Roll of googleapis as of 4/7/2015.

discovery/googleapis_beta/genomics__v1beta2.json

 {
     "auth": {
         "oauth2": {
             "scopes": {
                 "https://www.googleapis.com/auth/bigquery": {
                     "description": "View and manage your data in Google BigQuery"
                 },
                 "https://www.googleapis.com/auth/devstorage.read_write": {
                     "description": "Manage your data in Google Cloud Storage"
                 },
                 "https://www.googleapis.com/auth/genomics": {
                     "description": "View and manage Genomics data"
                 },
                 "https://www.googleapis.com/auth/genomics.readonly": {
                     "description": "View Genomics data"
                 }
             }
         }
     },
     "basePath": "/genomics/v1beta2/",
     "baseUrl": "https://www.googleapis.com/genomics/v1beta2/",
     "batchPath": "batch",
     "description": "Provides access to Genomics data.",
     "discoveryVersion": "v1",
     "documentationLink": "https://developers.google.com/genomics/v1beta2/reference",
-    "etag": "\"ye6orv2F-1npMW3u9suM3a7C5Bo/wfhG0otVobUDwlejJM3hCJTIZzM\"",
+    "etag": "\"ye6orv2F-1npMW3u9suM3a7C5Bo/zxM6l4gLCm-vFIvi5lr-kFXGmmI\"",
     "icons": {
         "x16": "http://www.google.com/images/icons/product/search-16.gif",
         "x32": "http://www.google.com/images/icons/product/search-32.gif"
     },
     "id": "genomics:v1beta2",
     "kind": "discovery#restDescription",
     "name": "genomics",
     "ownerDomain": "google.com",
     "ownerName": "Google",
     "parameters": {
@@ skipping 124 matching lines @@
                         "$ref": "AnnotationSet"
                     },
                     "response": {
                         "$ref": "AnnotationSet"
                     },
                     "scopes": [
                         "https://www.googleapis.com/auth/genomics"
                     ]
                 },
                 "search": {
-                    "description": "Searches for annotation sets which match the given criteria. Results are returned in a deterministic order. Caller must have READ permission for the queried datasets.",
+                    "description": "Searches for annotation sets that match the given criteria. Results are returned in a deterministic order. Caller must have READ permission for the queried datasets.",
                     "httpMethod": "POST",
                     "id": "genomics.annotationSets.search",
                     "path": "annotationSets/search",
                     "request": {
                         "$ref": "SearchAnnotationSetsRequest"
                     },
                     "response": {
                         "$ref": "SearchAnnotationSetsResponse"
                     },
                     "scopes": [
@@ skipping 125 matching lines @@
                         "$ref": "Annotation"
                     },
                     "response": {
                         "$ref": "Annotation"
                     },
                     "scopes": [
                         "https://www.googleapis.com/auth/genomics"
                     ]
                 },
                 "search": {
-                    "description": "Searches for annotations which match the given criteria. Results are returned ordered by start position. Annotations which have matching start positions are ordered deterministically. Caller must have READ permission for the queried annotation sets.",
+                    "description": "Searches for annotations that match the given criteria. Results are returned ordered by start position. Annotations that have matching start positions are ordered deterministically. Caller must have READ permission for the queried annotation sets.",
                     "httpMethod": "POST",
                     "id": "genomics.annotations.search",
                     "path": "annotations/search",
                     "request": {
                         "$ref": "SearchAnnotationsRequest"
                     },
                     "response": {
                         "$ref": "SearchAnnotationsResponse"
                     },
                     "scopes": [
@@ skipping 215 matching lines @@
                     "path": "datasets/{datasetId}",
                     "response": {
                         "$ref": "Dataset"
                     },
                     "scopes": [
                         "https://www.googleapis.com/auth/genomics",
                         "https://www.googleapis.com/auth/genomics.readonly"
                     ]
                 },
                 "list": {
-                    "description": "Lists all datasets.",
+                    "description": "Lists datasets within a project.",
                     "httpMethod": "GET",
                     "id": "genomics.datasets.list",
                     "parameters": {
                         "pageSize": {
-                            "default": "50",
-                            "description": "The maximum number of results returned by this request.",
+                            "description": "The maximum number of results returned by this request. If unspecified, defaults to 50.",
                             "format": "int32",
                             "location": "query",
                             "type": "integer"
                         },
                         "pageToken": {
                             "description": "The continuation token, which is used to page through large result sets. To get the next page of results, set this parameter to the value of nextPageToken from the previous response.",
                             "location": "query",
                             "type": "string"
                         },
                         "projectNumber": {
-                            "description": "Only return datasets which belong to this Google Developers Console project. Only accepts project numbers. Returns all public projects if no project number is specified.",
+                            "description": "The project to list datasets for.",
                             "format": "int64",
                             "location": "query",
                             "type": "string"
                         }
                     },
                     "path": "datasets",
                     "response": {
                         "$ref": "ListDatasetsResponse"
                     },
                     "scopes": [
@@ skipping 350 matching lines @@
                     "methods": {
                         "list": {
                             "description": "Lists fixed width coverage buckets for a read group set, each of which correspond to a range of a reference sequence. Each bucket summarizes coverage information across its corresponding genomic range.\n\nCoverage is defined as the number of reads which are aligned to a given base in the reference sequence. Coverage buckets are available at several precomputed bucket widths, enabling retrieval of various coverage 'zoom levels'. The caller must have READ permissions for the target read group set.",
                             "httpMethod": "GET",
                             "id": "genomics.readgroupsets.coveragebuckets.list",
                             "parameterOrder": [
                                 "readGroupSetId"
                             ],
                             "parameters": {
                                 "pageSize": {
-                                    "default": "1024",
                                     "description": "The maximum number of results to return in a single page. If unspecified, defaults to 1024. The maximum value is 2048.",
                                     "format": "int32",
                                     "location": "query",
                                     "type": "integer"
                                 },
                                 "pageToken": {
                                     "description": "The continuation token, which is used to page through large result sets. To get the next page of results, set this parameter to the value of nextPageToken from the previous response.",
                                     "location": "query",
                                     "type": "string"
                                 },
@@ skipping 114 matching lines @@
                                 "referenceId"
                             ],
                             "parameters": {
                                 "end": {
                                     "description": "The end position (0-based, exclusive) of this query. Defaults to the length of this reference.",
                                     "format": "int64",
                                     "location": "query",
                                     "type": "string"
                                 },
                                 "pageSize": {
-                                    "default": "200000",
                                     "description": "Specifies the maximum number of bases to return in a single page.",
                                     "format": "int32",
                                     "location": "query",
                                     "type": "integer"
                                 },
                                 "pageToken": {
                                     "description": "The continuation token, which is used to page through large result sets. To get the next page of results, set this parameter to the value of nextPageToken from the previous response.",
                                     "location": "query",
                                     "type": "string"
                                 },
@@ skipping 60 matching lines @@
                     "response": {
                         "$ref": "SearchReferenceSetsResponse"
                     },
                     "scopes": [
                         "https://www.googleapis.com/auth/genomics",
                         "https://www.googleapis.com/auth/genomics.readonly"
                     ]
                 }
             }
         },
+        "streamingVariantStore": {
+            "methods": {
+                "streamvariants": {
+                    "description": "Returns a stream of all the variants matching the search request, ordered by reference name, position, and ID.",
+                    "httpMethod": "POST",
+                    "id": "genomics.streamingVariantStore.streamvariants",
+                    "path": "streamingVariantStore/streamvariants",
+                    "request": {
+                        "$ref": "StreamVariantsRequest"
+                    },
+                    "response": {
+                        "$ref": "Variant"
+                    }
+                }
+            }
+        },
         "variants": {
             "methods": {
                 "create": {
                     "description": "Creates a new variant.",
                     "httpMethod": "POST",
                     "id": "genomics.variants.create",
                     "path": "variants",
                     "request": {
                         "$ref": "Variant"
                     },
@@ skipping 279 matching lines @@
                     "response": {
                         "$ref": "VariantSet"
                     },
                     "scopes": [
                         "https://www.googleapis.com/auth/genomics"
                     ]
                 }
             }
         }
     },
-    "revision": "20150223",
+    "revision": "20150326",
     "rootUrl": "https://www.googleapis.com/",
     "schemas": {
         "AlignReadGroupSetsRequest": {
             "description": "The read group set align request.",
             "id": "AlignReadGroupSetsRequest",
             "properties": {
                 "bamSourceUris": {
                     "description": "The BAM source files for alignment. Exactly one of readGroupSetId, bamSourceUris, interleavedFastqSource or pairedFastqSource must be provided. The caller must have READ permissions for these files.",
                     "items": {
                         "type": "string"
@@ skipping 24 matching lines @@
             "id": "AlignReadGroupSetsResponse",
             "properties": {
                 "jobId": {
                     "description": "A job ID that can be used to get status information.",
                     "type": "string"
                 }
             },
             "type": "object"
         },
         "Annotation": {
-            "description": "An annotation describes a region of reference genome. The value of an annotation may be one of several canonical types, supplemented by arbitrary info tags. A variant annotation is represented by one or more of these canonical types. An annotation is not inherently associated with a specific sample/individual (though a client could choose to use annotations in this way). Example canonical annotation types are 'Gene' and 'Variant'.",
+            "description": "An annotation describes a region of reference genome. The value of an annotation may be one of several canonical types, supplemented by arbitrary info tags. A variant annotation is represented by one or more of these canonical types. An annotation is not inherently associated with a specific sample or individual (though a client could choose to use annotations in this way). Example canonical annotation types are 'Gene' and 'Variant'.",
             "id": "Annotation",
             "properties": {
                 "annotationSetId": {
                     "description": "The ID of the containing annotation set.",
                     "type": "string"
                 },
                 "id": {
                     "description": "The generated unique ID for this annotation.",
                     "type": "string"
                 },
@@ skipping 11 matching lines @@
                 "name": {
                     "description": "The display name of this annotation.",
                     "type": "string"
                 },
                 "position": {
                     "$ref": "RangePosition",
                     "description": "The position of this annotation on the reference sequence."
                 },
                 "transcript": {
                     "$ref": "Transcript",
-                    "description": "A transcript value represents the assertion that a particular region of the reference genome may be transcribed as RNA. An alternate splicing pattern would be represented as separate transcript object. This field is only set for annotations of type TRANSCRIPT."
+                    "description": "A transcript value represents the assertion that a particular region of the reference genome may be transcribed as RNA. An alternative splicing pattern would be represented as a separate transcript object. This field is only set for annotations of type TRANSCRIPT."
                 },
                 "type": {
                     "description": "The data type for this annotation. Must match the containing annotation set's type.",
                     "enum": [
                         "GENE",
                         "GENERIC",
                         "TRANSCRIPT",
                         "VARIANT"
                     ],
                     "enumDescriptions": [
                         "",
                         "",
                         "",
                         ""
                     ],
                     "type": "string"
                 },
                 "variant": {
                     "$ref": "VariantAnnotation",
-                    "description": "A variant annotation which describes the effect of a variant on the genome, the coding sequence, and/or higher level consequences at the organism level e.g. pathogenicity. This field is only set for annotations of type VARIANT."
+                    "description": "A variant annotation, which describes the effect of a variant on the genome, the coding sequence, and/or higher level consequences at the organism level e.g. pathogenicity. This field is only set for annotations of type VARIANT."
                 }
             },
             "type": "object"
         },
         "AnnotationSet": {
-            "description": "An annotation set is a logical grouping of annotations which share consistent type information and provenance. An example would be 'all genes from refseq', or 'all variant annotations from ClinVar'.",
+            "description": "An annotation set is a logical grouping of annotations that share consistent type information and provenance. Examples of annotation sets include 'all genes from refseq', and 'all variant annotations from ClinVar'.",
             "id": "AnnotationSet",
             "properties": {
                 "datasetId": {
                     "description": "The ID of the containing dataset.",
                     "type": "string"
                 },
                 "id": {
                     "description": "The generated unique ID for this annotation set.",
                     "type": "string"
                 },
                 "info": {
                     "additionalProperties": {
                         "description": "A string which maps to an array of values.",
                         "items": {
                             "type": "string"
                         },
                         "type": "array"
                     },
                     "description": "A map of additional data for this annotation set.",
                     "type": "object"
                 },
                 "name": {
                     "description": "The display name for this annotation set.",
                     "type": "string"
                 },
                 "referenceSetId": {
-                    "description": "The ID of the reference set which defines the coordinate-space for this set's annotations.",
+                    "description": "The ID of the reference set that defines the coordinate space for this set's annotations.",
                     "type": "string"
                 },
                 "sourceUri": {
                     "description": "The source URI describing the file from which this annotation set was generated, if any.",
                     "type": "string"
                 },
                 "type": {
                     "description": "The type of annotations contained within this set.",
                     "enum": [
                         "GENE",
@@ skipping 317 matching lines @@
                     "type": "string"
                 }
             },
             "type": "object"
         },
         "ExportReadGroupSetsRequest": {
             "description": "The read group set export request.",
             "id": "ExportReadGroupSetsRequest",
             "properties": {
                 "exportUri": {
-                    "description": "A Google Cloud Storage URI where the exported BAM file will be created. The currently authenticated user must have write access to the new file location. An error will be returned if the URI already contains data.",
+                    "description": "A Google Cloud Storage URI for the exported BAM file. The currently authenticated user must have write access to the new file. An error will be returned if the URI already contains data.",
                     "type": "string"
                 },
                 "projectNumber": {
                     "description": "The Google Developers Console project number that owns this export.",
                     "format": "int64",
                     "type": "string"
                 },
                 "readGroupSetIds": {
                     "description": "The IDs of the read group sets to export.",
                     "items": {
@@ skipping 911 matching lines @@
         },
         "ReferenceSet": {
             "description": "A reference set is a set of references which typically comprise a reference assembly for a species, such as GRCh38 which is representative of the human genome. A reference set defines a common coordinate space for comparing reference-aligned experimental data. A reference set contains 1 or more references.",
             "id": "ReferenceSet",
             "properties": {
                 "assemblyId": {
                     "description": "Public id of this reference set, such as GRCh37.",
                     "type": "string"
                 },
                 "description": {
-                    "description": "Optional free text description of this reference set.",
+                    "description": "Free text description of this reference set.",
                     "type": "string"
                 },
                 "id": {
                     "description": "The Google generated immutable ID of the reference set.",
                     "type": "string"
                 },
                 "md5checksum": {
                     "description": "Order-independent MD5 checksum which identifies this reference set. The checksum is computed by sorting all lower case hexidecimal string reference.md5checksum (for all reference in this set) in ascending lexicographic order, concatenating, and taking the MD5 of that value. The resulting value is represented in lower case hexadecimal format.",
                     "type": "string"
                 },
@@ skipping 44 matching lines @@
                 },
                 "pageToken": {
                     "description": "The continuation token, which is used to page through large result sets. To get the next page of results, set this parameter to the value of nextPageToken from the previous response.",
                     "type": "string"
                 },
                 "referenceSetId": {
                     "description": "If specified, only annotation sets associated with the given reference set are returned.",
                     "type": "string"
                 },
                 "types": {
-                    "description": "If specified, only annotation sets which have any of these types are returned.",
+                    "description": "If specified, only annotation sets that have any of these types are returned.",
                     "items": {
                         "enum": [
                             "GENE",
                             "GENERIC",
                             "TRANSCRIPT",
                             "VARIANT"
                         ],
                         "enumDescriptions": [
                             "",
                             "",
@@ skipping 38 matching lines @@
                     "description": "Specifies number of results to return in a single page. If unspecified, it will default to 256. The maximum value is 2048.",
                     "format": "int32",
                     "type": "integer"
                 },
                 "pageToken": {
                     "description": "The continuation token, which is used to page through large result sets. To get the next page of results, set this parameter to the value of nextPageToken from the previous response.",
                     "type": "string"
                 },
                 "range": {
                     "$ref": "QueryRange",
-                    "description": "If specified, this query matches only annotations which overlap this range."
+                    "description": "If specified, this query matches only annotations that overlap this range."
                 }
             },
             "type": "object"
         },
         "SearchAnnotationsResponse": {
             "id": "SearchAnnotationsResponse",
             "properties": {
                 "annotations": {
                     "description": "The matching annotations.",
                     "items": {
@@ skipping 136 matching lines @@
                     "items": {
                         "type": "string"
                     },
                     "type": "array"
                 },
                 "name": {
                     "description": "Only return read group sets for which a substring of the name matches this string.",
                     "type": "string"
                 },
                 "pageSize": {
-                    "description": "Specifies number of results to return in a single page. If unspecified, it will default to 128. The maximum value is 1024.",
+                    "description": "Specifies number of results to return in a single page. If unspecified, it will default to 256. The maximum value is 1024.",
                     "format": "int32",
                     "type": "integer"
                 },
                 "pageToken": {
                     "description": "The continuation token, which is used to page through large result sets. To get the next page of results, set this parameter to the value of nextPageToken from the previous response.",
                     "type": "string"
                 }
             },
             "type": "object"
         },
@@ skipping 284 matching lines @@
                 "variants": {
                     "description": "The list of matching Variants.",
                     "items": {
                         "$ref": "Variant"
                     },
                     "type": "array"
                 }
             },
             "type": "object"
         },
+        "StreamVariantsRequest": {
+            "description": "The stream variants request.",
+            "id": "StreamVariantsRequest",
+            "properties": {
+                "callSetIds": {
+                    "description": "Only return variant calls which belong to call sets with these ids. Leaving this blank returns all variant calls.",
+                    "items": {
+                        "type": "string"
+                    },
+                    "type": "array"
+                },
+                "end": {
+                    "description": "The end of the window (0-based, exclusive) for which overlapping variants should be returned.",
+                    "format": "int64",
+                    "type": "string"
+                },
+                "referenceName": {
+                    "description": "Required. Only return variants in this reference sequence.",
+                    "type": "string"
+                },
+                "start": {
+                    "description": "The beginning of the window (0-based, inclusive) for which overlapping variants should be returned.",
+                    "format": "int64",
+                    "type": "string"
+                },
+                "variantSetIds": {
+                    "description": "Exactly one variant set ID must be provided. Only variants from this variant set will be returned.",
+                    "items": {
+                        "type": "string"
+                    },
+                    "type": "array"
+                }
+            },
+            "type": "object"
+        },
         "Transcript": {
             "description": "A transcript represents the assertion that a particular region of the reference genome may be transcribed as RNA.",
             "id": "Transcript",
             "properties": {
                 "codingSequence": {
                     "$ref": "TranscriptCodingSequence",
                     "description": "The range of the coding sequence for this transcript, if any. To determine the exact ranges of coding sequence, intersect this range with those of the exons, if any. If there are any exons, the codingSequence must start and end within them.\n\nNote that in some cases, the reference genome will not exactly match the observed mRNA transcript e.g. due to variance in the source genome from reference. In these cases, exon.frame will not necessarily match the expected reference reading frame and coding exon reference bases cannot necessarily be concatenated to produce the original transcript mRNA."
                 },
                 "exons": {
-                    "description": "The exons which compose this transcript. Exons are the pieces of the transcript which are spliced together, may be exported from a cell's nucleus, and may then be translated to protein. This field should be unset for genomes where transcript splicing does not occur, for example prokaryotes.\n\n\nIntrons are regions of the transcript which are not included in the spliced RNA product. Though not explicitly modeled here, intron ranges can be deduced; all regions of this transcript which are not exons are introns.\n\n\nExonic sequences do not necessarily code for a translational product (amino acids). Only the regions of exons bounded by the codingSequence correspond to coding DNA sequence.\n\n\nExons are ordered by start position and may not overlap.",
+                    "description": "The exons that compose this transcript. This field should be unset for genomes where transcript splicing does not occur, for example prokaryotes.\n\n\nIntrons are regions of the transcript that are not included in the spliced RNA product. Though not explicitly modeled here, intron ranges can be deduced; all regions of this transcript that are not exons are introns.\n\n\nExonic sequences do not necessarily code for a translational product (amino acids). Only the regions of exons bounded by the codingSequence correspond to coding DNA sequence.\n\n\nExons are ordered by start position and may not overlap.",
                     "items": {
                         "$ref": "TranscriptExon"
                     },
                     "type": "array"
                 },
                 "geneId": {
                     "description": "The annotation ID of the gene from which this transcript is transcribed.",
                     "type": "string"
                 }
             },
@@ skipping 18 matching lines @@
         "TranscriptExon": {
             "id": "TranscriptExon",
             "properties": {
                 "end": {
                     "description": "The end position of the exon on this annotation's reference sequence, 0-based exclusive. Note that this is relative to the reference start, and not the containing annotation start.",
                     "format": "int64",
                     "type": "string"
                 },
                 "frame": {
                     "$ref": "Int32Value",
-                    "description": "The frame of this exon. Contains a value of 0, 1, or 2 which indicates the offset of the first coding base of the exon within the reading frame of the coding DNA sequence, if any. This field is dependent on the strandedness of this annotation (see Annotation.position.reverseStrand). For forward stranded annotations, this offset is relative to the exon.start. For reverse strand annotations, this offset is relative to the exon.end-1.\n\nUnset if this exon does not intersect the coding sequence. Upon creation of a transcript, the frame must be populated for all or none of the coding exons."
+                    "description": "The frame of this exon. Contains a value of 0, 1, or 2, which indicates the offset of the first coding base of the exon within the reading frame of the coding DNA sequence, if any. This field is dependent on the strandedness of this annotation (see Annotation.position.reverseStrand). For forward stranded annotations, this offset is relative to the exon.start. For reverse strand annotations, this offset is relative to the exon.end-1.\n\nUnset if this exon does not intersect the coding sequence. Upon creation of a transcript, the frame must be populated for all or none of the coding exons."
                 },
                 "start": {
                     "description": "The start position of the exon on this annotation's reference sequence, 0-based inclusive. Note that this is relative to the reference start, and not the containing annotation start.",
                     "format": "int64",
                     "type": "string"
                 }
             },
             "type": "object"
         },
         "Variant": {
@@ skipping 153 matching lines @@
                         "",
                         ""
                     ],
                     "type": "string"
                 },
                 "geneId": {
                     "description": "Google annotation ID of the gene affected by this variant. This should be provided when the variant is created.",
                     "type": "string"
                 },
                 "transcriptIds": {
-                    "description": "Google annotation ID of the transcripts affected by this variant. These should be provided when the variant is created.",
+                    "description": "Google annotation IDs of the transcripts affected by this variant. These should be provided when the variant is created.",
                     "items": {
                         "type": "string"
                     },
                     "type": "array"
                 },
                 "type": {
                     "description": "Type has been adapted from ClinVar's list of variant types.",
                     "enum": [
                         "CNV",
                         "DELETION",
@@ skipping 21 matching lines @@
         },
         "VariantAnnotationCondition": {
             "description": "",
             "id": "VariantAnnotationCondition",
             "properties": {
                 "conceptId": {
                     "description": "The MedGen concept id associated with this gene. Search for these IDs at http://www.ncbi.nlm.nih.gov/medgen/",
                     "type": "string"
                 },
                 "externalIds": {
-                    "description": "The set of external ids for this condition.",
+                    "description": "The set of external IDs for this condition.",
                     "items": {
                         "$ref": "ExternalId"
                     },
                     "type": "array"
                 },
                 "names": {
                     "description": "A set of names for the condition.",
                     "items": {
                         "type": "string"
                     },
@@ skipping 33 matching lines @@
                     "type": "array"
                 }
             },
             "type": "object"
         }
     },
     "servicePath": "genomics/v1beta2/",
     "title": "Genomics API",
     "version": "v1beta2"
 }