@@ -509,7 +509,7 @@ data Annotation = Annotation'
509509 , _aName :: !(Maybe Text)
510510 , _aEnd :: !(Maybe (Textual Int64))
511511 , _aId :: !(Maybe Text)
512− , _aType :: !(Maybe Text)
512+ , _aType :: !(Maybe AnnotationType)
513513 , _aTranscript :: !(Maybe Transcript)
514514 , _aInfo :: !(Maybe AnnotationInfo)
515515 } deriving (Eq,Show,Data,Typeable,Generic)
@@ -614,7 +614,7 @@ aId = lens _aId (\ s a -> s{_aId = a})
614614
615615-- | The data type for this annotation. Must match the containing annotation
616616-- set\'s type.
617−aType :: Lens' Annotation (Maybe Text)
617+aType :: Lens' Annotation (Maybe AnnotationType)
618618aType = lens _aType (\ s a -> s{_aType = a})
619619
620620-- | A transcript value represents the assertion that a particular region of
@@ -829,7 +829,7 @@ data DataSet = DataSet'
829829 { _dsName :: !(Maybe Text)
830830 , _dsId :: !(Maybe Text)
831831 , _dsProjectId :: !(Maybe Text)
832− , _dsCreateTime :: !(Maybe Text)
832+ , _dsCreateTime :: !(Maybe DateTime')
833833 } deriving (Eq,Show,Data,Typeable,Generic)
834834
835835-- | Creates a value of 'DataSet' with the minimum fields required to make a request.
@@ -867,9 +867,10 @@ dsProjectId
867867 = lens _dsProjectId (\ s a -> s{_dsProjectId = a})
868868
869869-- | The time this dataset was created, in seconds from the epoch.
870−dsCreateTime :: Lens' DataSet (Maybe Text)
870+dsCreateTime :: Lens' DataSet (Maybe UTCTime)
871871dsCreateTime
872872 = lens _dsCreateTime (\ s a -> s{_dsCreateTime = a})
873+ . mapping _DateTime
873874
874875instance FromJSON DataSet where
875876 parseJSON
@@ -1196,6 +1197,41 @@ instance ToJSON Read' where
11961197 ("readNumber" .=) <$> _rReadNumber,
11971198 ("alignedQuality" .=) <$> _rAlignedQuality])
11981199
1200+-- | Optionally provided by the caller when submitting the request that
1201+-- creates the operation.
1202+--
1203+-- /See:/ 'operationMetadataLabels' smart constructor.
1204+newtype OperationMetadataLabels = OperationMetadataLabels'
1205+ { _omlAddtional :: HashMap Text Text
1206+ } deriving (Eq,Show,Data,Typeable,Generic)
1207+
1208+-- | Creates a value of 'OperationMetadataLabels' with the minimum fields required to make a request.
1209+--
1210+-- Use one of the following lenses to modify other fields as desired:
1211+--
1212+-- * 'omlAddtional'
1213+operationMetadataLabels
1214+ :: HashMap Text Text -- ^ 'omlAddtional'
1215+ -> OperationMetadataLabels
1216+operationMetadataLabels pOmlAddtional_ =
1217+ OperationMetadataLabels'
1218+ { _omlAddtional = _Coerce # pOmlAddtional_
1219+ }
1220+
1221+omlAddtional :: Lens' OperationMetadataLabels (HashMap Text Text)
1222+omlAddtional
1223+ = lens _omlAddtional (\ s a -> s{_omlAddtional = a})
1224+ . _Coerce
1225+
1226+instance FromJSON OperationMetadataLabels where
1227+ parseJSON
1228+ = withObject "OperationMetadataLabels"
1229+ (\ o ->
1230+ OperationMetadataLabels' <$> (parseJSONObject o))
1231+
1232+instance ToJSON OperationMetadataLabels where
1233+ toJSON = toJSON . _omlAddtional
1234+
11991235-- | A call represents the determination of genotype with respect to a
12001236-- particular variant. It may include associated information such as
12011237-- quality and phasing. For example, a call might assign a probability of
@@ -1637,7 +1673,7 @@ oError = lens _oError (\ s a -> s{_oError = a})
16371673
16381674-- | If importing ReadGroupSets, an ImportReadGroupSetsResponse is returned.
16391675-- If importing Variants, an ImportVariantsResponse is returned. For
1640−-- exports, an empty response is returned.
1676+-- pipelines and exports, an empty response is returned.
16411677oResponse :: Lens' Operation (Maybe OperationResponse)
16421678oResponse
16431679 = lens _oResponse (\ s a -> s{_oResponse = a})
@@ -1855,7 +1891,7 @@ data VariantSetMetadata = VariantSetMetadata'
18551891 { _vsmValue :: !(Maybe Text)
18561892 , _vsmKey :: !(Maybe Text)
18571893 , _vsmId :: !(Maybe Text)
1858− , _vsmType :: !(Maybe Text)
1894+ , _vsmType :: !(Maybe VariantSetMetadataType)
18591895 , _vsmNumber :: !(Maybe Text)
18601896 , _vsmDescription :: !(Maybe Text)
18611897 , _vsmInfo :: !(Maybe VariantSetMetadataInfo)
@@ -1907,7 +1943,7 @@ vsmId = lens _vsmId (\ s a -> s{_vsmId = a})
19071943
19081944-- | The type of data. Possible types include: Integer, Float, Flag,
19091945-- Character, and String.
1910−vsmType :: Lens' VariantSetMetadata (Maybe Text)
1946+vsmType :: Lens' VariantSetMetadata (Maybe VariantSetMetadataType)
19111947vsmType = lens _vsmType (\ s a -> s{_vsmType = a})
19121948
19131949-- | The number of values that can be included in a field described by this
@@ -2098,12 +2134,12 @@ instance ToJSON CoverageBucket where
20982134--
20992135-- /See:/ 'variantAnnotation' smart constructor.
21002136data VariantAnnotation = VariantAnnotation'
2101− { _vaEffect :: !(Maybe Text)
2102− , _vaClinicalSignificance :: !(Maybe Text)
2137+ { _vaEffect :: !(Maybe VariantAnnotationEffect)
2138+ , _vaClinicalSignificance :: !(Maybe VariantAnnotationClinicalSignificance)
21032139 , _vaAlternateBases :: !(Maybe Text)
21042140 , _vaGeneId :: !(Maybe Text)
21052141 , _vaConditions :: !(Maybe [ClinicalCondition])
2106− , _vaType :: !(Maybe Text)
2142+ , _vaType :: !(Maybe VariantAnnotationType)
21072143 , _vaTranscriptIds :: !(Maybe [Text])
21082144 } deriving (Eq,Show,Data,Typeable,Generic)
21092145
@@ -2138,13 +2174,13 @@ variantAnnotation =
21382174 }
21392175
21402176-- | Effect of the variant on the coding sequence.
2141−vaEffect :: Lens' VariantAnnotation (Maybe Text)
2177+vaEffect :: Lens' VariantAnnotation (Maybe VariantAnnotationEffect)
21422178vaEffect = lens _vaEffect (\ s a -> s{_vaEffect = a})
21432179
21442180-- | Describes the clinical significance of a variant. It is adapted from the
21452181-- ClinVar controlled vocabulary for clinical significance described at:
21462182-- http:\/\/www.ncbi.nlm.nih.gov\/clinvar\/docs\/clinsig\/
2147−vaClinicalSignificance :: Lens' VariantAnnotation (Maybe Text)
2183+vaClinicalSignificance :: Lens' VariantAnnotation (Maybe VariantAnnotationClinicalSignificance)
21482184vaClinicalSignificance
21492185 = lens _vaClinicalSignificance
21502186 (\ s a -> s{_vaClinicalSignificance = a})
@@ -2171,7 +2207,7 @@ vaConditions
21712207 . _Coerce
21722208
21732209-- | Type has been adapted from ClinVar\'s list of variant types.
2174−vaType :: Lens' VariantAnnotation (Maybe Text)
2210+vaType :: Lens' VariantAnnotation (Maybe VariantAnnotationType)
21752211vaType = lens _vaType (\ s a -> s{_vaType = a})
21762212
21772213-- | Google annotation IDs of the transcripts affected by this variant. These
@@ -2474,42 +2510,6 @@ instance FromJSON ReadGroupInfo where
24742510instance ToJSON ReadGroupInfo where
24752511 toJSON = toJSON . _rgiAddtional
24762512
2477−--
2478−-- /See:/ 'streamVariantsResponse' smart constructor.
2479−newtype StreamVariantsResponse = StreamVariantsResponse'
2480− { _svrVariants :: Maybe [Variant]
2481− } deriving (Eq,Show,Data,Typeable,Generic)
2482−
2483−-- | Creates a value of 'StreamVariantsResponse' with the minimum fields required to make a request.
2484−--
2485−-- Use one of the following lenses to modify other fields as desired:
2486−--
2487−-- * 'svrVariants'
2488−streamVariantsResponse
2489− :: StreamVariantsResponse
2490−streamVariantsResponse =
2491− StreamVariantsResponse'
2492− { _svrVariants = Nothing
2493− }
2494−
2495−svrVariants :: Lens' StreamVariantsResponse [Variant]
2496−svrVariants
2497− = lens _svrVariants (\ s a -> s{_svrVariants = a}) .
2498− _Default
2499− . _Coerce
2500−
2501−instance FromJSON StreamVariantsResponse where
2502− parseJSON
2503− = withObject "StreamVariantsResponse"
2504− (\ o ->
2505− StreamVariantsResponse' <$>
2506− (o .:? "variants" .!= mempty))
2507−
2508−instance ToJSON StreamVariantsResponse where
2509− toJSON StreamVariantsResponse'{..}
2510− = object
2511− (catMaybes [("variants" .=) <$> _svrVariants])
2512−
25132513--
25142514-- /See:/ 'statusDetailsItem' smart constructor.
25152515newtype StatusDetailsItem = StatusDetailsItem'
@@ -2543,43 +2543,6 @@ instance FromJSON StatusDetailsItem where
25432543instance ToJSON StatusDetailsItem where
25442544 toJSON = toJSON . _sdiAddtional
25452545
2546−--
2547−-- /See:/ 'streamReadsResponse' smart constructor.
2548−newtype StreamReadsResponse = StreamReadsResponse'
2549− { _srrAlignments :: Maybe [Read']
2550− } deriving (Eq,Show,Data,Typeable,Generic)
2551−
2552−-- | Creates a value of 'StreamReadsResponse' with the minimum fields required to make a request.
2553−--
2554−-- Use one of the following lenses to modify other fields as desired:
2555−--
2556−-- * 'srrAlignments'
2557−streamReadsResponse
2558− :: StreamReadsResponse
2559−streamReadsResponse =
2560− StreamReadsResponse'
2561− { _srrAlignments = Nothing
2562− }
2563−
2564−srrAlignments :: Lens' StreamReadsResponse [Read']
2565−srrAlignments
2566− = lens _srrAlignments
2567− (\ s a -> s{_srrAlignments = a})
2568− . _Default
2569− . _Coerce
2570−
2571−instance FromJSON StreamReadsResponse where
2572− parseJSON
2573− = withObject "StreamReadsResponse"
2574− (\ o ->
2575− StreamReadsResponse' <$>
2576− (o .:? "alignments" .!= mempty))
2577−
2578−instance ToJSON StreamReadsResponse where
2579− toJSON StreamReadsResponse'{..}
2580− = object
2581− (catMaybes [("alignments" .=) <$> _srrAlignments])
2582−
25832546-- | The call set search response.
25842547--
25852548-- /See:/ 'searchCallSetsResponse' smart constructor.
@@ -3247,29 +3210,29 @@ instance ToJSON SearchAnnotationSetsRequest where
32473210--
32483211-- /See:/ 'searchVariantsResponse' smart constructor.
32493212data SearchVariantsResponse = SearchVariantsResponse'
3250− { _sVariants :: !(Maybe [Variant])
3251− , _sNextPageToken :: !(Maybe Text)
3213+ { _svrVariants :: !(Maybe [Variant])
3214+ , _svrNextPageToken :: !(Maybe Text)
32523215 } deriving (Eq,Show,Data,Typeable,Generic)
32533216
32543217-- | Creates a value of 'SearchVariantsResponse' with the minimum fields required to make a request.
32553218--
32563219-- Use one of the following lenses to modify other fields as desired:
32573220--
3258−-- * 'sVariants'
3221+-- * 'svrVariants'
32593222--
3260−-- * 'sNextPageToken'
3223+-- * 'svrNextPageToken'
32613224searchVariantsResponse
32623225 :: SearchVariantsResponse
32633226searchVariantsResponse =
32643227 SearchVariantsResponse'
3265− { _sVariants = Nothing
3266− , _sNextPageToken = Nothing
3228+ { _svrVariants = Nothing
3229+ , _svrNextPageToken = Nothing
32673230 }
32683231
32693232-- | The list of matching Variants.
3270−sVariants :: Lens' SearchVariantsResponse [Variant]
3271−sVariants
3272− = lens _sVariants (\ s a -> s{_sVariants = a}) .
3233+svrVariants :: Lens' SearchVariantsResponse [Variant]
3234+svrVariants
3235+ = lens _svrVariants (\ s a -> s{_svrVariants = a}) .
32733236 _Default
32743237 . _Coerce
32753238
@@ -3277,10 +3240,10 @@ sVariants
32773240-- Provide this value in a subsequent request to return the next page of
32783241-- results. This field will be empty if there aren\'t any additional
32793242-- results.
3280−sNextPageToken :: Lens' SearchVariantsResponse (Maybe Text)
3281−sNextPageToken
3282− = lens _sNextPageToken
3283− (\ s a -> s{_sNextPageToken = a})
3243+svrNextPageToken :: Lens' SearchVariantsResponse (Maybe Text)
3244+svrNextPageToken
3245+ = lens _svrNextPageToken
3246+ (\ s a -> s{_svrNextPageToken = a})
32843247
32853248instance FromJSON SearchVariantsResponse where
32863249 parseJSON
@@ -3294,8 +3257,8 @@ instance ToJSON SearchVariantsResponse where
32943257 toJSON SearchVariantsResponse'{..}
32953258 = object
32963259 (catMaybes
3297− [("variants" .=) <$> _sVariants,
3298− ("nextPageToken" .=) <$> _sNextPageToken])
3260+ [("variants" .=) <$> _svrVariants,
3261+ ("nextPageToken" .=) <$> _svrNextPageToken])
32993262
33003263-- | Runtime metadata on this Operation.
33013264--
@@ -3410,134 +3373,6 @@ instance ToJSON ClinicalCondition where
34103373 ("conceptId" .=) <$> _ccConceptId,
34113374 ("omimId" .=) <$> _ccOmimId])
34123375
3413−-- | The stream reads request.
3414−--
3415−-- /See:/ 'streamReadsRequest' smart constructor.
3416−data StreamReadsRequest = StreamReadsRequest'
3417− { _sShard :: !(Maybe (Textual Int32))
3418− , _sReadGroupSetId :: !(Maybe Text)
3419− , _sTotalShards :: !(Maybe (Textual Int32))
3420− , _sStart :: !(Maybe (Textual Int64))
3421− , _sReferenceName :: !(Maybe Text)
3422− , _sEnd :: !(Maybe (Textual Int64))
3423− , _sProjectId :: !(Maybe Text)
3424− } deriving (Eq,Show,Data,Typeable,Generic)
3425−
3426−-- | Creates a value of 'StreamReadsRequest' with the minimum fields required to make a request.
3427−--
3428−-- Use one of the following lenses to modify other fields as desired:
3429−--
3430−-- * 'sShard'
3431−--
3432−-- * 'sReadGroupSetId'
3433−--
3434−-- * 'sTotalShards'
3435−--
3436−-- * 'sStart'
3437−--
3438−-- * 'sReferenceName'
3439−--
3440−-- * 'sEnd'
3441−--
3442−-- * 'sProjectId'
3443−streamReadsRequest
3444− :: StreamReadsRequest
3445−streamReadsRequest =
3446− StreamReadsRequest'
3447− { _sShard = Nothing
3448− , _sReadGroupSetId = Nothing
3449− , _sTotalShards = Nothing
3450− , _sStart = Nothing
3451− , _sReferenceName = Nothing
3452− , _sEnd = Nothing
3453− , _sProjectId = Nothing
3454− }
3455−
3456−-- | Restricts results to a shard containing approximately \`1\/totalShards\`
3457−-- of the normal response payload for this query. Results from a sharded
3458−-- request are disjoint from those returned by all queries which differ
3459−-- only in their shard parameter. A shard may yield 0 results; this is
3460−-- especially likely for large values of \`totalShards\`. Valid values are
3461−-- \`[0, totalShards)\`.
3462−sShard :: Lens' StreamReadsRequest (Maybe Int32)
3463−sShard
3464− = lens _sShard (\ s a -> s{_sShard = a}) .
3465− mapping _Coerce
3466−
3467−-- | The ID of the read group set from which to stream reads.
3468−sReadGroupSetId :: Lens' StreamReadsRequest (Maybe Text)
3469−sReadGroupSetId
3470− = lens _sReadGroupSetId
3471− (\ s a -> s{_sReadGroupSetId = a})
3472−
3473−-- | Specifying \`totalShards\` causes a disjoint subset of the normal
3474−-- response payload to be returned for each query with a unique \`shard\`
3475−-- parameter specified. A best effort is made to yield equally sized
3476−-- shards. Sharding can be used to distribute processing amongst workers,
3477−-- where each worker is assigned a unique \`shard\` number and all workers
3478−-- specify the same \`totalShards\` number. The union of reads returned for
3479−-- all sharded queries \`[0, totalShards)\` is equal to those returned by a
3480−-- single unsharded query. Queries for different values of \`totalShards\`
3481−-- with common divisors will share shard boundaries. For example, streaming
3482−-- \`shard\` 2 of 5 \`totalShards\` yields the same results as streaming
3483−-- \`shard\`s 4 and 5 of 10 \`totalShards\`. This property can be leveraged
3484−-- for adaptive retries.
3485−sTotalShards :: Lens' StreamReadsRequest (Maybe Int32)
3486−sTotalShards
3487− = lens _sTotalShards (\ s a -> s{_sTotalShards = a})
3488− . mapping _Coerce
3489−
3490−-- | The start position of the range on the reference, 0-based inclusive. If
3491−-- specified, \`referenceName\` must also be specified.
3492−sStart :: Lens' StreamReadsRequest (Maybe Int64)
3493−sStart
3494− = lens _sStart (\ s a -> s{_sStart = a}) .
3495− mapping _Coerce
3496−
3497−-- | The reference sequence name, for example \`chr1\`, \`1\`, or \`chrX\`.
3498−-- If set to *, only unmapped reads are returned.
3499−sReferenceName :: Lens' StreamReadsRequest (Maybe Text)
3500−sReferenceName
3501− = lens _sReferenceName
3502− (\ s a -> s{_sReferenceName = a})
3503−
3504−-- | The end position of the range on the reference, 0-based exclusive. If
3505−-- specified, \`referenceName\` must also be specified.
3506−sEnd :: Lens' StreamReadsRequest (Maybe Int64)
3507−sEnd
3508− = lens _sEnd (\ s a -> s{_sEnd = a}) .
3509− mapping _Coerce
3510−
3511−-- | The Google Cloud project ID which will be billed for this access. The
3512−-- caller must have WRITE access to this project. Required.
3513−sProjectId :: Lens' StreamReadsRequest (Maybe Text)
3514−sProjectId
3515− = lens _sProjectId (\ s a -> s{_sProjectId = a})
3516−
3517−instance FromJSON StreamReadsRequest where
3518− parseJSON
3519− = withObject "StreamReadsRequest"
3520− (\ o ->
3521− StreamReadsRequest' <$>
3522− (o .:? "shard") <*> (o .:? "readGroupSetId") <*>
3523− (o .:? "totalShards")
3524− <*> (o .:? "start")
3525− <*> (o .:? "referenceName")
3526− <*> (o .:? "end")
3527− <*> (o .:? "projectId"))
3528−
3529−instance ToJSON StreamReadsRequest where
3530− toJSON StreamReadsRequest'{..}
3531− = object
3532− (catMaybes
3533− [("shard" .=) <$> _sShard,
3534− ("readGroupSetId" .=) <$> _sReadGroupSetId,
3535− ("totalShards" .=) <$> _sTotalShards,
3536− ("start" .=) <$> _sStart,
3537− ("referenceName" .=) <$> _sReferenceName,
3538− ("end" .=) <$> _sEnd,
3539− ("projectId" .=) <$> _sProjectId])
3540−
35413376-- | The call set search request.
35423377--
35433378-- /See:/ 'searchCallSetsRequest' smart constructor.
@@ -3664,43 +3499,42 @@ instance ToJSON Entry where
36643499--
36653500-- /See:/ 'searchReadsResponse' smart constructor.
36663501data SearchReadsResponse = SearchReadsResponse'
3667− { _seaNextPageToken :: !(Maybe Text)
3668− , _seaAlignments :: !(Maybe [Read'])
3502+ { _sNextPageToken :: !(Maybe Text)
3503+ , _sAlignments :: !(Maybe [Read'])
36693504 } deriving (Eq,Show,Data,Typeable,Generic)
36703505
36713506-- | Creates a value of 'SearchReadsResponse' with the minimum fields required to make a request.
36723507--
36733508-- Use one of the following lenses to modify other fields as desired:
36743509--
3675−-- * 'seaNextPageToken'
3510+-- * 'sNextPageToken'
36763511--
3677−-- * 'seaAlignments'
3512+-- * 'sAlignments'
36783513searchReadsResponse
36793514 :: SearchReadsResponse
36803515searchReadsResponse =
36813516 SearchReadsResponse'
3682− { _seaNextPageToken = Nothing
3683− , _seaAlignments = Nothing
3517+ { _sNextPageToken = Nothing
3518+ , _sAlignments = Nothing
36843519 }
36853520
36863521-- | The continuation token, which is used to page through large result sets.
36873522-- Provide this value in a subsequent request to return the next page of
36883523-- results. This field will be empty if there aren\'t any additional
36893524-- results.
3690−seaNextPageToken :: Lens' SearchReadsResponse (Maybe Text)
3691−seaNextPageToken
3692− = lens _seaNextPageToken
3693− (\ s a -> s{_seaNextPageToken = a})
3525+sNextPageToken :: Lens' SearchReadsResponse (Maybe Text)
3526+sNextPageToken
3527+ = lens _sNextPageToken
3528+ (\ s a -> s{_sNextPageToken = a})
36943529
36953530-- | The list of matching alignments sorted by mapped genomic coordinate, if
36963531-- any, ascending in position within the same reference. Unmapped reads,
36973532-- which have no position, are returned contiguously and are sorted in
36983533-- ascending lexicographic order by fragment name.
3699−seaAlignments :: Lens' SearchReadsResponse [Read']
3700−seaAlignments
3701− = lens _seaAlignments
3702− (\ s a -> s{_seaAlignments = a})
3703− . _Default
3534+sAlignments :: Lens' SearchReadsResponse [Read']
3535+sAlignments
3536+ = lens _sAlignments (\ s a -> s{_sAlignments = a}) .
3537+ _Default
37043538 . _Coerce
37053539
37063540instance FromJSON SearchReadsResponse where
@@ -3715,8 +3549,8 @@ instance ToJSON SearchReadsResponse where
37153549 toJSON SearchReadsResponse'{..}
37163550 = object
37173551 (catMaybes
3718− [("nextPageToken" .=) <$> _seaNextPageToken,
3719− ("alignments" .=) <$> _seaAlignments])
3552+ [("nextPageToken" .=) <$> _sNextPageToken,
3553+ ("alignments" .=) <$> _sAlignments])
37203554
37213555--
37223556-- /See:/ 'program' smart constructor.
@@ -4546,7 +4380,7 @@ data AnnotationSet = AnnotationSet'
45464380 , _asName :: !(Maybe Text)
45474381 , _asDataSetId :: !(Maybe Text)
45484382 , _asId :: !(Maybe Text)
4549− , _asType :: !(Maybe Text)
4383+ , _asType :: !(Maybe AnnotationSetType)
45504384 , _asSourceURI :: !(Maybe Text)
45514385 , _asInfo :: !(Maybe AnnotationSetInfo)
45524386 } deriving (Eq,Show,Data,Typeable,Generic)
@@ -4603,7 +4437,7 @@ asId :: Lens' AnnotationSet (Maybe Text)
46034437asId = lens _asId (\ s a -> s{_asId = a})
46044438
46054439-- | The type of annotations contained within this set.
4606−asType :: Lens' AnnotationSet (Maybe Text)
4440+asType :: Lens' AnnotationSet (Maybe AnnotationSetType)
46074441asType = lens _asType (\ s a -> s{_asType = a})
46084442
46094443-- | The source URI describing the file from which this annotation set was
@@ -4861,7 +4695,7 @@ data ImportReadGroupSetsRequest = ImportReadGroupSetsRequest'
48614695 { _irgsrReferenceSetId :: !(Maybe Text)
48624696 , _irgsrDataSetId :: !(Maybe Text)
48634697 , _irgsrSourceURIs :: !(Maybe [Text])
4864− , _irgsrPartitionStrategy :: !(Maybe Text)
4698+ , _irgsrPartitionStrategy :: !(Maybe ImportReadGroupSetsRequestPartitionStrategy)
48654699 } deriving (Eq,Show,Data,Typeable,Generic)
48664700
48674701-- | Creates a value of 'ImportReadGroupSetsRequest' with the minimum fields required to make a request.
@@ -4904,7 +4738,12 @@ irgsrDataSetId
49044738
49054739-- | A list of URIs pointing at [BAM
49064740-- files](https:\/\/samtools.github.io\/hts-specs\/SAMv1.pdf) in Google
4907−-- Cloud Storage.
4741+-- Cloud Storage. Those URIs can include wildcards (*), but do not add or
4742+-- remove matching files before import has completed. Note that Google
4743+-- Cloud Storage object listing is only eventually consistent: files added
4744+-- may be not be immediately visible to everyone. Thus, if using a wildcard
4745+-- it is preferable not to start the import immediately after the files are
4746+-- created.
49084747irgsrSourceURIs :: Lens' ImportReadGroupSetsRequest [Text]
49094748irgsrSourceURIs
49104749 = lens _irgsrSourceURIs
@@ -4914,7 +4753,7 @@ irgsrSourceURIs
49144753
49154754-- | The partition strategy describes how read groups are partitioned into
49164755-- read group sets.
4917−irgsrPartitionStrategy :: Lens' ImportReadGroupSetsRequest (Maybe Text)
4756+irgsrPartitionStrategy :: Lens' ImportReadGroupSetsRequest (Maybe ImportReadGroupSetsRequestPartitionStrategy)
49184757irgsrPartitionStrategy
49194758 = lens _irgsrPartitionStrategy
49204759 (\ s a -> s{_irgsrPartitionStrategy = a})
@@ -4943,7 +4782,7 @@ instance ToJSON ImportReadGroupSetsRequest where
49434782-- /See:/ 'importVariantsRequest' smart constructor.
49444783data ImportVariantsRequest = ImportVariantsRequest'
49454784 { _ivrVariantSetId :: !(Maybe Text)
4946− , _ivrFormat :: !(Maybe Text)
4785+ , _ivrFormat :: !(Maybe ImportVariantsRequestFormat)
49474786 , _ivrInfoMergeConfig :: !(Maybe ImportVariantsRequestInfoMergeConfig)
49484787 , _ivrNormalizeReferenceNames :: !(Maybe Bool)
49494788 , _ivrSourceURIs :: !(Maybe [Text])
@@ -4981,7 +4820,7 @@ ivrVariantSetId
49814820
49824821-- | The format of the variant data being imported. If unspecified, defaults
49834822-- to to \`VCF\`.
4984−ivrFormat :: Lens' ImportVariantsRequest (Maybe Text)
4823+ivrFormat :: Lens' ImportVariantsRequest (Maybe ImportVariantsRequestFormat)
49854824ivrFormat
49864825 = lens _ivrFormat (\ s a -> s{_ivrFormat = a})
49874826
@@ -5086,7 +4925,7 @@ instance ToJSON ExternalId where
50864925--
50874926-- /See:/ 'cigarUnit' smart constructor.
50884927data CigarUnit = CigarUnit'
5089− { _cuOperation :: !(Maybe Text)
4928+ { _cuOperation :: !(Maybe CigarUnitOperation)
50904929 , _cuOperationLength :: !(Maybe (Textual Int64))
50914930 , _cuReferenceSequence :: !(Maybe Text)
50924931 } deriving (Eq,Show,Data,Typeable,Generic)
@@ -5109,7 +4948,7 @@ cigarUnit =
51094948 , _cuReferenceSequence = Nothing
51104949 }
51114950
5112−cuOperation :: Lens' CigarUnit (Maybe Text)
4951+cuOperation :: Lens' CigarUnit (Maybe CigarUnitOperation)
51134952cuOperation
51144953 = lens _cuOperation (\ s a -> s{_cuOperation = a})
51154954
@@ -5160,7 +4999,7 @@ instance ToJSON CigarUnit where
51604999--
51615000-- /See:/ 'policy' smart constructor.
51625001data Policy = Policy'
5163− { _polEtag :: !(Maybe Base64)
5002+ { _polEtag :: !(Maybe Bytes)
51645003 , _polVersion :: !(Maybe (Textual Int32))
51655004 , _polBindings :: !(Maybe [Binding])
51665005 } deriving (Eq,Show,Data,Typeable,Generic)
@@ -5195,7 +5034,7 @@ policy =
51955034polEtag :: Lens' Policy (Maybe ByteString)
51965035polEtag
51975036 = lens _polEtag (\ s a -> s{_polEtag = a}) .
5198− mapping _Base64
5037+ mapping _Bytes
51995038
52005039-- | Version of the \`Policy\`. The default version is 0.
52015040polVersion :: Lens' Policy (Maybe Int32)
@@ -5234,7 +5073,7 @@ instance ToJSON Policy where
52345073data ExportVariantSetRequest = ExportVariantSetRequest'
52355074 { _evsrBigQueryDataSet :: !(Maybe Text)
52365075 , _evsrBigQueryTable :: !(Maybe Text)
5237− , _evsrFormat :: !(Maybe Text)
5076+ , _evsrFormat :: !(Maybe ExportVariantSetRequestFormat)
52385077 , _evsrCallSetIds :: !(Maybe [Text])
52395078 , _evsrProjectId :: !(Maybe Text)
52405079 } deriving (Eq,Show,Data,Typeable,Generic)
@@ -5279,7 +5118,7 @@ evsrBigQueryTable
52795118 (\ s a -> s{_evsrBigQueryTable = a})
52805119
52815120-- | The format for the exported data.
5282−evsrFormat :: Lens' ExportVariantSetRequest (Maybe Text)
5121+evsrFormat :: Lens' ExportVariantSetRequest (Maybe ExportVariantSetRequestFormat)
52835122evsrFormat
52845123 = lens _evsrFormat (\ s a -> s{_evsrFormat = a})
52855124
@@ -5325,11 +5164,12 @@ instance ToJSON ExportVariantSetRequest where
53255164-- /See:/ 'operationMetadata' smart constructor.
53265165data OperationMetadata = OperationMetadata'
53275166 { _omClientId :: !(Maybe Text)
5328− , _omStartTime :: !(Maybe Text)
5167+ , _omStartTime :: !(Maybe DateTime')
53295168 , _omEvents :: !(Maybe [OperationEvent])
5330− , _omEndTime :: !(Maybe Text)
5169+ , _omEndTime :: !(Maybe DateTime')
5170+ , _omLabels :: !(Maybe OperationMetadataLabels)
53315171 , _omProjectId :: !(Maybe Text)
5332− , _omCreateTime :: !(Maybe Text)
5172+ , _omCreateTime :: !(Maybe DateTime')
53335173 , _omRuntimeMetadata :: !(Maybe OperationMetadataRuntimeMetadata)
53345174 , _omRequest :: !(Maybe OperationMetadataRequest)
53355175 } deriving (Eq,Show,Data,Typeable,Generic)
@@ -5346,6 +5186,8 @@ data OperationMetadata = OperationMetadata'
53465186--
53475187-- * 'omEndTime'
53485188--
5189+-- * 'omLabels'
5190+--
53495191-- * 'omProjectId'
53505192--
53515193-- * 'omCreateTime'
@@ -5361,22 +5203,24 @@ operationMetadata =
53615203 , _omStartTime = Nothing
53625204 , _omEvents = Nothing
53635205 , _omEndTime = Nothing
5206+ , _omLabels = Nothing
53645207 , _omProjectId = Nothing
53655208 , _omCreateTime = Nothing
53665209 , _omRuntimeMetadata = Nothing
53675210 , _omRequest = Nothing
53685211 }
53695212
5370−-- | Optionally provided by the caller when submitting the request that
5371−-- creates the operation.
5213+-- | This field is deprecated. Use \`labels\` instead. Optionally provided by
5214+-- the caller when submitting the request that creates the operation.
53725215omClientId :: Lens' OperationMetadata (Maybe Text)
53735216omClientId
53745217 = lens _omClientId (\ s a -> s{_omClientId = a})
53755218
53765219-- | The time at which the job began to run.
5377−omStartTime :: Lens' OperationMetadata (Maybe Text)
5220+omStartTime :: Lens' OperationMetadata (Maybe UTCTime)
53785221omStartTime
5379− = lens _omStartTime (\ s a -> s{_omStartTime = a})
5222+ = lens _omStartTime (\ s a -> s{_omStartTime = a}) .
5223+ mapping _DateTime
53805224
53815225-- | Optional event messages that were generated during the job\'s execution.
53825226-- This also contains any warnings that were generated during import or
@@ -5388,9 +5232,15 @@ omEvents
53885232 . _Coerce
53895233
53905234-- | The time at which the job stopped running.
5391−omEndTime :: Lens' OperationMetadata (Maybe Text)
5235+omEndTime :: Lens' OperationMetadata (Maybe UTCTime)
53925236omEndTime
5393− = lens _omEndTime (\ s a -> s{_omEndTime = a})
5237+ = lens _omEndTime (\ s a -> s{_omEndTime = a}) .
5238+ mapping _DateTime
5239+
5240+-- | Optionally provided by the caller when submitting the request that
5241+-- creates the operation.
5242+omLabels :: Lens' OperationMetadata (Maybe OperationMetadataLabels)
5243+omLabels = lens _omLabels (\ s a -> s{_omLabels = a})
53945244
53955245-- | The Google Cloud Project in which the job is scoped.
53965246omProjectId :: Lens' OperationMetadata (Maybe Text)
@@ -5398,9 +5248,10 @@ omProjectId
53985248 = lens _omProjectId (\ s a -> s{_omProjectId = a})
53995249
54005250-- | The time at which the job was submitted to the Genomics service.
5401−omCreateTime :: Lens' OperationMetadata (Maybe Text)
5251+omCreateTime :: Lens' OperationMetadata (Maybe UTCTime)
54025252omCreateTime
54035253 = lens _omCreateTime (\ s a -> s{_omCreateTime = a})
5254+ . mapping _DateTime
54045255
54055256-- | Runtime metadata on this Operation.
54065257omRuntimeMetadata :: Lens' OperationMetadata (Maybe OperationMetadataRuntimeMetadata)
@@ -5424,6 +5275,7 @@ instance FromJSON OperationMetadata where
54245275 (o .:? "clientId") <*> (o .:? "startTime") <*>
54255276 (o .:? "events" .!= mempty)
54265277 <*> (o .:? "endTime")
5278+ <*> (o .:? "labels")
54275279 <*> (o .:? "projectId")
54285280 <*> (o .:? "createTime")
54295281 <*> (o .:? "runtimeMetadata")
@@ -5437,6 +5289,7 @@ instance ToJSON OperationMetadata where
54375289 ("startTime" .=) <$> _omStartTime,
54385290 ("events" .=) <$> _omEvents,
54395291 ("endTime" .=) <$> _omEndTime,
5292+ ("labels" .=) <$> _omLabels,
54405293 ("projectId" .=) <$> _omProjectId,
54415294 ("createTime" .=) <$> _omCreateTime,
54425295 ("runtimeMetadata" .=) <$> _omRuntimeMetadata,
@@ -5997,7 +5850,7 @@ instance ToJSON VariantSetMetadataInfo where
59975850
59985851-- | If importing ReadGroupSets, an ImportReadGroupSetsResponse is returned.
59995852-- If importing Variants, an ImportVariantsResponse is returned. For
6000−-- exports, an empty response is returned.
5853+-- pipelines and exports, an empty response is returned.
60015854--
60025855-- /See:/ 'operationResponse' smart constructor.
60035856newtype OperationResponse = OperationResponse'
@@ -6077,15 +5930,15 @@ tCodingSequence
60775930 = lens _tCodingSequence
60785931 (\ s a -> s{_tCodingSequence = a})
60795932
6080−-- | The exons that compose this transcript. This field should be unset for
6081−-- genomes where transcript splicing does not occur, for example
6082−-- prokaryotes. Introns are regions of the transcript that are not included
6083−-- in the spliced RNA product. Though not explicitly modeled here, intron
6084−-- ranges can be deduced; all regions of this transcript that are not exons
6085−-- are introns. Exonic sequences do not necessarily code for a
6086−-- translational product (amino acids). Only the regions of exons bounded
6087−-- by the codingSequence correspond to coding DNA sequence. Exons are
6088−-- ordered by start position and may not overlap.
5933+-- | The <http://en.wikipedia.org/wiki/Exon exons> that compose this
5934+-- transcript. This field should be unset for genomes where transcript
5935+-- splicing does not occur, for example prokaryotes. Introns are regions of
5936+-- the transcript that are not included in the spliced RNA product. Though
5937+-- not explicitly modeled here, intron ranges can be deduced; all regions
5938+-- of this transcript that are not exons are introns. Exonic sequences do
5939+-- not necessarily code for a translational product (amino acids). Only the
5940+-- regions of exons bounded by the codingSequence correspond to coding DNA
5941+-- sequence. Exons are ordered by start position and may not overlap.
60895942tExons :: Lens' Transcript [Exon]
60905943tExons
60915944 = lens _tExons (\ s a -> s{_tExons = a}) . _Default .
@@ -6111,8 +5964,8 @@ instance ToJSON Transcript where
61115964--
61125965-- /See:/ 'operationEvent' smart constructor.
61135966data OperationEvent = OperationEvent'
6114− { _oeStartTime :: !(Maybe Text)
6115− , _oeEndTime :: !(Maybe Text)
5967+ { _oeStartTime :: !(Maybe DateTime')
5968+ , _oeEndTime :: !(Maybe DateTime')
61165969 , _oeDescription :: !(Maybe Text)
61175970 } deriving (Eq,Show,Data,Typeable,Generic)
61185971
@@ -6135,16 +5988,18 @@ operationEvent =
61355988 }
61365989
61375990-- | Optional time of when event started.
6138−oeStartTime :: Lens' OperationEvent (Maybe Text)
5991+oeStartTime :: Lens' OperationEvent (Maybe UTCTime)
61395992oeStartTime
6140− = lens _oeStartTime (\ s a -> s{_oeStartTime = a})
5993+ = lens _oeStartTime (\ s a -> s{_oeStartTime = a}) .
5994+ mapping _DateTime
61415995
61425996-- | Optional time of when event finished. An event can have a start time and
61435997-- no finish time. If an event has a finish time, there must be a start
61445998-- time.
6145−oeEndTime :: Lens' OperationEvent (Maybe Text)
5999+oeEndTime :: Lens' OperationEvent (Maybe UTCTime)
61466000oeEndTime
6147− = lens _oeEndTime (\ s a -> s{_oeEndTime = a})
6001+ = lens _oeEndTime (\ s a -> s{_oeEndTime = a}) .
6002+ mapping _DateTime
61486003
61496004-- | Required description of event.
61506005oeDescription :: Lens' OperationEvent (Maybe Text)
@@ -6168,108 +6023,6 @@ instance ToJSON OperationEvent where
61686023 ("endTime" .=) <$> _oeEndTime,
61696024 ("description" .=) <$> _oeDescription])
61706025
6171−-- | The stream variants request.
6172−--
6173−-- /See:/ 'streamVariantsRequest' smart constructor.
6174−data StreamVariantsRequest = StreamVariantsRequest'
6175− { _strVariantSetId :: !(Maybe Text)
6176− , _strStart :: !(Maybe (Textual Int64))
6177− , _strCallSetIds :: !(Maybe [Text])
6178− , _strReferenceName :: !(Maybe Text)
6179− , _strEnd :: !(Maybe (Textual Int64))
6180− , _strProjectId :: !(Maybe Text)
6181− } deriving (Eq,Show,Data,Typeable,Generic)
6182−
6183−-- | Creates a value of 'StreamVariantsRequest' with the minimum fields required to make a request.
6184−--
6185−-- Use one of the following lenses to modify other fields as desired:
6186−--
6187−-- * 'strVariantSetId'
6188−--
6189−-- * 'strStart'
6190−--
6191−-- * 'strCallSetIds'
6192−--
6193−-- * 'strReferenceName'
6194−--
6195−-- * 'strEnd'
6196−--
6197−-- * 'strProjectId'
6198−streamVariantsRequest
6199− :: StreamVariantsRequest
6200−streamVariantsRequest =
6201− StreamVariantsRequest'
6202− { _strVariantSetId = Nothing
6203− , _strStart = Nothing
6204− , _strCallSetIds = Nothing
6205− , _strReferenceName = Nothing
6206− , _strEnd = Nothing
6207− , _strProjectId = Nothing
6208− }
6209−
6210−-- | The variant set ID from which to stream variants.
6211−strVariantSetId :: Lens' StreamVariantsRequest (Maybe Text)
6212−strVariantSetId
6213− = lens _strVariantSetId
6214− (\ s a -> s{_strVariantSetId = a})
6215−
6216−-- | The beginning of the window (0-based, inclusive) for which overlapping
6217−-- variants should be returned.
6218−strStart :: Lens' StreamVariantsRequest (Maybe Int64)
6219−strStart
6220− = lens _strStart (\ s a -> s{_strStart = a}) .
6221− mapping _Coerce
6222−
6223−-- | Only return variant calls which belong to call sets with these IDs.
6224−-- Leaving this blank returns all variant calls.
6225−strCallSetIds :: Lens' StreamVariantsRequest [Text]
6226−strCallSetIds
6227− = lens _strCallSetIds
6228− (\ s a -> s{_strCallSetIds = a})
6229− . _Default
6230− . _Coerce
6231−
6232−-- | Required. Only return variants in this reference sequence.
6233−strReferenceName :: Lens' StreamVariantsRequest (Maybe Text)
6234−strReferenceName
6235− = lens _strReferenceName
6236− (\ s a -> s{_strReferenceName = a})
6237−
6238−-- | The end of the window (0-based, exclusive) for which overlapping
6239−-- variants should be returned.
6240−strEnd :: Lens' StreamVariantsRequest (Maybe Int64)
6241−strEnd
6242− = lens _strEnd (\ s a -> s{_strEnd = a}) .
6243− mapping _Coerce
6244−
6245−-- | The Google Cloud project ID which will be billed for this access. The
6246−-- caller must have WRITE access to this project. Required.
6247−strProjectId :: Lens' StreamVariantsRequest (Maybe Text)
6248−strProjectId
6249− = lens _strProjectId (\ s a -> s{_strProjectId = a})
6250−
6251−instance FromJSON StreamVariantsRequest where
6252− parseJSON
6253− = withObject "StreamVariantsRequest"
6254− (\ o ->
6255− StreamVariantsRequest' <$>
6256− (o .:? "variantSetId") <*> (o .:? "start") <*>
6257− (o .:? "callSetIds" .!= mempty)
6258− <*> (o .:? "referenceName")
6259− <*> (o .:? "end")
6260− <*> (o .:? "projectId"))
6261−
6262−instance ToJSON StreamVariantsRequest where
6263− toJSON StreamVariantsRequest'{..}
6264− = object
6265− (catMaybes
6266− [("variantSetId" .=) <$> _strVariantSetId,
6267− ("start" .=) <$> _strStart,
6268− ("callSetIds" .=) <$> _strCallSetIds,
6269− ("referenceName" .=) <$> _strReferenceName,
6270− ("end" .=) <$> _strEnd,
6271− ("projectId" .=) <$> _strProjectId])
6272−
62736026-- | ReferenceBound records an upper bound for the starting coordinate of
62746027-- variants in a particular reference.
62756028--