- specified here, in an order that matches the first of each paired file
3539−-- specified in firstSourceUris. For example: firstSourceUris: [file1_1.fq,
3540−-- file2_1.fq], secondSourceUris: [file1_2.fq, file2_2.fq]. The caller must
3541−-- have READ permissions for these files.
3542−pfsSecondSourceURIs :: Lens' PairedFastqSource [Text]
3543−pfsSecondSourceURIs
3544− = lens _pfsSecondSourceURIs
3545− (\ s a -> s{_pfsSecondSourceURIs = a})
3546− . _Default
3547− . _Coerce
2505+-- | The name of the program.
2506+pName :: Lens' Program (Maybe Text)
2507+pName = lens _pName (\ s a -> s{_pName = a})
2508+
2509+-- | The version of the program run.
2510+pVersion :: Lens' Program (Maybe Text)
2511+pVersion = lens _pVersion (\ s a -> s{_pVersion = a})
2512+
2513+-- | The user specified locally unique ID of the program. Used along with
2514+-- \`prevProgramId\` to define an ordering between programs.
2515+pId :: Lens' Program (Maybe Text)
2516+pId = lens _pId (\ s a -> s{_pId = a})
35482517
3549−instance FromJSON PairedFastqSource where
2518+-- | The command line used to run this program.
2519+pCommandLine :: Lens' Program (Maybe Text)
2520+pCommandLine
2521+ = lens _pCommandLine (\ s a -> s{_pCommandLine = a})
2522+
2523+instance FromJSON Program where
35502524 parseJSON
3551− = withObject "PairedFastqSource"
2525+ = withObject "Program"
35522526 (\ o ->
3553− PairedFastqSource <$>
3554− (o .:? "firstSourceUris" .!= mempty) <*>
3555− (o .:? "metadata")
3556− <*> (o .:? "secondSourceUris" .!= mempty))
2527+ Program <$>
2528+ (o .:? "prevProgramId") <*> (o .:? "name") <*>
2529+ (o .:? "version")
2530+ <*> (o .:? "id")
2531+ <*> (o .:? "commandLine"))
35572532
3558−instance ToJSON PairedFastqSource where
3559− toJSON PairedFastqSource{..}
2533+instance ToJSON Program where
2534+ toJSON Program{..}
35602535 = object
35612536 (catMaybes
3562− [("firstSourceUris" .=) <$> _pfsFirstSourceURIs,
3563− ("metadata" .=) <$> _pfsMetadata,
3564− ("secondSourceUris" .=) <$> _pfsSecondSourceURIs])
2537+ [("prevProgramId" .=) <$> _pPrevProgramId,
2538+ ("name" .=) <$> _pName, ("version" .=) <$> _pVersion,
2539+ ("id" .=) <$> _pId,
2540+ ("commandLine" .=) <$> _pCommandLine])
35652541
3566−-- |
35672542--
35682543-- /See:/ 'searchReferencesRequest' smart constructor.
35692544data SearchReferencesRequest = SearchReferencesRequest
@@ -3604,8 +2579,8 @@ sReferenceSetId
36042579 = lens _sReferenceSetId
36052580 (\ s a -> s{_sReferenceSetId = a})
36062581
3607−-- | If present, return references for which the md5checksum matches. See
3608−-- Reference.md5checksum for construction details.
2582+-- | If present, return references for which the \`md5checksum\` matches. See
2583+-- \`Reference.md5checksum\` for construction details.
36092584sMD5checksums :: Lens' SearchReferencesRequest [Text]
36102585sMD5checksums
36112586 = lens _sMD5checksums
@@ -3614,9 +2589,9 @@ sMD5checksums
36142589 . _Coerce
36152590
36162591-- | If present, return references for which the accession matches this
3617−-- string. Best to give a version number, for example GCF_000001405.26. If
3618−-- only the main accession number is given then all records with that main
3619−-- accession will be returned, whichever version. Note that different
2592+-- string. Best to give a version number, for example \`GCF_000001405.26\`.
2593+-- If only the main accession number is given then all records with that
2594+-- main accession will be returned, whichever version. Note that different
36202595-- versions will have different sequences.
36212596sAccessions :: Lens' SearchReferencesRequest [Text]
36222597sAccessions
@@ -3626,7 +2601,7 @@ sAccessions
36262601
36272602-- | The continuation token, which is used to page through large result sets.
36282603-- To get the next page of results, set this parameter to the value of
3629−-- nextPageToken from the previous response.
2604+-- \`nextPageToken\` from the previous response.
36302605sPageToken :: Lens' SearchReferencesRequest (Maybe Text)
36312606sPageToken
36322607 = lens _sPageToken (\ s a -> s{_sPageToken = a})
@@ -3711,7 +2686,7 @@ instance ToJSON SearchReferenceSetsResponse where
37112686 [("nextPageToken" .=) <$> _srsrNextPageToken,
37122687 ("referenceSets" .=) <$> _srsrReferenceSets])
37132688
3714−-- | A 0-based half-open genomic coordinate range over a reference sequence.
2689+-- | A 0-based half-open genomic coordinate range for search requests.
37152690--
37162691-- /See:/ 'range' smart constructor.
37172692data Range = Range
@@ -3738,19 +2713,17 @@ range =
37382713 , _rEnd = Nothing
37392714 }
37402715
3741−-- | The start position of the range on the reference, 0-based inclusive. If
3742−-- specified, referenceName must also be specified.
2716+-- | The start position of the range on the reference, 0-based inclusive.
37432717rStart :: Lens' Range (Maybe Int64)
37442718rStart = lens _rStart (\ s a -> s{_rStart = a})
37452719
3746−-- | The reference sequence name, for example chr1, 1, or chrX.
2720+-- | The reference sequence name, for example \`chr1\`, \`1\`, or \`chrX\`.
37472721rReferenceName :: Lens' Range (Maybe Text)
37482722rReferenceName
37492723 = lens _rReferenceName
37502724 (\ s a -> s{_rReferenceName = a})
37512725
3752−-- | The end position of the range on the reference, 0-based exclusive. If
3753−-- specified, referenceName must also be specified.
2726+-- | The end position of the range on the reference, 0-based exclusive.
37542727rEnd :: Lens' Range (Maybe Int64)
37552728rEnd = lens _rEnd (\ s a -> s{_rEnd = a})
37562729
@@ -3773,8 +2746,8 @@ instance ToJSON Range where
37732746-- | A read group set is a logical collection of read groups, which are
37742747-- collections of reads produced by a sequencer. A read group set typically
37752748-- models reads corresponding to one sample, sequenced one way, and aligned
3776−-- one way. - A read group set belongs to one dataset. - A read group
3777−-- belongs to one read group set. - A read belongs to one read group.
2749+-- one way. * A read group set belongs to one dataset. * A read group
2750+-- belongs to one read group set. * A read belongs to one read group.
37782751--
37792752-- /See:/ 'readGroupSet' smart constructor.
37802753data ReadGroupSet = ReadGroupSet
@@ -3833,11 +2806,11 @@ rgsDatasetId :: Lens' ReadGroupSet (Maybe Text)
38332806rgsDatasetId
38342807 = lens _rgsDatasetId (\ s a -> s{_rgsDatasetId = a})
38352808
3836−-- | The read group set ID.
2809+-- | The server-generated read group set ID, unique for all read group sets.
38372810rgsId :: Lens' ReadGroupSet (Maybe Text)
38382811rgsId = lens _rgsId (\ s a -> s{_rgsId = a})
38392812
3840−-- | A string which maps to an array of values.
2813+-- | A map of additional read group set information.
38412814rgsInfo :: Lens' ReadGroupSet (Maybe ReadGroupSetInfo)
38422815rgsInfo = lens _rgsInfo (\ s a -> s{_rgsInfo = a})
38432816
@@ -3879,232 +2852,113 @@ instance ToJSON ReadGroupSet where
38792852 ("readGroups" .=) <$> _rgsReadGroups,
38802853 ("filename" .=) <$> _rgsFilename])
38812854
3882−-- | A Job represents an ongoing process that can be monitored for status
3883−-- information.
3884−--
3885−-- /See:/ 'job' smart constructor.
3886−data Job = Job
3887− { _jDetailedStatus :: !(Maybe Text)
3888− , _jStatus :: !(Maybe JobStatus)
3889− , _jCreated :: !(Maybe Int64)
3890− , _jProjectNumber :: !(Maybe Int64)
3891− , _jWarnings :: !(Maybe [Text])
3892− , _jImportedIds :: !(Maybe [Text])
3893− , _jId :: !(Maybe Text)
3894− , _jErrors :: !(Maybe [Text])
3895− , _jRequest :: !(Maybe JobRequest)
2855+-- | The read group set export request.
2856+--
2857+-- /See:/ 'exportReadGroupSetRequest' smart constructor.
2858+data ExportReadGroupSetRequest = ExportReadGroupSetRequest
2859+ { _ergsrReferenceNames :: !(Maybe [Text])
2860+ , _ergsrExportURI :: !(Maybe Text)
2861+ , _ergsrProjectId :: !(Maybe Text)
38962862 } deriving (Eq,Show,Data,Typeable,Generic)
38972863
3898−-- | Creates a value of 'Job' with the minimum fields required to make a request.
2864+-- | Creates a value of 'ExportReadGroupSetRequest' with the minimum fields required to make a request.
38992865--
39002866-- Use one of the following lenses to modify other fields as desired:
39012867--
3902−-- * 'jDetailedStatus'
3903−--
3904−-- * 'jStatus'
3905−--
3906−-- * 'jCreated'
3907−--
3908−-- * 'jProjectNumber'
3909−--
3910−-- * 'jWarnings'
3911−--
3912−-- * 'jImportedIds'
3913−--
3914−-- * 'jId'
2868+-- * 'ergsrReferenceNames'
39152869--
3916−-- * 'jErrors'
2870+-- * 'ergsrExportURI'
39172871--
3918−-- * 'jRequest'
3919−job
3920− :: Job
3921−job =
3922− Job
3923− { _jDetailedStatus = Nothing
3924− , _jStatus = Nothing
3925− , _jCreated = Nothing
3926− , _jProjectNumber = Nothing
3927− , _jWarnings = Nothing
3928− , _jImportedIds = Nothing
3929− , _jId = Nothing
3930− , _jErrors = Nothing
3931− , _jRequest = Nothing
2872+-- * 'ergsrProjectId'
2873+exportReadGroupSetRequest
2874+ :: ExportReadGroupSetRequest
2875+exportReadGroupSetRequest =
2876+ ExportReadGroupSetRequest
2877+ { _ergsrReferenceNames = Nothing
2878+ , _ergsrExportURI = Nothing
2879+ , _ergsrProjectId = Nothing
39322880 }
39332881
3934−-- | A more detailed description of this job\'s current status.
3935−jDetailedStatus :: Lens' Job (Maybe Text)
3936−jDetailedStatus
3937− = lens _jDetailedStatus
3938− (\ s a -> s{_jDetailedStatus = a})
3939−
3940−-- | The status of this job.
3941−jStatus :: Lens' Job (Maybe JobStatus)
3942−jStatus = lens _jStatus (\ s a -> s{_jStatus = a})
3943−
3944−-- | The date this job was created, in milliseconds from the epoch.
3945−jCreated :: Lens' Job (Maybe Int64)
3946−jCreated = lens _jCreated (\ s a -> s{_jCreated = a})
3947−
3948−-- | The Google Developers Console project number to which this job belongs.
3949−jProjectNumber :: Lens' Job (Maybe Int64)
3950−jProjectNumber
3951− = lens _jProjectNumber
3952− (\ s a -> s{_jProjectNumber = a})
3953−
3954−-- | Any warnings that occurred during processing.
3955−jWarnings :: Lens' Job [Text]
3956−jWarnings
3957− = lens _jWarnings (\ s a -> s{_jWarnings = a}) .
3958− _Default
3959− . _Coerce
3960−
3961−-- | If this Job represents an import, this field will contain the IDs of the
3962−-- objects that were successfully imported.
3963−jImportedIds :: Lens' Job [Text]
3964−jImportedIds
3965− = lens _jImportedIds (\ s a -> s{_jImportedIds = a})
2882+-- | The reference names to export. If this is not specified, all reference
2883+-- sequences, including unmapped reads, are exported. Use \`*\` to export
2884+-- only unmapped reads.
2885+ergsrReferenceNames :: Lens' ExportReadGroupSetRequest [Text]
2886+ergsrReferenceNames
2887+ = lens _ergsrReferenceNames
2888+ (\ s a -> s{_ergsrReferenceNames = a})
39662889 . _Default
39672890 . _Coerce
39682891
3969−-- | The job ID.
3970−jId :: Lens' Job (Maybe Text)
3971−jId = lens _jId (\ s a -> s{_jId = a})
3972−
3973−-- | Any errors that occurred during processing.
3974−jErrors :: Lens' Job [Text]
3975−jErrors
3976− = lens _jErrors (\ s a -> s{_jErrors = a}) . _Default
3977− . _Coerce
2892+-- | Required. A Google Cloud Storage URI for the exported BAM file. The
2893+-- currently authenticated user must have write access to the new file. An
2894+-- error will be returned if the URI already contains data.
2895+ergsrExportURI :: Lens' ExportReadGroupSetRequest (Maybe Text)
2896+ergsrExportURI
2897+ = lens _ergsrExportURI
2898+ (\ s a -> s{_ergsrExportURI = a})
39782899
3979−-- | A summarized representation of the original service request.
3980−jRequest :: Lens' Job (Maybe JobRequest)
3981−jRequest = lens _jRequest (\ s a -> s{_jRequest = a})
2900+-- | Required. The Google Developers Console project ID that owns this
2901+-- export.
2902+ergsrProjectId :: Lens' ExportReadGroupSetRequest (Maybe Text)
2903+ergsrProjectId
2904+ = lens _ergsrProjectId
2905+ (\ s a -> s{_ergsrProjectId = a})
39822906
3983−instance FromJSON Job where
2907+instance FromJSON ExportReadGroupSetRequest where
39842908 parseJSON
3985− = withObject "Job"
2909+ = withObject "ExportReadGroupSetRequest"
39862910 (\ o ->
3987− Job <$>
3988− (o .:? "detailedStatus") <*> (o .:? "status") <*>
3989− (o .:? "created")
3990− <*> (o .:? "projectNumber")
3991− <*> (o .:? "warnings" .!= mempty)
3992− <*> (o .:? "importedIds" .!= mempty)
3993− <*> (o .:? "id")
3994− <*> (o .:? "errors" .!= mempty)
3995− <*> (o .:? "request"))
2911+ ExportReadGroupSetRequest <$>
2912+ (o .:? "referenceNames" .!= mempty) <*>
2913+ (o .:? "exportUri")
2914+ <*> (o .:? "projectId"))
39962915
3997−instance ToJSON Job where
3998− toJSON Job{..}
2916+instance ToJSON ExportReadGroupSetRequest where
2917+ toJSON ExportReadGroupSetRequest{..}
39992918 = object
40002919 (catMaybes
4001− [("detailedStatus" .=) <$> _jDetailedStatus,
4002− ("status" .=) <$> _jStatus,
4003− ("created" .=) <$> _jCreated,
4004− ("projectNumber" .=) <$> _jProjectNumber,
4005− ("warnings" .=) <$> _jWarnings,
4006− ("importedIds" .=) <$> _jImportedIds,
4007− ("id" .=) <$> _jId, ("errors" .=) <$> _jErrors,
4008− ("request" .=) <$> _jRequest])
4009−
4010−-- | The variant data export response.
4011−--
4012−-- /See:/ 'exportVariantSetResponse' smart constructor.
4013−newtype ExportVariantSetResponse = ExportVariantSetResponse
4014− { _evsrJobId :: Maybe Text
4015− } deriving (Eq,Show,Data,Typeable,Generic)
4016−
4017−-- | Creates a value of 'ExportVariantSetResponse' with the minimum fields required to make a request.
4018−--
4019−-- Use one of the following lenses to modify other fields as desired:
4020−--
4021−-- * 'evsrJobId'
4022−exportVariantSetResponse
4023− :: ExportVariantSetResponse
4024−exportVariantSetResponse =
4025− ExportVariantSetResponse
4026− { _evsrJobId = Nothing
4027− }
4028−
4029−-- | A job ID that can be used to get status information.
4030−evsrJobId :: Lens' ExportVariantSetResponse (Maybe Text)
4031−evsrJobId
4032− = lens _evsrJobId (\ s a -> s{_evsrJobId = a})
4033−
4034−instance FromJSON ExportVariantSetResponse where
4035− parseJSON
4036− = withObject "ExportVariantSetResponse"
4037− (\ o -> ExportVariantSetResponse <$> (o .:? "jobId"))
4038−
4039−instance ToJSON ExportVariantSetResponse where
4040− toJSON ExportVariantSetResponse{..}
4041− = object (catMaybes [("jobId" .=) <$> _evsrJobId])
4042−
4043−-- | The read group set align response.
4044−--
4045−-- /See:/ 'alignReadGroupSetsResponse' smart constructor.
4046−newtype AlignReadGroupSetsResponse = AlignReadGroupSetsResponse
4047− { _argsrJobId :: Maybe Text
4048− } deriving (Eq,Show,Data,Typeable,Generic)
4049−
4050−-- | Creates a value of 'AlignReadGroupSetsResponse' with the minimum fields required to make a request.
4051−--
4052−-- Use one of the following lenses to modify other fields as desired:
4053−--
4054−-- * 'argsrJobId'
4055−alignReadGroupSetsResponse
4056− :: AlignReadGroupSetsResponse
4057−alignReadGroupSetsResponse =
4058− AlignReadGroupSetsResponse
4059− { _argsrJobId = Nothing
4060− }
4061−
4062−-- | A job ID that can be used to get status information.
4063−argsrJobId :: Lens' AlignReadGroupSetsResponse (Maybe Text)
4064−argsrJobId
4065− = lens _argsrJobId (\ s a -> s{_argsrJobId = a})
4066−
4067−instance FromJSON AlignReadGroupSetsResponse where
4068− parseJSON
4069− = withObject "AlignReadGroupSetsResponse"
4070− (\ o ->
4071− AlignReadGroupSetsResponse <$> (o .:? "jobId"))
4072−
4073−instance ToJSON AlignReadGroupSetsResponse where
4074− toJSON AlignReadGroupSetsResponse{..}
4075− = object (catMaybes [("jobId" .=) <$> _argsrJobId])
2920+ [("referenceNames" .=) <$> _ergsrReferenceNames,
2921+ ("exportUri" .=) <$> _ergsrExportURI,
2922+ ("projectId" .=) <$> _ergsrProjectId])
40762923
40772924-- | The variant data import response.
40782925--
40792926-- /See:/ 'importVariantsResponse' smart constructor.
40802927newtype ImportVariantsResponse = ImportVariantsResponse
4081− { _ivrJobId :: Maybe Text
2928+ { _ivrCallSetIds :: Maybe [Text]
40822929 } deriving (Eq,Show,Data,Typeable,Generic)
40832930
40842931-- | Creates a value of 'ImportVariantsResponse' with the minimum fields required to make a request.
40852932--
40862933-- Use one of the following lenses to modify other fields as desired:
40872934--
4088−-- * 'ivrJobId'
2935+-- * 'ivrCallSetIds'
40892936importVariantsResponse
40902937 :: ImportVariantsResponse
40912938importVariantsResponse =
40922939 ImportVariantsResponse
4093− { _ivrJobId = Nothing
2940+ { _ivrCallSetIds = Nothing
40942941 }
40952942
4096−-- | A job ID that can be used to get status information.
4097−ivrJobId :: Lens' ImportVariantsResponse (Maybe Text)
4098−ivrJobId = lens _ivrJobId (\ s a -> s{_ivrJobId = a})
2943+-- | IDs of the call sets that were created.
2944+ivrCallSetIds :: Lens' ImportVariantsResponse [Text]
2945+ivrCallSetIds
2946+ = lens _ivrCallSetIds
2947+ (\ s a -> s{_ivrCallSetIds = a})
2948+ . _Default
2949+ . _Coerce
40992950
41002951instance FromJSON ImportVariantsResponse where
41012952 parseJSON
41022953 = withObject "ImportVariantsResponse"
4103− (\ o -> ImportVariantsResponse <$> (o .:? "jobId"))
2954+ (\ o ->
2955+ ImportVariantsResponse <$>
2956+ (o .:? "callSetIds" .!= mempty))
41042957
41052958instance ToJSON ImportVariantsResponse where
41062959 toJSON ImportVariantsResponse{..}
4107− = object (catMaybes [("jobId" .=) <$> _ivrJobId])
2960+ = object
2961+ (catMaybes [("callSetIds" .=) <$> _ivrCallSetIds])
41082962
41092963--
41102964-- /See:/ 'listCoverageBucketsResponse' smart constructor.
@@ -4144,7 +2998,7 @@ lcbrNextPageToken
41442998-- | The length of each coverage bucket in base pairs. Note that buckets at
41452999-- the end of a reference sequence may be shorter. This value is omitted if
41463000-- the bucket width is infinity (the default behaviour, with no range or
4147−-- targetBucketWidth).
3001+-- \`targetBucketWidth\`).
41483002lcbrBucketWidth :: Lens' ListCoverageBucketsResponse (Maybe Int64)
41493003lcbrBucketWidth
41503004 = lens _lcbrBucketWidth
@@ -4152,8 +3006,8 @@ lcbrBucketWidth
41523006
41533007-- | The coverage buckets. The list of buckets is sparse; a bucket with 0
41543008-- overlapping reads is not returned. A bucket never crosses more than one
4155−-- reference sequence. Each bucket has width bucketWidth, unless its end is
4156−-- the end of the reference sequence.
3009+-- reference sequence. Each bucket has width \`bucketWidth\`, unless its
3010+-- end is the end of the reference sequence.
41573011lcbrCoverageBuckets :: Lens' ListCoverageBucketsResponse [CoverageBucket]
41583012lcbrCoverageBuckets
41593013 = lens _lcbrCoverageBuckets
@@ -4177,39 +3031,89 @@ instance ToJSON ListCoverageBucketsResponse where
41773031 ("bucketWidth" .=) <$> _lcbrBucketWidth,
41783032 ("coverageBuckets" .=) <$> _lcbrCoverageBuckets])
41793033
3034+-- | Request message for \`TestIamPermissions\` method.
3035+--
3036+-- /See:/ 'testIAMPermissionsRequest' smart constructor.
3037+newtype TestIAMPermissionsRequest = TestIAMPermissionsRequest
3038+ { _tiprPermissions :: Maybe [Text]
3039+ } deriving (Eq,Show,Data,Typeable,Generic)
3040+
3041+-- | Creates a value of 'TestIAMPermissionsRequest' with the minimum fields required to make a request.
3042+--
3043+-- Use one of the following lenses to modify other fields as desired:
3044+--
3045+-- * 'tiprPermissions'
3046+testIAMPermissionsRequest
3047+ :: TestIAMPermissionsRequest
3048+testIAMPermissionsRequest =
3049+ TestIAMPermissionsRequest
3050+ { _tiprPermissions = Nothing
3051+ }
3052+
3053+-- | REQUIRED: The set of permissions to check for the \'resource\'.
3054+-- Permissions with wildcards (such as \'*\' or \'storage.*\') are not
3055+-- allowed. Allowed permissions are: * \`genomics.datasets.create\` *
3056+-- \`genomics.datasets.delete\` * \`genomics.datasets.get\` *
3057+-- \`genomics.datasets.list\` * \`genomics.datasets.update\` *
3058+-- \`genomics.datasets.getIamPolicy\` * \`genomics.datasets.setIamPolicy\`
3059+tiprPermissions :: Lens' TestIAMPermissionsRequest [Text]
3060+tiprPermissions
3061+ = lens _tiprPermissions
3062+ (\ s a -> s{_tiprPermissions = a})
3063+ . _Default
3064+ . _Coerce
3065+
3066+instance FromJSON TestIAMPermissionsRequest where
3067+ parseJSON
3068+ = withObject "TestIAMPermissionsRequest"
3069+ (\ o ->
3070+ TestIAMPermissionsRequest <$>
3071+ (o .:? "permissions" .!= mempty))
3072+
3073+instance ToJSON TestIAMPermissionsRequest where
3074+ toJSON TestIAMPermissionsRequest{..}
3075+ = object
3076+ (catMaybes [("permissions" .=) <$> _tiprPermissions])
3077+
41803078-- | The read group set import response.
41813079--
41823080-- /See:/ 'importReadGroupSetsResponse' smart constructor.
41833081newtype ImportReadGroupSetsResponse = ImportReadGroupSetsResponse
4184− { _irgsrJobId :: Maybe Text
3082+ { _irgsrReadGroupSetIds :: Maybe [Text]
41853083 } deriving (Eq,Show,Data,Typeable,Generic)
41863084
41873085-- | Creates a value of 'ImportReadGroupSetsResponse' with the minimum fields required to make a request.
41883086--
41893087-- Use one of the following lenses to modify other fields as desired:
41903088--
4191−-- * 'irgsrJobId'
3089+-- * 'irgsrReadGroupSetIds'
41923090importReadGroupSetsResponse
41933091 :: ImportReadGroupSetsResponse
41943092importReadGroupSetsResponse =
41953093 ImportReadGroupSetsResponse
4196− { _irgsrJobId = Nothing
3094+ { _irgsrReadGroupSetIds = Nothing
41973095 }
41983096
4199−-- | A job ID that can be used to get status information.
4200−irgsrJobId :: Lens' ImportReadGroupSetsResponse (Maybe Text)
4201−irgsrJobId
4202− = lens _irgsrJobId (\ s a -> s{_irgsrJobId = a})
3097+-- | IDs of the read group sets that were created.
3098+irgsrReadGroupSetIds :: Lens' ImportReadGroupSetsResponse [Text]
3099+irgsrReadGroupSetIds
3100+ = lens _irgsrReadGroupSetIds
3101+ (\ s a -> s{_irgsrReadGroupSetIds = a})
3102+ . _Default
3103+ . _Coerce
42033104
42043105instance FromJSON ImportReadGroupSetsResponse where
42053106 parseJSON
42063107 = withObject "ImportReadGroupSetsResponse"
42073108 (\ o ->
4208− ImportReadGroupSetsResponse <$> (o .:? "jobId"))
3109+ ImportReadGroupSetsResponse <$>
3110+ (o .:? "readGroupSetIds" .!= mempty))
42093111
42103112instance ToJSON ImportReadGroupSetsResponse where
42113113 toJSON ImportReadGroupSetsResponse{..}
4212− = object (catMaybes [("jobId" .=) <$> _irgsrJobId])
3114+ = object
3115+ (catMaybes
3116+ [("readGroupSetIds" .=) <$> _irgsrReadGroupSetIds])
42133117
42143118-- | A linear alignment can be represented by one CIGAR string. Describes the
42153119-- mapped position and local alignment of the read to the reference.
@@ -4236,280 +3140,44 @@ linearAlignment =
42363140 LinearAlignment
42373141 { _laCigar = Nothing
42383142 , _laMAppingQuality = Nothing
4239− , _laPosition = Nothing
4240− }
4241−
4242−-- | Represents the local alignment of this sequence (alignment matches,
4243−-- indels, etc) against the reference.
4244−laCigar :: Lens' LinearAlignment [CigarUnit]
4245−laCigar
4246− = lens _laCigar (\ s a -> s{_laCigar = a}) . _Default
4247− . _Coerce
4248−
4249−-- | The mapping quality of this alignment. Represents how likely the read
4250−-- maps to this position as opposed to other locations.
4251−laMAppingQuality :: Lens' LinearAlignment (Maybe Int32)
4252−laMAppingQuality
4253− = lens _laMAppingQuality
4254− (\ s a -> s{_laMAppingQuality = a})
4255−
4256−-- | The position of this alignment.
4257−laPosition :: Lens' LinearAlignment (Maybe Position)
4258−laPosition
4259− = lens _laPosition (\ s a -> s{_laPosition = a})
4260−
4261−instance FromJSON LinearAlignment where
4262− parseJSON
4263− = withObject "LinearAlignment"
4264− (\ o ->
4265− LinearAlignment <$>
4266− (o .:? "cigar" .!= mempty) <*>
4267− (o .:? "mappingQuality")
4268− <*> (o .:? "position"))
4269−
4270−instance ToJSON LinearAlignment where
4271− toJSON LinearAlignment{..}
4272− = object
4273− (catMaybes
4274− [("cigar" .=) <$> _laCigar,
4275− ("mappingQuality" .=) <$> _laMAppingQuality,
4276− ("position" .=) <$> _laPosition])
4277−
4278−-- | Metadata describes a single piece of variant call metadata. These data
4279−-- include a top level key and either a single value string (value) or a
4280−-- list of key-value pairs (info.) Value and info are mutually exclusive.
4281−--
4282−-- /See:/ 'metadata' smart constructor.
4283−data Metadata = Metadata
4284− { _mValue :: !(Maybe Text)
4285− , _mKey :: !(Maybe Text)
4286− , _mId :: !(Maybe Text)
4287− , _mType :: !(Maybe MetadataType)
4288− , _mNumber :: !(Maybe Text)
4289− , _mDescription :: !(Maybe Text)
4290− , _mInfo :: !(Maybe MetadataInfo)
4291− } deriving (Eq,Show,Data,Typeable,Generic)
4292−
4293−-- | Creates a value of 'Metadata' with the minimum fields required to make a request.
4294−--
4295−-- Use one of the following lenses to modify other fields as desired:
4296−--
4297−-- * 'mValue'
4298−--
4299−-- * 'mKey'
4300−--
4301−-- * 'mId'
4302−--
4303−-- * 'mType'
4304−--
4305−-- * 'mNumber'
4306−--
4307−-- * 'mDescription'
4308−--
4309−-- * 'mInfo'
4310−metadata
4311− :: Metadata
4312−metadata =
4313− Metadata
4314− { _mValue = Nothing
4315− , _mKey = Nothing
4316− , _mId = Nothing
4317− , _mType = Nothing
4318− , _mNumber = Nothing
4319− , _mDescription = Nothing
4320− , _mInfo = Nothing
4321− }
4322−
4323−-- | The value field for simple metadata
4324−mValue :: Lens' Metadata (Maybe Text)
4325−mValue = lens _mValue (\ s a -> s{_mValue = a})
4326−
4327−-- | The top-level key.
4328−mKey :: Lens' Metadata (Maybe Text)
4329−mKey = lens _mKey (\ s a -> s{_mKey = a})
4330−
4331−-- | User-provided ID field, not enforced by this API. Two or more pieces of
4332−-- structured metadata with identical id and key fields are considered
4333−-- equivalent.
4334−mId :: Lens' Metadata (Maybe Text)
4335−mId = lens _mId (\ s a -> s{_mId = a})
4336−
4337−-- | The type of data. Possible types include: Integer, Float, Flag,
4338−-- Character, and String.
4339−mType :: Lens' Metadata (Maybe MetadataType)
4340−mType = lens _mType (\ s a -> s{_mType = a})
4341−
4342−-- | The number of values that can be included in a field described by this
4343−-- metadata.
4344−mNumber :: Lens' Metadata (Maybe Text)
4345−mNumber = lens _mNumber (\ s a -> s{_mNumber = a})
4346−
4347−-- | A textual description of this metadata.
4348−mDescription :: Lens' Metadata (Maybe Text)
4349−mDescription
4350− = lens _mDescription (\ s a -> s{_mDescription = a})
4351−
4352−-- | A string which maps to an array of values.
4353−mInfo :: Lens' Metadata (Maybe MetadataInfo)
4354−mInfo = lens _mInfo (\ s a -> s{_mInfo = a})
4355−
4356−instance FromJSON Metadata where
4357− parseJSON
4358− = withObject "Metadata"
4359− (\ o ->
4360− Metadata <$>
4361− (o .:? "value") <*> (o .:? "key") <*> (o .:? "id")
4362− <*> (o .:? "type")
4363− <*> (o .:? "number")
4364− <*> (o .:? "description")
4365− <*> (o .:? "info"))
4366−
4367−instance ToJSON Metadata where
4368− toJSON Metadata{..}
4369− = object
4370− (catMaybes
4371− [("value" .=) <$> _mValue, ("key" .=) <$> _mKey,
4372− ("id" .=) <$> _mId, ("type" .=) <$> _mType,
4373− ("number" .=) <$> _mNumber,
4374− ("description" .=) <$> _mDescription,
4375− ("info" .=) <$> _mInfo])
4376−
4377−-- | The read group set call response.
4378−--
4379−-- /See:/ 'callReadGroupSetsResponse' smart constructor.
4380−newtype CallReadGroupSetsResponse = CallReadGroupSetsResponse
4381− { _crgsrJobId :: Maybe Text
4382− } deriving (Eq,Show,Data,Typeable,Generic)
4383−
4384−-- | Creates a value of 'CallReadGroupSetsResponse' with the minimum fields required to make a request.
4385−--
4386−-- Use one of the following lenses to modify other fields as desired:
4387−--
4388−-- * 'crgsrJobId'
4389−callReadGroupSetsResponse
4390− :: CallReadGroupSetsResponse
4391−callReadGroupSetsResponse =
4392− CallReadGroupSetsResponse
4393− { _crgsrJobId = Nothing
4394− }
4395−
4396−-- | A job ID that can be used to get status information.
4397−crgsrJobId :: Lens' CallReadGroupSetsResponse (Maybe Text)
4398−crgsrJobId
4399− = lens _crgsrJobId (\ s a -> s{_crgsrJobId = a})
4400−
4401−instance FromJSON CallReadGroupSetsResponse where
4402− parseJSON
4403− = withObject "CallReadGroupSetsResponse"
4404− (\ o ->
4405− CallReadGroupSetsResponse <$> (o .:? "jobId"))
4406−
4407−instance ToJSON CallReadGroupSetsResponse where
4408− toJSON CallReadGroupSetsResponse{..}
4409− = object (catMaybes [("jobId" .=) <$> _crgsrJobId])
4410−
4411−-- | An annotation set is a logical grouping of annotations that share
4412−-- consistent type information and provenance. Examples of annotation sets
4413−-- include \'all genes from refseq\', and \'all variant annotations from
4414−-- ClinVar\'.
4415−--
4416−-- /See:/ 'annotationSet' smart constructor.
4417−data AnnotationSet = AnnotationSet
4418− { _asReferenceSetId :: !(Maybe Text)
4419− , _asName :: !(Maybe Text)
4420− , _asDatasetId :: !(Maybe Text)
4421− , _asId :: !(Maybe Text)
4422− , _asType :: !(Maybe AnnotationSetType)
4423− , _asSourceURI :: !(Maybe Text)
4424− , _asInfo :: !(Maybe AnnotationSetInfo)
4425− } deriving (Eq,Show,Data,Typeable,Generic)
4426−
4427−-- | Creates a value of 'AnnotationSet' with the minimum fields required to make a request.
4428−--
4429−-- Use one of the following lenses to modify other fields as desired:
4430−--
4431−-- * 'asReferenceSetId'
4432−--
4433−-- * 'asName'
4434−--
4435−-- * 'asDatasetId'
4436−--
4437−-- * 'asId'
4438−--
4439−-- * 'asType'
4440−--
4441−-- * 'asSourceURI'
4442−--
4443−-- * 'asInfo'
4444−annotationSet
4445− :: AnnotationSet
4446−annotationSet =
4447− AnnotationSet
4448− { _asReferenceSetId = Nothing
4449− , _asName = Nothing
4450− , _asDatasetId = Nothing
4451− , _asId = Nothing
4452− , _asType = Nothing
4453− , _asSourceURI = Nothing
4454− , _asInfo = Nothing
3143+ , _laPosition = Nothing
44553144 }
44563145
4457−-- | The ID of the reference set that defines the coordinate space for this
4458−-- set\'s annotations.
4459−asReferenceSetId :: Lens' AnnotationSet (Maybe Text)
4460−asReferenceSetId
4461− = lens _asReferenceSetId
4462− (\ s a -> s{_asReferenceSetId = a})
4463−
4464−-- | The display name for this annotation set.
4465−asName :: Lens' AnnotationSet (Maybe Text)
4466−asName = lens _asName (\ s a -> s{_asName = a})
4467−
4468−-- | The ID of the containing dataset.
4469−asDatasetId :: Lens' AnnotationSet (Maybe Text)
4470−asDatasetId
4471− = lens _asDatasetId (\ s a -> s{_asDatasetId = a})
4472−
4473−-- | The generated unique ID for this annotation set.
4474−asId :: Lens' AnnotationSet (Maybe Text)
4475−asId = lens _asId (\ s a -> s{_asId = a})
4476−
4477−-- | The type of annotations contained within this set.
4478−asType :: Lens' AnnotationSet (Maybe AnnotationSetType)
4479−asType = lens _asType (\ s a -> s{_asType = a})
4480−
4481−-- | The source URI describing the file from which this annotation set was
4482−-- generated, if any.
4483−asSourceURI :: Lens' AnnotationSet (Maybe Text)
4484−asSourceURI
4485− = lens _asSourceURI (\ s a -> s{_asSourceURI = a})
4486−
4487−-- | A string which maps to an array of values.
4488−asInfo :: Lens' AnnotationSet (Maybe AnnotationSetInfo)
4489−asInfo = lens _asInfo (\ s a -> s{_asInfo = a})
4490−
4491−instance FromJSON AnnotationSet where
3146+-- | Represents the local alignment of this sequence (alignment matches,
3147+-- indels, etc) against the reference.
3148+laCigar :: Lens' LinearAlignment [CigarUnit]
3149+laCigar
3150+ = lens _laCigar (\ s a -> s{_laCigar = a}) . _Default
3151+ . _Coerce
3152+
3153+-- | The mapping quality of this alignment. Represents how likely the read
3154+-- maps to this position as opposed to other locations.
3155+laMAppingQuality :: Lens' LinearAlignment (Maybe Int32)
3156+laMAppingQuality
3157+ = lens _laMAppingQuality
3158+ (\ s a -> s{_laMAppingQuality = a})
3159+
3160+-- | The position of this alignment.
3161+laPosition :: Lens' LinearAlignment (Maybe Position)
3162+laPosition
3163+ = lens _laPosition (\ s a -> s{_laPosition = a})
3164+
3165+instance FromJSON LinearAlignment where
44923166 parseJSON
4493− = withObject "AnnotationSet"
3167+ = withObject "LinearAlignment"
44943168 (\ o ->
4495− AnnotationSet <$>
4496− (o .:? "referenceSetId") <*> (o .:? "name") <*>
4497− (o .:? "datasetId")
4498− <*> (o .:? "id")
4499− <*> (o .:? "type")
4500− <*> (o .:? "sourceUri")
4501− <*> (o .:? "info"))
3169+ LinearAlignment <$>
3170+ (o .:? "cigar" .!= mempty) <*>
3171+ (o .:? "mappingQuality")
3172+ <*> (o .:? "position"))
45023173
4503−instance ToJSON AnnotationSet where
4504− toJSON AnnotationSet{..}
3174+instance ToJSON LinearAlignment where
3175+ toJSON LinearAlignment{..}
45053176 = object
45063177 (catMaybes
4507− [("referenceSetId" .=) <$> _asReferenceSetId,
4508− ("name" .=) <$> _asName,
4509− ("datasetId" .=) <$> _asDatasetId,
4510− ("id" .=) <$> _asId, ("type" .=) <$> _asType,
4511− ("sourceUri" .=) <$> _asSourceURI,
4512− ("info" .=) <$> _asInfo])
3178+ [("cigar" .=) <$> _laCigar,
3179+ ("mappingQuality" .=) <$> _laMAppingQuality,
3180+ ("position" .=) <$> _laPosition])
45133181
45143182-- | A variant set is a collection of call sets and variants. It contains
45153183-- summary statistics of those contents. A variant set belongs to a
@@ -4519,7 +3187,7 @@ instance ToJSON AnnotationSet where
45193187data VariantSet = VariantSet
45203188 { _vsDatasetId :: !(Maybe Text)
45213189 , _vsReferenceBounds :: !(Maybe [ReferenceBound])
4522− , _vsMetadata :: !(Maybe [Metadata])
3190+ , _vsMetadata :: !(Maybe [VariantSetMetadata])
45233191 , _vsId :: !(Maybe Text)
45243192 } deriving (Eq,Show,Data,Typeable,Generic)
45253193
@@ -4544,7 +3212,7 @@ variantSet =
45443212 , _vsId = Nothing
45453213 }
45463214
4547−-- | The dataset to which this variant set belongs. Immutable.
3215+-- | The dataset to which this variant set belongs.
45483216vsDatasetId :: Lens' VariantSet (Maybe Text)
45493217vsDatasetId
45503218 = lens _vsDatasetId (\ s a -> s{_vsDatasetId = a})
@@ -4559,13 +3227,13 @@ vsReferenceBounds
45593227 . _Coerce
45603228
45613229-- | The metadata associated with this variant set.
4562−vsMetadata :: Lens' VariantSet [Metadata]
3230+vsMetadata :: Lens' VariantSet [VariantSetMetadata]
45633231vsMetadata
45643232 = lens _vsMetadata (\ s a -> s{_vsMetadata = a}) .
45653233 _Default
45663234 . _Coerce
45673235
4568−-- | The Google-generated ID of the variant set. Immutable.
3236+-- | The server-generated variant set ID, unique across all variant sets.
45693237vsId :: Lens' VariantSet (Maybe Text)
45703238vsId = lens _vsId (\ s a -> s{_vsId = a})
45713239
@@ -4588,6 +3256,47 @@ instance ToJSON VariantSet where
45883256 ("metadata" .=) <$> _vsMetadata,
45893257 ("id" .=) <$> _vsId])
45903258
3259+-- | Response message for \`TestIamPermissions\` method.
3260+--
3261+-- /See:/ 'testIAMPermissionsResponse' smart constructor.
3262+newtype TestIAMPermissionsResponse = TestIAMPermissionsResponse
3263+ { _tiamprPermissions :: Maybe [Text]
3264+ } deriving (Eq,Show,Data,Typeable,Generic)
3265+
3266+-- | Creates a value of 'TestIAMPermissionsResponse' with the minimum fields required to make a request.
3267+--
3268+-- Use one of the following lenses to modify other fields as desired:
3269+--
3270+-- * 'tiamprPermissions'
3271+testIAMPermissionsResponse
3272+ :: TestIAMPermissionsResponse
3273+testIAMPermissionsResponse =
3274+ TestIAMPermissionsResponse
3275+ { _tiamprPermissions = Nothing
3276+ }
3277+
3278+-- | A subset of \`TestPermissionsRequest.permissions\` that the caller is
3279+-- allowed.
3280+tiamprPermissions :: Lens' TestIAMPermissionsResponse [Text]
3281+tiamprPermissions
3282+ = lens _tiamprPermissions
3283+ (\ s a -> s{_tiamprPermissions = a})
3284+ . _Default
3285+ . _Coerce
3286+
3287+instance FromJSON TestIAMPermissionsResponse where
3288+ parseJSON
3289+ = withObject "TestIAMPermissionsResponse"
3290+ (\ o ->
3291+ TestIAMPermissionsResponse <$>
3292+ (o .:? "permissions" .!= mempty))
3293+
3294+instance ToJSON TestIAMPermissionsResponse where
3295+ toJSON TestIAMPermissionsResponse{..}
3296+ = object
3297+ (catMaybes
3298+ [("permissions" .=) <$> _tiamprPermissions])
3299+
45913300-- | The dataset list response.
45923301--
45933302-- /See:/ 'listDatasetsResponse' smart constructor.
@@ -4649,7 +3358,7 @@ data ImportReadGroupSetsRequest = ImportReadGroupSetsRequest
46493358 { _irgsrReferenceSetId :: !(Maybe Text)
46503359 , _irgsrDatasetId :: !(Maybe Text)
46513360 , _irgsrSourceURIs :: !(Maybe [Text])
4652− , _irgsrPartitionStrategy :: !(Maybe ImportReadGroupSetsRequestPartitionStrategy)
3361+ , _irgsrPartitionStrategy :: !(Maybe Text)
46533362 } deriving (Eq,Show,Data,Typeable,Generic)
46543363
46553364-- | Creates a value of 'ImportReadGroupSetsRequest' with the minimum fields required to make a request.
@@ -4690,7 +3399,9 @@ irgsrDatasetId
46903399 = lens _irgsrDatasetId
46913400 (\ s a -> s{_irgsrDatasetId = a})
46923401
4693−-- | A list of URIs pointing at BAM files in Google Cloud Storage.
3402+-- | A list of URIs pointing at [BAM
3403+-- files](https:\/\/samtools.github.io\/hts-specs\/SAMv1.pdf) in Google
3404+-- Cloud Storage.
46943405irgsrSourceURIs :: Lens' ImportReadGroupSetsRequest [Text]
46953406irgsrSourceURIs
46963407 = lens _irgsrSourceURIs
@@ -4700,7 +3411,7 @@ irgsrSourceURIs
47003411
47013412-- | The partition strategy describes how read groups are partitioned into
47023413-- read group sets.
4703−irgsrPartitionStrategy :: Lens' ImportReadGroupSetsRequest (Maybe ImportReadGroupSetsRequestPartitionStrategy)
3414+irgsrPartitionStrategy :: Lens' ImportReadGroupSetsRequest (Maybe Text)
47043415irgsrPartitionStrategy
47053416 = lens _irgsrPartitionStrategy
47063417 (\ s a -> s{_irgsrPartitionStrategy = a})
@@ -4728,7 +3439,8 @@ instance ToJSON ImportReadGroupSetsRequest where
47283439--
47293440-- /See:/ 'importVariantsRequest' smart constructor.
47303441data ImportVariantsRequest = ImportVariantsRequest
4731− { _ivrFormat :: !(Maybe ImportVariantsRequestFormat)
3442+ { _ivrVariantSetId :: !(Maybe Text)
3443+ , _ivrFormat :: !(Maybe Text)
47323444 , _ivrNormalizeReferenceNames :: !(Maybe Bool)
47333445 , _ivrSourceURIs :: !(Maybe [Text])
47343446 } deriving (Eq,Show,Data,Typeable,Generic)
@@ -4737,6 +3449,8 @@ data ImportVariantsRequest = ImportVariantsRequest
47373449--
47383450-- Use one of the following lenses to modify other fields as desired:
47393451--
3452+-- * 'ivrVariantSetId'
3453+--
47403454-- * 'ivrFormat'
47413455--
47423456-- * 'ivrNormalizeReferenceNames'
@@ -4746,14 +3460,21 @@ importVariantsRequest
47463460 :: ImportVariantsRequest
47473461importVariantsRequest =
47483462 ImportVariantsRequest
4749− { _ivrFormat = Nothing
3463+ { _ivrVariantSetId = Nothing
3464+ , _ivrFormat = Nothing
47503465 , _ivrNormalizeReferenceNames = Nothing
47513466 , _ivrSourceURIs = Nothing
47523467 }
47533468
3469+-- | Required. The variant set to which variant data should be imported.
3470+ivrVariantSetId :: Lens' ImportVariantsRequest (Maybe Text)
3471+ivrVariantSetId
3472+ = lens _ivrVariantSetId
3473+ (\ s a -> s{_ivrVariantSetId = a})
3474+
47543475-- | The format of the variant data being imported. If unspecified, defaults
4755−-- to to \"VCF\".
4756−ivrFormat :: Lens' ImportVariantsRequest (Maybe ImportVariantsRequestFormat)
3476+-- to to \`VCF\`.
3477+ivrFormat :: Lens' ImportVariantsRequest (Maybe Text)
47573478ivrFormat
47583479 = lens _ivrFormat (\ s a -> s{_ivrFormat = a})
47593480
@@ -4770,8 +3491,9 @@ ivrNormalizeReferenceNames
47703491 (\ s a -> s{_ivrNormalizeReferenceNames = a})
47713492
47723493-- | A list of URIs referencing variant files in Google Cloud Storage. URIs
4773−-- can include wildcards as described here. Note that recursive wildcards
4774−-- (\'**\') are not supported.
3494+-- can include wildcards [as described
3495+-- here](https:\/\/cloud.google.com\/storage\/docs\/gsutil\/addlhelp\/WildcardNames).
3496+-- Note that recursive wildcards (\'**\') are not supported.
47753497ivrSourceURIs :: Lens' ImportVariantsRequest [Text]
47763498ivrSourceURIs
47773499 = lens _ivrSourceURIs
@@ -4784,7 +3506,7 @@ instance FromJSON ImportVariantsRequest where
47843506 = withObject "ImportVariantsRequest"
47853507 (\ o ->
47863508 ImportVariantsRequest <$>
4787− (o .:? "format") <*>
3509+ (o .:? "variantSetId") <*> (o .:? "format") <*>
47883510 (o .:? "normalizeReferenceNames")
47893511 <*> (o .:? "sourceUris" .!= mempty))
47903512
@@ -4792,61 +3514,17 @@ instance ToJSON ImportVariantsRequest where
47923514 toJSON ImportVariantsRequest{..}
47933515 = object
47943516 (catMaybes
4795− [("format" .=) <$> _ivrFormat,
3517+ [("variantSetId" .=) <$> _ivrVariantSetId,
3518+ ("format" .=) <$> _ivrFormat,
47963519 ("normalizeReferenceNames" .=) <$>
47973520 _ivrNormalizeReferenceNames,
47983521 ("sourceUris" .=) <$> _ivrSourceURIs])
47993522
4800−-- |
4801−--
4802−-- /See:/ 'externalId' smart constructor.
4803−data ExternalId = ExternalId
4804− { _eiSourceName :: !(Maybe Text)
4805− , _eiId :: !(Maybe Text)
4806− } deriving (Eq,Show,Data,Typeable,Generic)
4807−
4808−-- | Creates a value of 'ExternalId' with the minimum fields required to make a request.
4809−--
4810−-- Use one of the following lenses to modify other fields as desired:
4811−--
4812−-- * 'eiSourceName'
4813−--
4814−-- * 'eiId'
4815−externalId
4816− :: ExternalId
4817−externalId =
4818− ExternalId
4819− { _eiSourceName = Nothing
4820− , _eiId = Nothing
4821− }
4822−
4823−-- | The name of the source of this data.
4824−eiSourceName :: Lens' ExternalId (Maybe Text)
4825−eiSourceName
4826− = lens _eiSourceName (\ s a -> s{_eiSourceName = a})
4827−
4828−-- | The id used by the source of this data.
4829−eiId :: Lens' ExternalId (Maybe Text)
4830−eiId = lens _eiId (\ s a -> s{_eiId = a})
4831−
4832−instance FromJSON ExternalId where
4833− parseJSON
4834− = withObject "ExternalId"
4835− (\ o ->
4836− ExternalId <$> (o .:? "sourceName") <*> (o .:? "id"))
4837−
4838−instance ToJSON ExternalId where
4839− toJSON ExternalId{..}
4840− = object
4841− (catMaybes
4842− [("sourceName" .=) <$> _eiSourceName,
4843− ("id" .=) <$> _eiId])
4844−
48453523-- | A single CIGAR operation.
48463524--
48473525-- /See:/ 'cigarUnit' smart constructor.
48483526data CigarUnit = CigarUnit
4849− { _cuOperation :: !(Maybe CigarUnitOperation)
3527+ { _cuOperation :: !(Maybe Text)
48503528 , _cuOperationLength :: !(Maybe Int64)
48513529 , _cuReferenceSequence :: !(Maybe Text)
48523530 } deriving (Eq,Show,Data,Typeable,Generic)
@@ -4869,19 +3547,19 @@ cigarUnit =
48693547 , _cuReferenceSequence = Nothing
48703548 }
48713549
4872−cuOperation :: Lens' CigarUnit (Maybe CigarUnitOperation)
3550+cuOperation :: Lens' CigarUnit (Maybe Text)
48733551cuOperation
48743552 = lens _cuOperation (\ s a -> s{_cuOperation = a})
48753553
4876−-- | The number of bases that the operation runs for. Required.
3554+-- | The number of genomic bases that the operation runs for. Required.
48773555cuOperationLength :: Lens' CigarUnit (Maybe Int64)
48783556cuOperationLength
48793557 = lens _cuOperationLength
48803558 (\ s a -> s{_cuOperationLength = a})
48813559
4882−-- | referenceSequence is only used at mismatches (SEQUENCE_MISMATCH) and
4883−-- deletions (DELETE). Filling this field replaces SAM\'s MD tag. If the
4884−-- relevant information is not available, this field is unset.
3560+-- | \`referenceSequence\` is only used at mismatches (\`SEQUENCE_MISMATCH\`)
3561+-- and deletions (\`DELETE\`). Filling this field replaces SAM\'s MD tag.
3562+-- If the relevant information is not available, this field is unset.
48853563cuReferenceSequence :: Lens' CigarUnit (Maybe Text)
48863564cuReferenceSequence
48873565 = lens _cuReferenceSequence
@@ -4903,107 +3581,78 @@ instance ToJSON CigarUnit where
49033581 ("operationLength" .=) <$> _cuOperationLength,
49043582 ("referenceSequence" .=) <$> _cuReferenceSequence])
49053583
4906−-- | The read group set align request.
4907−--
4908−-- /See:/ 'alignReadGroupSetsRequest' smart constructor.
4909−data AlignReadGroupSetsRequest = AlignReadGroupSetsRequest
4910− { _argsrInterleavedFastqSource :: !(Maybe InterleavedFastqSource)
4911− , _argsrReadGroupSetId :: !(Maybe Text)
4912− , _argsrBamSourceURIs :: !(Maybe [Text])
4913− , _argsrPairedFastqSource :: !(Maybe PairedFastqSource)
4914− , _argsrDatasetId :: !(Maybe Text)
3584+-- | Defines an Identity and Access Management (IAM) policy. It is used to
3585+-- specify access control policies for Cloud Platform resources. A
3586+-- \`Policy\` consists of a list of \`bindings\`. A \`Binding\` binds a
3587+-- list of \`members\` to a \`role\`, where the members can be user
3588+-- accounts, Google groups, Google domains, and service accounts. A
3589+-- \`role\` is a named list of permissions defined by IAM. **Example** {
3590+-- \"bindings\": [ { \"role\": \"roles\/owner\", \"members\": [
3591+-- \"user:mike\'example.com\", \"group:admins\'example.com\",
3592+-- \"domain:google.com\",
3593+-- \"serviceAccount:my-other-app\'appspot.gserviceaccount.com\"] }, {
3594+-- \"role\": \"roles\/viewer\", \"members\": [\"user:sean\'example.com\"] }
3595+-- ] } For a description of IAM and its features, see the [IAM developer\'s
3596+-- guide](https:\/\/cloud.google.com\/iam).
3597+--
3598+-- /See:/ 'policy' smart constructor.
3599+data Policy = Policy
3600+ { _polEtag :: !(Maybe Word8)
3601+ , _polVersion :: !(Maybe Int32)
3602+ , _polBindings :: !(Maybe [Binding])
49153603 } deriving (Eq,Show,Data,Typeable,Generic)
49163604
4917−-- | Creates a value of 'AlignReadGroupSetsRequest' with the minimum fields required to make a request.
3605+-- | Creates a value of 'Policy' with the minimum fields required to make a request.
49183606--
49193607-- Use one of the following lenses to modify other fields as desired:
49203608--
4921−-- * 'argsrInterleavedFastqSource'
4922−--
4923−-- * 'argsrReadGroupSetId'
3609+-- * 'polEtag'
49243610--
4925−-- * 'argsrBamSourceURIs'
3611+-- * 'polVersion'
49263612--
4927−-- * 'argsrPairedFastqSource'
4928−--
4929−-- * 'argsrDatasetId'
4930−alignReadGroupSetsRequest
4931− :: AlignReadGroupSetsRequest
4932−alignReadGroupSetsRequest =
4933− AlignReadGroupSetsRequest
4934− { _argsrInterleavedFastqSource = Nothing
4935− , _argsrReadGroupSetId = Nothing
4936− , _argsrBamSourceURIs = Nothing
4937− , _argsrPairedFastqSource = Nothing
4938− , _argsrDatasetId = Nothing
3613+-- * 'polBindings'
3614+policy
3615+ :: Policy
3616+policy =
3617+ Policy
3618+ { _polEtag = Nothing
3619+ , _polVersion = Nothing
3620+ , _polBindings = Nothing
49393621 }
49403622
4941−-- | The interleaved FASTQ source files for alignment, where both members of
4942−-- each pair of reads are found on consecutive records within the same
4943−-- FASTQ file. Exactly one of readGroupSetId, bamSourceUris,
4944−-- interleavedFastqSource or pairedFastqSource must be provided.
4945−argsrInterleavedFastqSource :: Lens' AlignReadGroupSetsRequest (Maybe InterleavedFastqSource)
4946−argsrInterleavedFastqSource
4947− = lens _argsrInterleavedFastqSource
4948− (\ s a -> s{_argsrInterleavedFastqSource = a})
4949−
4950−-- | The ID of the read group set which will be aligned. A new read group set
4951−-- will be generated to hold the aligned data, the originals will not be
4952−-- modified. The caller must have READ permissions for this read group set.
4953−-- Exactly one of readGroupSetId, bamSourceUris, interleavedFastqSource or
4954−-- pairedFastqSource must be provided.
4955−argsrReadGroupSetId :: Lens' AlignReadGroupSetsRequest (Maybe Text)
4956−argsrReadGroupSetId
4957− = lens _argsrReadGroupSetId
4958− (\ s a -> s{_argsrReadGroupSetId = a})
4959−
4960−-- | The BAM source files for alignment. Exactly one of readGroupSetId,
4961−-- bamSourceUris, interleavedFastqSource or pairedFastqSource must be
4962−-- provided. The caller must have READ permissions for these files.
4963−argsrBamSourceURIs :: Lens' AlignReadGroupSetsRequest [Text]
4964−argsrBamSourceURIs
4965− = lens _argsrBamSourceURIs
4966− (\ s a -> s{_argsrBamSourceURIs = a})
4967− . _Default
3623+-- | Can be used to perform a read-modify-write.
3624+polEtag :: Lens' Policy (Maybe Word8)
3625+polEtag = lens _polEtag (\ s a -> s{_polEtag = a})
3626+
3627+-- | Version of the \`Policy\`. The default version is 0.
3628+polVersion :: Lens' Policy (Maybe Int32)
3629+polVersion
3630+ = lens _polVersion (\ s a -> s{_polVersion = a})
3631+
3632+-- | Associates a list of \`members\` to a \`role\`. Multiple \`bindings\`
3633+-- must not be specified for the same \`role\`. \`bindings\` with no
3634+-- members will result in an error.
3635+polBindings :: Lens' Policy [Binding]
3636+polBindings
3637+ = lens _polBindings (\ s a -> s{_polBindings = a}) .
3638+ _Default
49683639 . _Coerce
49693640
4970−-- | The paired end FASTQ source files for alignment, where each member of a
4971−-- pair of reads are found in separate files. Exactly one of
4972−-- readGroupSetId, bamSourceUris, interleavedFastqSource or
4973−-- pairedFastqSource must be provided.
4974−argsrPairedFastqSource :: Lens' AlignReadGroupSetsRequest (Maybe PairedFastqSource)
4975−argsrPairedFastqSource
4976− = lens _argsrPairedFastqSource
4977− (\ s a -> s{_argsrPairedFastqSource = a})
4978−
4979−-- | Required. The ID of the dataset the newly aligned read group sets will
4980−-- belong to. The caller must have WRITE permissions to this dataset.
4981−argsrDatasetId :: Lens' AlignReadGroupSetsRequest (Maybe Text)
4982−argsrDatasetId
4983− = lens _argsrDatasetId
4984− (\ s a -> s{_argsrDatasetId = a})
4985−
4986−instance FromJSON AlignReadGroupSetsRequest where
3641+instance FromJSON Policy where
49873642 parseJSON
4988− = withObject "AlignReadGroupSetsRequest"
3643+ = withObject "Policy"
49893644 (\ o ->
4990− AlignReadGroupSetsRequest <$>
4991− (o .:? "interleavedFastqSource") <*>
4992− (o .:? "readGroupSetId")
4993− <*> (o .:? "bamSourceUris" .!= mempty)
4994− <*> (o .:? "pairedFastqSource")
4995− <*> (o .:? "datasetId"))
4996−
4997−instance ToJSON AlignReadGroupSetsRequest where
4998− toJSON AlignReadGroupSetsRequest{..}
3645+ Policy <$>
3646+ (o .:? "etag") <*> (o .:? "version") <*>
3647+ (o .:? "bindings" .!= mempty))
3648+
3649+instance ToJSON Policy where
3650+ toJSON Policy{..}
49993651 = object
50003652 (catMaybes
5001− [("interleavedFastqSource" .=) <$>
5002− _argsrInterleavedFastqSource,
5003− ("readGroupSetId" .=) <$> _argsrReadGroupSetId,
5004− ("bamSourceUris" .=) <$> _argsrBamSourceURIs,
5005− ("pairedFastqSource" .=) <$> _argsrPairedFastqSource,
5006− ("datasetId" .=) <$> _argsrDatasetId])
3653+ [("etag" .=) <$> _polEtag,
3654+ ("version" .=) <$> _polVersion,
3655+ ("bindings" .=) <$> _polBindings])
50073656
50083657-- | The variant data export request.
50093658--
@@ -5011,9 +3660,9 @@ instance ToJSON AlignReadGroupSetsRequest where
50113660data ExportVariantSetRequest = ExportVariantSetRequest
50123661 { _evsrBigQueryDataset :: !(Maybe Text)
50133662 , _evsrBigQueryTable :: !(Maybe Text)
5014− , _evsrFormat :: !(Maybe ExportVariantSetRequestFormat)
5015− , _evsrProjectNumber :: !(Maybe Int64)
3663+ , _evsrFormat :: !(Maybe Text)
50163664 , _evsrCallSetIds :: !(Maybe [Text])
3665+ , _evsrProjectId :: !(Maybe Text)
50173666 } deriving (Eq,Show,Data,Typeable,Generic)
50183667
50193668-- | Creates a value of 'ExportVariantSetRequest' with the minimum fields required to make a request.
@@ -5026,9 +3675,9 @@ data ExportVariantSetRequest = ExportVariantSetRequest
50263675--
50273676-- * 'evsrFormat'
50283677--
5029−-- * 'evsrProjectNumber'
5030−--
50313678-- * 'evsrCallSetIds'
3679+--
3680+-- * 'evsrProjectId'
50323681exportVariantSetRequest
50333682 :: ExportVariantSetRequest
50343683exportVariantSetRequest =
@@ -5036,8 +3685,8 @@ exportVariantSetRequest =
50363685 { _evsrBigQueryDataset = Nothing
50373686 , _evsrBigQueryTable = Nothing
50383687 , _evsrFormat = Nothing
5039− , _evsrProjectNumber = Nothing
50403688 , _evsrCallSetIds = Nothing
3689+ , _evsrProjectId = Nothing
50413690 }
50423691
50433692-- | Required. The BigQuery dataset to export data to. This dataset must
@@ -5056,18 +3705,10 @@ evsrBigQueryTable
50563705 (\ s a -> s{_evsrBigQueryTable = a})
50573706
50583707-- | The format for the exported data.
5059−evsrFormat :: Lens' ExportVariantSetRequest (Maybe ExportVariantSetRequestFormat)
3708+evsrFormat :: Lens' ExportVariantSetRequest (Maybe Text)
50603709evsrFormat
50613710 = lens _evsrFormat (\ s a -> s{_evsrFormat = a})
50623711
5063−-- | Required. The Google Cloud project number that owns the destination
5064−-- BigQuery dataset. The caller must have WRITE access to this project.
5065−-- This project will also own the resulting export job.
5066−evsrProjectNumber :: Lens' ExportVariantSetRequest (Maybe Int64)
5067−evsrProjectNumber
5068− = lens _evsrProjectNumber
5069− (\ s a -> s{_evsrProjectNumber = a})
5070−
50713712-- | If provided, only variant call information from the specified call sets
50723713-- will be exported. By default all variant calls are exported.
50733714evsrCallSetIds :: Lens' ExportVariantSetRequest [Text]
@@ -5077,6 +3718,14 @@ evsrCallSetIds
50773718 . _Default
50783719 . _Coerce
50793720
3721+-- | Required. The Google Cloud project ID that owns the destination BigQuery
3722+-- dataset. The caller must have WRITE access to this project. This project
3723+-- will also own the resulting export job.
3724+evsrProjectId :: Lens' ExportVariantSetRequest (Maybe Text)
3725+evsrProjectId
3726+ = lens _evsrProjectId
3727+ (\ s a -> s{_evsrProjectId = a})
3728+
50803729instance FromJSON ExportVariantSetRequest where
50813730 parseJSON
50823731 = withObject "ExportVariantSetRequest"
@@ -5084,8 +3733,8 @@ instance FromJSON ExportVariantSetRequest where
50843733 ExportVariantSetRequest <$>
50853734 (o .:? "bigqueryDataset") <*> (o .:? "bigqueryTable")
50863735 <*> (o .:? "format")
5087− <*> (o .:? "projectNumber")
5088− <*> (o .:? "callSetIds" .!= mempty))
3736+ <*> (o .:? "callSetIds" .!= mempty)
3737+ <*> (o .:? "projectId"))
50893738
50903739instance ToJSON ExportVariantSetRequest where
50913740 toJSON ExportVariantSetRequest{..}
@@ -5094,139 +3743,84 @@ instance ToJSON ExportVariantSetRequest where
50943743 [("bigqueryDataset" .=) <$> _evsrBigQueryDataset,
50953744 ("bigqueryTable" .=) <$> _evsrBigQueryTable,
50963745 ("format" .=) <$> _evsrFormat,
5097− ("projectNumber" .=) <$> _evsrProjectNumber,
5098− ("callSetIds" .=) <$> _evsrCallSetIds])
5099−
5100−-- | The read group set export response.
5101−--
5102−-- /See:/ 'exportReadGroupSetsResponse' smart constructor.
5103−newtype ExportReadGroupSetsResponse = ExportReadGroupSetsResponse
5104− { _ergsrJobId :: Maybe Text
5105− } deriving (Eq,Show,Data,Typeable,Generic)
5106−
5107−-- | Creates a value of 'ExportReadGroupSetsResponse' with the minimum fields required to make a request.
5108−--
5109−-- Use one of the following lenses to modify other fields as desired:
5110−--
5111−-- * 'ergsrJobId'
5112−exportReadGroupSetsResponse
5113− :: ExportReadGroupSetsResponse
5114−exportReadGroupSetsResponse =
5115− ExportReadGroupSetsResponse
5116− { _ergsrJobId = Nothing
5117− }
5118−
5119−-- | A job ID that can be used to get status information.
5120−ergsrJobId :: Lens' ExportReadGroupSetsResponse (Maybe Text)
5121−ergsrJobId
5122− = lens _ergsrJobId (\ s a -> s{_ergsrJobId = a})
5123−
5124−instance FromJSON ExportReadGroupSetsResponse where
5125− parseJSON
5126− = withObject "ExportReadGroupSetsResponse"
5127− (\ o ->
5128− ExportReadGroupSetsResponse <$> (o .:? "jobId"))
5129−
5130−instance ToJSON ExportReadGroupSetsResponse where
5131− toJSON ExportReadGroupSetsResponse{..}
5132− = object (catMaybes [("jobId" .=) <$> _ergsrJobId])
3746+ ("callSetIds" .=) <$> _evsrCallSetIds,
3747+ ("projectId" .=) <$> _evsrProjectId])
51333748
3749+-- | Metadata describing an Operation.
51343750--
5135−-- /See:/ 'searchAnnotationsRequest' smart constructor.
5136−data SearchAnnotationsRequest = SearchAnnotationsRequest
5137− { _sarRange :: !(Maybe QueryRange)
5138− , _sarPageToken :: !(Maybe Text)
5139− , _sarAnnotationSetIds :: !(Maybe [Text])
5140− , _sarPageSize :: !(Maybe Int32)
3751+-- /See:/ 'operationMetadata' smart constructor.
3752+data OperationMetadata = OperationMetadata
3753+ { _omEvents :: !(Maybe [OperationEvent])
3754+ , _omProjectId :: !(Maybe Text)
3755+ , _omCreateTime :: !(Maybe Text)
3756+ , _omRequest :: !(Maybe OperationMetadataRequest)
51413757 } deriving (Eq,Show,Data,Typeable,Generic)
51423758
5143−-- | Creates a value of 'SearchAnnotationsRequest' with the minimum fields required to make a request.
3759+-- | Creates a value of 'OperationMetadata' with the minimum fields required to make a request.
51443760--
51453761-- Use one of the following lenses to modify other fields as desired:
51463762--
5147−-- * 'sarRange'
3763+-- * 'omEvents'
51483764--
5149−-- * 'sarPageToken'
3765+-- * 'omProjectId'
51503766--
5151−-- * 'sarAnnotationSetIds'
3767+-- * 'omCreateTime'
51523768--
5153−-- * 'sarPageSize'
5154−searchAnnotationsRequest
5155− :: SearchAnnotationsRequest
5156−searchAnnotationsRequest =
5157− SearchAnnotationsRequest
5158− { _sarRange = Nothing
5159− , _sarPageToken = Nothing
5160− , _sarAnnotationSetIds = Nothing
5161− , _sarPageSize = Nothing
3769+-- * 'omRequest'
3770+operationMetadata
3771+ :: OperationMetadata
3772+operationMetadata =
3773+ OperationMetadata
3774+ { _omEvents = Nothing
3775+ , _omProjectId = Nothing
3776+ , _omCreateTime = Nothing
3777+ , _omRequest = Nothing
51623778 }
51633779
5164−-- | If specified, this query matches only annotations that overlap this
5165−-- range.
5166−sarRange :: Lens' SearchAnnotationsRequest (Maybe QueryRange)
5167−sarRange = lens _sarRange (\ s a -> s{_sarRange = a})
5168−
5169−-- | The continuation token, which is used to page through large result sets.
5170−-- To get the next page of results, set this parameter to the value of
5171−-- nextPageToken from the previous response.
5172−sarPageToken :: Lens' SearchAnnotationsRequest (Maybe Text)
5173−sarPageToken
5174− = lens _sarPageToken (\ s a -> s{_sarPageToken = a})
5175−
5176−-- | The annotation sets to search within. The caller must have READ access
5177−-- to these annotation sets. Required. All queried annotation sets must
5178−-- have the same type.
5179−sarAnnotationSetIds :: Lens' SearchAnnotationsRequest [Text]
5180−sarAnnotationSetIds
5181− = lens _sarAnnotationSetIds
5182− (\ s a -> s{_sarAnnotationSetIds = a})
5183− . _Default
3780+-- | Optional event messages that were generated during the job\'s execution.
3781+-- This also contains any warnings that were generated during import or
3782+-- export.
3783+omEvents :: Lens' OperationMetadata [OperationEvent]
3784+omEvents
3785+ = lens _omEvents (\ s a -> s{_omEvents = a}) .
3786+ _Default
51843787 . _Coerce
51853788
5186−-- | Specifies number of results to return in a single page. If unspecified,
5187−-- it will default to 256. The maximum value is 2048.
5188−sarPageSize :: Lens' SearchAnnotationsRequest (Maybe Int32)
5189−sarPageSize
5190− = lens _sarPageSize (\ s a -> s{_sarPageSize = a})
3789+-- | The Google Cloud Project in which the job is scoped.
3790+omProjectId :: Lens' OperationMetadata (Maybe Text)
3791+omProjectId
3792+ = lens _omProjectId (\ s a -> s{_omProjectId = a})
3793+
3794+-- | The time at which the job was submitted to the Genomics service.
3795+omCreateTime :: Lens' OperationMetadata (Maybe Text)
3796+omCreateTime
3797+ = lens _omCreateTime (\ s a -> s{_omCreateTime = a})
3798+
3799+-- | The original request that started the operation. Note that this will be
3800+-- in current version of the API. If the operation was started with v1beta2
3801+-- API and a GetOperation is performed on v1 API, a v1 request will be
3802+-- returned.
3803+omRequest :: Lens' OperationMetadata (Maybe OperationMetadataRequest)
3804+omRequest
3805+ = lens _omRequest (\ s a -> s{_omRequest = a})
51913806
5192−instance FromJSON SearchAnnotationsRequest where
3807+instance FromJSON OperationMetadata where
51933808 parseJSON
5194− = withObject "SearchAnnotationsRequest"
3809+ = withObject "OperationMetadata"
51953810 (\ o ->
5196− SearchAnnotationsRequest <$>
5197− (o .:? "range") <*> (o .:? "pageToken") <*>
5198− (o .:? "annotationSetIds" .!= mempty)
5199− <*> (o .:? "pageSize"))
3811+ OperationMetadata <$>
3812+ (o .:? "events" .!= mempty) <*> (o .:? "projectId")
3813+ <*> (o .:? "createTime")
3814+ <*> (o .:? "request"))
52003815
5201−instance ToJSON SearchAnnotationsRequest where
5202− toJSON SearchAnnotationsRequest{..}
3816+instance ToJSON OperationMetadata where
3817+ toJSON OperationMetadata{..}
52033818 = object
52043819 (catMaybes
5205− [("range" .=) <$> _sarRange,
5206− ("pageToken" .=) <$> _sarPageToken,
5207− ("annotationSetIds" .=) <$> _sarAnnotationSetIds,
5208− ("pageSize" .=) <$> _sarPageSize])
5209−
5210−-- | A string which maps to an array of values.
5211−--
5212−-- /See:/ 'metadataInfo' smart constructor.
5213−data MetadataInfo =
5214− MetadataInfo
5215− deriving (Eq,Show,Data,Typeable,Generic)
5216−
5217−-- | Creates a value of 'MetadataInfo' with the minimum fields required to make a request.
5218−--
5219−metadataInfo
5220− :: MetadataInfo
5221−metadataInfo = MetadataInfo
5222−
5223−instance FromJSON MetadataInfo where
5224− parseJSON
5225− = withObject "MetadataInfo"
5226− (\ o -> pure MetadataInfo)
5227−
5228−instance ToJSON MetadataInfo where
5229− toJSON = const emptyObject
3820+ [("events" .=) <$> _omEvents,
3821+ ("projectId" .=) <$> _omProjectId,
3822+ ("createTime" .=) <$> _omCreateTime,
3823+ ("request" .=) <$> _omRequest])
52303824
52313825-- | The search variant sets response.
52323826--
@@ -5371,7 +3965,7 @@ svrMaxCalls
53713965
53723966-- | The continuation token, which is used to page through large result sets.
53733967-- To get the next page of results, set this parameter to the value of
5374−-- nextPageToken from the previous response.
3968+-- \`nextPageToken\` from the previous response.
53753969svrPageToken :: Lens' SearchVariantsRequest (Maybe Text)
53763970svrPageToken
53773971 = lens _svrPageToken (\ s a -> s{_svrPageToken = a})
@@ -5426,159 +4020,8 @@ instance ToJSON SearchVariantsRequest where
54264020 ("variantSetIds" .=) <$> _svrVariantSetIds,
54274021 ("pageSize" .=) <$> _svrPageSize])
54284022
5429−-- | A string which maps to an array of values.
5430−--
5431−-- /See:/ 'annotationSetInfo' smart constructor.
5432−data AnnotationSetInfo =
5433− AnnotationSetInfo
5434− deriving (Eq,Show,Data,Typeable,Generic)
5435−
5436−-- | Creates a value of 'AnnotationSetInfo' with the minimum fields required to make a request.
5437−--
5438−annotationSetInfo
5439− :: AnnotationSetInfo
5440−annotationSetInfo = AnnotationSetInfo
5441−
5442−instance FromJSON AnnotationSetInfo where
5443− parseJSON
5444− = withObject "AnnotationSetInfo"
5445− (\ o -> pure AnnotationSetInfo)
5446−
5447−instance ToJSON AnnotationSetInfo where
5448− toJSON = const emptyObject
5449−
5450−-- |
5451−--
5452−-- /See:/ 'variantAnnotationCondition' smart constructor.
5453−data VariantAnnotationCondition = VariantAnnotationCondition
5454− { _vacExternalIds :: !(Maybe [ExternalId])
5455− , _vacNames :: !(Maybe [Text])
5456− , _vacConceptId :: !(Maybe Text)
5457− , _vacOmimId :: !(Maybe Text)
5458− } deriving (Eq,Show,Data,Typeable,Generic)
5459−
5460−-- | Creates a value of 'VariantAnnotationCondition' with the minimum fields required to make a request.
5461−--
5462−-- Use one of the following lenses to modify other fields as desired:
5463−--
5464−-- * 'vacExternalIds'
5465−--
5466−-- * 'vacNames'
5467−--
5468−-- * 'vacConceptId'
5469−--
5470−-- * 'vacOmimId'
5471−variantAnnotationCondition
5472− :: VariantAnnotationCondition
5473−variantAnnotationCondition =
5474− VariantAnnotationCondition
5475− { _vacExternalIds = Nothing
5476− , _vacNames = Nothing
5477− , _vacConceptId = Nothing
5478− , _vacOmimId = Nothing
5479− }
5480−
5481−-- | The set of external IDs for this condition.
5482−vacExternalIds :: Lens' VariantAnnotationCondition [ExternalId]
5483−vacExternalIds
5484− = lens _vacExternalIds
5485− (\ s a -> s{_vacExternalIds = a})
5486− . _Default
5487− . _Coerce
5488−
5489−-- | A set of names for the condition.
5490−vacNames :: Lens' VariantAnnotationCondition [Text]
5491−vacNames
5492− = lens _vacNames (\ s a -> s{_vacNames = a}) .
5493− _Default
5494− . _Coerce
5495−
5496−-- | The MedGen concept id associated with this gene. Search for these IDs at
5497−-- http:\/\/www.ncbi.nlm.nih.gov\/medgen\/
5498−vacConceptId :: Lens' VariantAnnotationCondition (Maybe Text)
5499−vacConceptId
5500− = lens _vacConceptId (\ s a -> s{_vacConceptId = a})
5501−
5502−-- | The OMIM id for this condition. Search for these IDs at
5503−-- http:\/\/omim.org\/
5504−vacOmimId :: Lens' VariantAnnotationCondition (Maybe Text)
5505−vacOmimId
5506− = lens _vacOmimId (\ s a -> s{_vacOmimId = a})
5507−
5508−instance FromJSON VariantAnnotationCondition where
5509− parseJSON
5510− = withObject "VariantAnnotationCondition"
5511− (\ o ->
5512− VariantAnnotationCondition <$>
5513− (o .:? "externalIds" .!= mempty) <*>
5514− (o .:? "names" .!= mempty)
5515− <*> (o .:? "conceptId")
5516− <*> (o .:? "omimId"))
5517−
5518−instance ToJSON VariantAnnotationCondition where
5519− toJSON VariantAnnotationCondition{..}
5520− = object
5521− (catMaybes
5522− [("externalIds" .=) <$> _vacExternalIds,
5523− ("names" .=) <$> _vacNames,
5524− ("conceptId" .=) <$> _vacConceptId,
5525− ("omimId" .=) <$> _vacOmimId])
5526−
5527−--
5528−-- /See:/ 'searchAnnotationSetsResponse' smart constructor.
5529−data SearchAnnotationSetsResponse = SearchAnnotationSetsResponse
5530− { _sasrNextPageToken :: !(Maybe Text)
5531− , _sasrAnnotationSets :: !(Maybe [AnnotationSet])
5532− } deriving (Eq,Show,Data,Typeable,Generic)
5533−
5534−-- | Creates a value of 'SearchAnnotationSetsResponse' with the minimum fields required to make a request.
5535−--
5536−-- Use one of the following lenses to modify other fields as desired:
5537−--
5538−-- * 'sasrNextPageToken'
5539−--
5540−-- * 'sasrAnnotationSets'
5541−searchAnnotationSetsResponse
5542− :: SearchAnnotationSetsResponse
5543−searchAnnotationSetsResponse =
5544− SearchAnnotationSetsResponse
5545− { _sasrNextPageToken = Nothing
5546− , _sasrAnnotationSets = Nothing
5547− }
5548−
5549−-- | The continuation token, which is used to page through large result sets.
5550−-- Provide this value in a subsequent request to return the next page of
5551−-- results. This field will be empty if there aren\'t any additional
5552−-- results.
5553−sasrNextPageToken :: Lens' SearchAnnotationSetsResponse (Maybe Text)
5554−sasrNextPageToken
5555− = lens _sasrNextPageToken
5556− (\ s a -> s{_sasrNextPageToken = a})
5557−
5558−-- | The matching annotation sets.
5559−sasrAnnotationSets :: Lens' SearchAnnotationSetsResponse [AnnotationSet]
5560−sasrAnnotationSets
5561− = lens _sasrAnnotationSets
5562− (\ s a -> s{_sasrAnnotationSets = a})
5563− . _Default
5564− . _Coerce
5565−
5566−instance FromJSON SearchAnnotationSetsResponse where
5567− parseJSON
5568− = withObject "SearchAnnotationSetsResponse"
5569− (\ o ->
5570− SearchAnnotationSetsResponse <$>
5571− (o .:? "nextPageToken") <*>
5572− (o .:? "annotationSets" .!= mempty))
5573−
5574−instance ToJSON SearchAnnotationSetsResponse where
5575− toJSON SearchAnnotationSetsResponse{..}
5576− = object
5577− (catMaybes
5578− [("nextPageToken" .=) <$> _sasrNextPageToken,
5579− ("annotationSets" .=) <$> _sasrAnnotationSets])
5580−
5581−-- | A string which maps to an array of values.
4023+-- | A map of additional call set information. This must be of the form map
4024+-- (string key mapping to a list of string values).
55824025--
55834026-- /See:/ 'callSetInfo' smart constructor.
55844027data CallSetInfo =
@@ -5598,265 +4041,85 @@ instance FromJSON CallSetInfo where
55984041instance ToJSON CallSetInfo where
55994042 toJSON = const emptyObject
56004043
5601−-- | A 0-based half-open genomic coordinate range over a reference sequence,
5602−-- for representing the position of a genomic resource.
4044+-- | Remaining structured metadata key-value pairs. This must be of the form
4045+-- map (string key mapping to a list of string values).
56034046--
5604−-- /See:/ 'rangePosition' smart constructor.
5605−data RangePosition = RangePosition
5606− { _rpStart :: !(Maybe Int64)
5607− , _rpReverseStrand :: !(Maybe Bool)
5608− , _rpReferenceId :: !(Maybe Text)
5609− , _rpReferenceName :: !(Maybe Text)
5610− , _rpEnd :: !(Maybe Int64)
5611− } deriving (Eq,Show,Data,Typeable,Generic)
5612−
5613−-- | Creates a value of 'RangePosition' with the minimum fields required to make a request.
5614−--
5615−-- Use one of the following lenses to modify other fields as desired:
5616−--
5617−-- * 'rpStart'
5618−--
5619−-- * 'rpReverseStrand'
5620−--
5621−-- * 'rpReferenceId'
5622−--
5623−-- * 'rpReferenceName'
5624−--
5625−-- * 'rpEnd'
5626−rangePosition
5627− :: RangePosition
5628−rangePosition =
5629− RangePosition
5630− { _rpStart = Nothing
5631− , _rpReverseStrand = Nothing
5632− , _rpReferenceId = Nothing
5633− , _rpReferenceName = Nothing
5634− , _rpEnd = Nothing
5635− }
5636−
5637−-- | The start position of the range on the reference, 0-based inclusive.
5638−rpStart :: Lens' RangePosition (Maybe Int64)
5639−rpStart = lens _rpStart (\ s a -> s{_rpStart = a})
5640−
5641−-- | Whether this range refers to the reverse strand, as opposed to the
5642−-- forward strand. Note that regardless of this field, the start\/end
5643−-- position of the range always refer to the forward strand.
5644−rpReverseStrand :: Lens' RangePosition (Maybe Bool)
5645−rpReverseStrand
5646− = lens _rpReverseStrand
5647− (\ s a -> s{_rpReverseStrand = a})
5648−
5649−-- | The ID of the Google Genomics reference associated with this range.
5650−rpReferenceId :: Lens' RangePosition (Maybe Text)
5651−rpReferenceId
5652− = lens _rpReferenceId
5653− (\ s a -> s{_rpReferenceId = a})
5654−
5655−-- | The display name corresponding to the reference specified by
5656−-- referenceId, for example chr1, 1, or chrX.
5657−rpReferenceName :: Lens' RangePosition (Maybe Text)
5658−rpReferenceName
5659− = lens _rpReferenceName
5660− (\ s a -> s{_rpReferenceName = a})
5661−
5662−-- | The end position of the range on the reference, 0-based exclusive.
5663−rpEnd :: Lens' RangePosition (Maybe Int64)
5664−rpEnd = lens _rpEnd (\ s a -> s{_rpEnd = a})
5665−
5666−instance FromJSON RangePosition where
5667− parseJSON
5668− = withObject "RangePosition"
5669− (\ o ->
5670− RangePosition <$>
5671− (o .:? "start") <*> (o .:? "reverseStrand") <*>
5672− (o .:? "referenceId")
5673− <*> (o .:? "referenceName")
5674− <*> (o .:? "end"))
5675−
5676−instance ToJSON RangePosition where
5677− toJSON RangePosition{..}
5678− = object
5679− (catMaybes
5680− [("start" .=) <$> _rpStart,
5681− ("reverseStrand" .=) <$> _rpReverseStrand,
5682− ("referenceId" .=) <$> _rpReferenceId,
5683− ("referenceName" .=) <$> _rpReferenceName,
5684− ("end" .=) <$> _rpEnd])
5685−
5686−-- | A transcript represents the assertion that a particular region of the
5687−-- reference genome may be transcribed as RNA.
5688−--
5689−-- /See:/ 'transcript' smart constructor.
5690−data Transcript = Transcript
5691− { _tGeneId :: !(Maybe Text)
5692− , _tCodingSequence :: !(Maybe TranscriptCodingSequence)
5693− , _tExons :: !(Maybe [TranscriptExon])
5694− } deriving (Eq,Show,Data,Typeable,Generic)
4047+-- /See:/ 'variantSetMetadataInfo' smart constructor.
4048+data VariantSetMetadataInfo =
4049+ VariantSetMetadataInfo
4050+ deriving (Eq,Show,Data,Typeable,Generic)
56954051
5696−-- | Creates a value of 'Transcript' with the minimum fields required to make a request.
5697−--
5698−-- Use one of the following lenses to modify other fields as desired:
5699−--
5700−-- * 'tGeneId'
4052+-- | Creates a value of 'VariantSetMetadataInfo' with the minimum fields required to make a request.
57014053--
5702−-- * 'tCodingSequence'
5703−--
5704−-- * 'tExons'
5705−transcript
5706− :: Transcript
5707−transcript =
5708− Transcript
5709− { _tGeneId = Nothing
5710− , _tCodingSequence = Nothing
5711− , _tExons = Nothing
5712− }
4054+variantSetMetadataInfo
4055+ :: VariantSetMetadataInfo
4056+variantSetMetadataInfo = VariantSetMetadataInfo
57134057
5714−-- | The annotation ID of the gene from which this transcript is transcribed.
5715−tGeneId :: Lens' Transcript (Maybe Text)
5716−tGeneId = lens _tGeneId (\ s a -> s{_tGeneId = a})
5717−
5718−-- | The range of the coding sequence for this transcript, if any. To
5719−-- determine the exact ranges of coding sequence, intersect this range with
5720−-- those of the exons, if any. If there are any exons, the codingSequence
5721−-- must start and end within them. Note that in some cases, the reference
5722−-- genome will not exactly match the observed mRNA transcript e.g. due to
5723−-- variance in the source genome from reference. In these cases, exon.frame
5724−-- will not necessarily match the expected reference reading frame and
5725−-- coding exon reference bases cannot necessarily be concatenated to
5726−-- produce the original transcript mRNA.
5727−tCodingSequence :: Lens' Transcript (Maybe TranscriptCodingSequence)
5728−tCodingSequence
5729− = lens _tCodingSequence
5730− (\ s a -> s{_tCodingSequence = a})
5731−
5732−-- | The exons that compose this transcript. This field should be unset for
5733−-- genomes where transcript splicing does not occur, for example
5734−-- prokaryotes. Introns are regions of the transcript that are not included
5735−-- in the spliced RNA product. Though not explicitly modeled here, intron
5736−-- ranges can be deduced; all regions of this transcript that are not exons
5737−-- are introns. Exonic sequences do not necessarily code for a
5738−-- translational product (amino acids). Only the regions of exons bounded
5739−-- by the codingSequence correspond to coding DNA sequence. Exons are
5740−-- ordered by start position and may not overlap.
5741−tExons :: Lens' Transcript [TranscriptExon]
5742−tExons
5743− = lens _tExons (\ s a -> s{_tExons = a}) . _Default .
5744− _Coerce
5745−
5746−instance FromJSON Transcript where
4058+instance FromJSON VariantSetMetadataInfo where
57474059 parseJSON
5748− = withObject "Transcript"
5749− (\ o ->
5750− Transcript <$>
5751− (o .:? "geneId") <*> (o .:? "codingSequence") <*>
5752− (o .:? "exons" .!= mempty))
4060+ = withObject "VariantSetMetadataInfo"
4061+ (\ o -> pure VariantSetMetadataInfo)
57534062
5754−instance ToJSON Transcript where
5755− toJSON Transcript{..}
5756− = object
5757− (catMaybes
5758− [("geneId" .=) <$> _tGeneId,
5759− ("codingSequence" .=) <$> _tCodingSequence,
5760− ("exons" .=) <$> _tExons])
4063+instance ToJSON VariantSetMetadataInfo where
4064+ toJSON = const emptyObject
57614065
4066+-- | If importing ReadGroupSets, an ImportReadGroupSetsResponse is returned.
4067+-- If importing Variants, an ImportVariantsResponse is returned. For
4068+-- exports, an empty response is returned.
57624069--
5763−-- /See:/ 'transcriptCodingSequence' smart constructor.
5764−data TranscriptCodingSequence = TranscriptCodingSequence
5765− { _tcsStart :: !(Maybe Int64)
5766− , _tcsEnd :: !(Maybe Int64)
5767− } deriving (Eq,Show,Data,Typeable,Generic)
4070+-- /See:/ 'operationResponse' smart constructor.
4071+data OperationResponse =
4072+ OperationResponse
4073+ deriving (Eq,Show,Data,Typeable,Generic)
57684074
5769−-- | Creates a value of 'TranscriptCodingSequence' with the minimum fields required to make a request.
4075+-- | Creates a value of 'OperationResponse' with the minimum fields required to make a request.
57704076--
5771−-- Use one of the following lenses to modify other fields as desired:
5772−--
5773−-- * 'tcsStart'
5774−--
5775−-- * 'tcsEnd'
5776−transcriptCodingSequence
5777− :: TranscriptCodingSequence
5778−transcriptCodingSequence =
5779− TranscriptCodingSequence
5780− { _tcsStart = Nothing
5781− , _tcsEnd = Nothing
5782− }
4077+operationResponse
4078+ :: OperationResponse
4079+operationResponse = OperationResponse
57834080
5784−-- | The start of the coding sequence on this annotation\'s reference
5785−-- sequence, 0-based inclusive. Note that this position is relative to the
5786−-- reference start, and not the containing annotation start.
5787−tcsStart :: Lens' TranscriptCodingSequence (Maybe Int64)
5788−tcsStart = lens _tcsStart (\ s a -> s{_tcsStart = a})
5789−
5790−-- | The end of the coding sequence on this annotation\'s reference sequence,
5791−-- 0-based exclusive. Note that this position is relative to the reference
5792−-- start, and not the containing annotation start.
5793−tcsEnd :: Lens' TranscriptCodingSequence (Maybe Int64)
5794−tcsEnd = lens _tcsEnd (\ s a -> s{_tcsEnd = a})
5795−
5796−instance FromJSON TranscriptCodingSequence where
4081+instance FromJSON OperationResponse where
57974082 parseJSON
5798− = withObject "TranscriptCodingSequence"
5799− (\ o ->
5800− TranscriptCodingSequence <$>
5801− (o .:? "start") <*> (o .:? "end"))
4083+ = withObject "OperationResponse"
4084+ (\ o -> pure OperationResponse)
58024085
5803−instance ToJSON TranscriptCodingSequence where
5804− toJSON TranscriptCodingSequence{..}
5805− = object
5806− (catMaybes
5807− [("start" .=) <$> _tcsStart, ("end" .=) <$> _tcsEnd])
4086+instance ToJSON OperationResponse where
4087+ toJSON = const emptyObject
58084088
5809−-- | The job search response.
4089+-- | An event that occurred during an Operation.
58104090--
5811−-- /See:/ 'searchJobsResponse' smart constructor.
5812−data SearchJobsResponse = SearchJobsResponse
5813− { _sjrNextPageToken :: !(Maybe Text)
5814− , _sjrJobs :: !(Maybe [Job])
4091+-- /See:/ 'operationEvent' smart constructor.
4092+newtype OperationEvent = OperationEvent
4093+ { _oeDescription :: Maybe Text
58154094 } deriving (Eq,Show,Data,Typeable,Generic)
58164095
5817−-- | Creates a value of 'SearchJobsResponse' with the minimum fields required to make a request.
4096+-- | Creates a value of 'OperationEvent' with the minimum fields required to make a request.
58184097--
58194098-- Use one of the following lenses to modify other fields as desired:
58204099--
5821−-- * 'sjrNextPageToken'
5822−--
5823−-- * 'sjrJobs'
5824−searchJobsResponse
5825− :: SearchJobsResponse
5826−searchJobsResponse =
5827− SearchJobsResponse
5828− { _sjrNextPageToken = Nothing
5829− , _sjrJobs = Nothing
4100+-- * 'oeDescription'
4101+operationEvent
4102+ :: OperationEvent
4103+operationEvent =
4104+ OperationEvent
4105+ { _oeDescription = Nothing
58304106 }
58314107
5832−-- | The continuation token which is used to page through large result sets.
5833−-- Provide this value is a subsequent request to return the next page of
5834−-- results. This field will be empty if there are no more results.
5835−sjrNextPageToken :: Lens' SearchJobsResponse (Maybe Text)
5836−sjrNextPageToken
5837− = lens _sjrNextPageToken
5838− (\ s a -> s{_sjrNextPageToken = a})
5839−
5840−-- | The list of jobs results, ordered newest to oldest.
5841−sjrJobs :: Lens' SearchJobsResponse [Job]
5842−sjrJobs
5843− = lens _sjrJobs (\ s a -> s{_sjrJobs = a}) . _Default
5844− . _Coerce
4108+-- | Required description of event.
4109+oeDescription :: Lens' OperationEvent (Maybe Text)
4110+oeDescription
4111+ = lens _oeDescription
4112+ (\ s a -> s{_oeDescription = a})
58454113
5846−instance FromJSON SearchJobsResponse where
4114+instance FromJSON OperationEvent where
58474115 parseJSON
5848− = withObject "SearchJobsResponse"
5849− (\ o ->
5850− SearchJobsResponse <$>
5851− (o .:? "nextPageToken") <*>
5852− (o .:? "jobs" .!= mempty))
4116+ = withObject "OperationEvent"
4117+ (\ o -> OperationEvent <$> (o .:? "description"))
58534118
5854−instance ToJSON SearchJobsResponse where
5855− toJSON SearchJobsResponse{..}
4119+instance ToJSON OperationEvent where
4120+ toJSON OperationEvent{..}
58564121 = object
5857− (catMaybes
5858− [("nextPageToken" .=) <$> _sjrNextPageToken,
5859− ("jobs" .=) <$> _sjrJobs])
4122+ (catMaybes [("description" .=) <$> _oeDescription])
58604123
58614124-- | ReferenceBound records an upper bound for the starting coordinate of
58624125-- variants in a particular reference.
@@ -5908,6 +4171,88 @@ instance ToJSON ReferenceBound where
59084171 [("upperBound" .=) <$> _rbUpperBound,
59094172 ("referenceName" .=) <$> _rbReferenceName])
59104173
4174+--
4175+-- /See:/ 'undeleteDatasetRequest' smart constructor.
4176+data UndeleteDatasetRequest =
4177+ UndeleteDatasetRequest
4178+ deriving (Eq,Show,Data,Typeable,Generic)
4179+
4180+-- | Creates a value of 'UndeleteDatasetRequest' with the minimum fields required to make a request.
4181+--
4182+undeleteDatasetRequest
4183+ :: UndeleteDatasetRequest
4184+undeleteDatasetRequest = UndeleteDatasetRequest
4185+
4186+instance FromJSON UndeleteDatasetRequest where
4187+ parseJSON
4188+ = withObject "UndeleteDatasetRequest"
4189+ (\ o -> pure UndeleteDatasetRequest)
4190+
4191+instance ToJSON UndeleteDatasetRequest where
4192+ toJSON = const emptyObject
4193+
4194+-- | Associates \`members\` with a \`role\`.
4195+--
4196+-- /See:/ 'binding' smart constructor.
4197+data Binding = Binding
4198+ { _bMembers :: !(Maybe [Text])
4199+ , _bRole :: !(Maybe Text)
4200+ } deriving (Eq,Show,Data,Typeable,Generic)
4201+
4202+-- | Creates a value of 'Binding' with the minimum fields required to make a request.
4203+--
4204+-- Use one of the following lenses to modify other fields as desired:
4205+--
4206+-- * 'bMembers'
4207+--
4208+-- * 'bRole'
4209+binding
4210+ :: Binding
4211+binding =
4212+ Binding
4213+ { _bMembers = Nothing
4214+ , _bRole = Nothing
4215+ }
4216+
4217+-- | Specifies the identities requesting access for a Cloud Platform
4218+-- resource. \`members\` can have the following formats: * \`allUsers\`: A
4219+-- special identifier that represents anyone who is on the internet; with
4220+-- or without a Google account. * \`allAuthenticatedUsers\`: A special
4221+-- identifier that represents anyone who is authenticated with a Google
4222+-- account or a service account. * \`user:{emailid}\`: An email address
4223+-- that represents a specific Google account. For example,
4224+-- \`alice\'gmail.com\` or \`joe\'example.com\`. *
4225+-- \`serviceAccount:{emailid}\`: An email address that represents a service
4226+-- account. For example, \`my-other-app\'appspot.gserviceaccount.com\`. *
4227+-- \`group:{emailid}\`: An email address that represents a Google group.
4228+-- For example, \`admins\'example.com\`. * \`domain:{domain}\`: A Google
4229+-- Apps domain name that represents all the users of that domain. For
4230+-- example, \`google.com\` or \`example.com\`.
4231+bMembers :: Lens' Binding [Text]
4232+bMembers
4233+ = lens _bMembers (\ s a -> s{_bMembers = a}) .
4234+ _Default
4235+ . _Coerce
4236+
4237+-- | Role that is assigned to \`members\`. For example, \`roles\/viewer\`,
4238+-- \`roles\/editor\`, or \`roles\/owner\`. Required
4239+bRole :: Lens' Binding (Maybe Text)
4240+bRole = lens _bRole (\ s a -> s{_bRole = a})
4241+
4242+instance FromJSON Binding where
4243+ parseJSON
4244+ = withObject "Binding"
4245+ (\ o ->
4246+ Binding <$>
4247+ (o .:? "members" .!= mempty) <*> (o .:? "role"))
4248+
4249+instance ToJSON Binding where
4250+ toJSON Binding{..}
4251+ = object
4252+ (catMaybes
4253+ [("members" .=) <$> _bMembers,
4254+ ("role" .=) <$> _bRole])
4255+
59114256-- | An abstraction for referring to a genomic position, in relation to some
59124257-- already known reference. For now, represents a genomic position as a
59134258-- reference name, a base number on that reference (0-based), and a
@@ -6028,7 +4373,7 @@ instance ToJSON SearchReadGroupSetsResponse where
60284373 [("nextPageToken" .=) <$> _srgsrNextPageToken,
60294374 ("readGroupSets" .=) <$> _srgsrReadGroupSets])
60304375
6031−-- | A string which maps to an array of values.
4376+-- | A map of additional read group set information.
60324377--
60334378-- /See:/ 'readGroupSetInfo' smart constructor.
60344379data ReadGroupSetInfo =
@@ -6050,10 +4395,10 @@ instance ToJSON ReadGroupSetInfo where
60504395 toJSON = const emptyObject
60514396
60524397-- | A reference set is a set of references which typically comprise a
6053−-- reference assembly for a species, such as GRCh38 which is representative
6054−-- of the human genome. A reference set defines a common coordinate space
6055−-- for comparing reference-aligned experimental data. A reference set
6056−-- contains 1 or more references.
4398+-- reference assembly for a species, such as \`GRCh38\` which is
4399+-- representative of the human genome. A reference set defines a common
4400+-- coordinate space for comparing reference-aligned experimental data. A
4401+-- reference set contains 1 or more references.
60574402--
60584403-- /See:/ 'referenceSet' smart constructor.
60594404data ReferenceSet = ReferenceSet
@@ -6101,7 +4446,7 @@ referenceSet =
61014446 }
61024447
61034448-- | All known corresponding accession IDs in INSDC (GenBank\/ENA\/DDBJ)
6104−-- ideally with a version number, for example NC_000001.11.
4449+-- ideally with a version number, for example \`NC_000001.11\`.
61054450rsSourceAccessions :: Lens' ReferenceSet [Text]
61064451rsSourceAccessions
61074452 = lens _rsSourceAccessions
@@ -6110,7 +4455,7 @@ rsSourceAccessions
61104455 . _Coerce
61114456
61124457-- | The IDs of the reference objects that are part of this set.
6113−-- Reference.md5checksum must be unique within this set.
4458+-- \`Reference.md5checksum\` must be unique within this set.
61144459rsReferenceIds :: Lens' ReferenceSet [Text]
61154460rsReferenceIds
61164461 = lens _rsReferenceIds
@@ -6120,7 +4465,7 @@ rsReferenceIds
61204465
61214466-- | Order-independent MD5 checksum which identifies this reference set. The
61224467-- checksum is computed by sorting all lower case hexidecimal string
6123−-- reference.md5checksum (for all reference in this set) in ascending
4468+-- \`reference.md5checksum\` (for all reference in this set) in ascending
61244469-- lexicographic order, concatenating, and taking the MD5 of that value.
61254470-- The resulting value is represented in lower case hexadecimal format.
61264471rsMD5checksum :: Lens' ReferenceSet (Maybe Text)
@@ -6130,7 +4475,7 @@ rsMD5checksum
61304475
61314476-- | ID from http:\/\/www.ncbi.nlm.nih.gov\/taxonomy (e.g. 9606->human)
61324477-- indicating the species which this assembly is intended to model. Note
6133−-- that contained references may specify a different ncbiTaxonId, as
4478+-- that contained references may specify a different \`ncbiTaxonId\`, as
61344479-- assemblies may contain reference sequences which do not belong to the
61354480-- modeled species, e.g. EBV in a human reference genome.
61364481rsNcbiTaxonId :: Lens' ReferenceSet (Maybe Int32)
@@ -6138,11 +4483,11 @@ rsNcbiTaxonId
61384483 = lens _rsNcbiTaxonId
61394484 (\ s a -> s{_rsNcbiTaxonId = a})
61404485
6141−-- | The Google generated immutable ID of the reference set.
4486+-- | The server-generated reference set ID, unique across all reference sets.
61424487rsId :: Lens' ReferenceSet (Maybe Text)
61434488rsId = lens _rsId (\ s a -> s{_rsId = a})
61444489
6145−-- | Public id of this reference set, such as GRCh37.
4490+-- | Public id of this reference set, such as \`GRCh37\`.
61464491rsAssemblyId :: Lens' ReferenceSet (Maybe Text)
61474492rsAssemblyId
61484493 = lens _rsAssemblyId (\ s a -> s{_rsAssemblyId = a})
@@ -6169,7 +4514,7 @@ instance FromJSON ReferenceSet where
61694514 <*> (o .:? "ncbiTaxonId")
61704515 <*> (o .:? "id")
61714516 <*> (o .:? "assemblyId")
6172− <*> (o .:? "sourceURI")
4517+ <*> (o .:? "sourceUri")
61734518 <*> (o .:? "description"))
61744519
61754520instance ToJSON ReferenceSet where
@@ -6182,5 +4527,5 @@ instance ToJSON ReferenceSet where
61824527 ("ncbiTaxonId" .=) <$> _rsNcbiTaxonId,
61834528 ("id" .=) <$> _rsId,
61844529 ("assemblyId" .=) <$> _rsAssemblyId,
6185− ("sourceURI" .=) <$> _rsSourceURI,
4530+ ("sourceUri" .=) <$> _rsSourceURI,
61864531 ("description" .=) <$> _rsDescription])