{"action":"created","comment":{"url":"https://api.github.com/repos/ga4gh/schemas/pulls/comments/31299580","id":31299580,"diff_hunk":"@@ -0,0 +1,244 @@\n+@namespace(\"org.ga4gh.methods\")\n+protocol AlleleAnnotationMethods {\n+\n+/*This protocol defines methods use to mine pre-calculated annotation sets.*/\n+\n+import idl \"methods.avdl\";\n+import idl \"variants.avdl\";\n+import idl \"alleleAnnotations.avdl\";\n+import idl \"sequenceAnnotations.avdl\";\n+import idl \"ontologies.avdl\";\n+\n+\n+\n+/******************  /variantannotations/search  *********************/\n+/** This request maps to the body of `POST /variantannotations/search` as JSON. */\n+record SearchVariantAnnotationsRequest {\n+  /** Required. The IDs of the annotation sets to search over. */\n+  array<string> annotationSetIds = [];\n+\n+  /**\n+  Only return annotation for variants which have exactly this name\n+  (case-sensitive, exact match).\n+  */\n+  union { null, string } name = null;\n+\n+  /**\n+  Only return variants with reference alleles on the reference with this name.\n+  One of this field or `referenceId` or `features` is required.\n+  (case-sensitive, exact match)\n+  */\n+  union { null, string } referenceName = null;\n+\n+  /**\n+  Only return variants with reference alleles on the reference with this ID. One\n+  of this field or `referenceName` or `features` is required.\n+  */\n+  union { null, string } referenceId = null;\n+\n+  /**\n+  Required if referenceName or referenceId supplied.\n+  The beginning of the window (0-based, inclusive) for which variants with\n+  overlapping reference alleles should be returned.\n+  Genomic positions are non-negative integers less than reference length.\n+  Requests spanning the join of circular genomes are represented as\n+  two requests one on each side of the join (position 0).\n+  */\n+  long start;\n+\n+  /**\n+  Required if referenceName or referenceId supplied.\n+  The end of the window (0-based, exclusive) for which variants with\n+  overlapping reference alleles should be returned.\n+  */\n+  long end;\n+\n+\n+  /**\n+  Only return variant annotations for any of these features\n+  If null, return all variant annotations in specified window.\n+  */\n+  union { null, array<org.ga4gh.models.Feature> } features;\n+\n+  /**\n+  Only return variant annotations including these effects (SO terms).\n+  If null, return all variant annotations.\n+  */\n+  union { null, array<org.ga4gh.models.OntologyTerm> } effects = null;\n+\n+\n+  /**\n+  Specifies the maximum number of results to return in a single page.\n+  If unspecified, a system default will be used.\n+  */\n+  union { null, int } pageSize = null;\n+\n+  /**\n+  The continuation token, which is used to page through large result sets.\n+  To get the next page of results, set this parameter to the value of\n+  `nextPageToken` from the previous response.\n+  */\n+  union { null, string } pageToken = null;\n+}\n+\n+\n+/** This is the response from `POST /variantannotations/search` expressed as JSON. */\n+record SearchVariantAnnotationsResponse {\n+  /**\n+  The list of matching variant annotations.\n+  */\n+  array<org.ga4gh.models.VariantAnnotation> variantAnnotations = [];\n+\n+  /**\n+  The continuation token, which is used to page through large result sets.\n+  Provide this value in a subsequent request to return the next page of\n+  results. This field will be empty if there aren't any additional results.\n+  */\n+  union { null, string } nextPageToken = null;\n+}\n+\n+/**\n+Gets a list of `VariantAnnotations` matching the search criteria.\n+\n+`POST /variantannotations/search` must accept a JSON version of `SearchVariantAnnotationsRequest`\n+as the post body and will return a JSON version of `SearchVariantAnnotationsResponse`.\n+*/\n+SearchVariantAnnotationsResponse searchVariantAnnotations(\n+  /** This request maps to the body of `POST /variantannotations/search` as JSON. */\n+  SearchVariantAnnotationsRequest request) throws GAException;\n+\n+\n+\n+/******************  /alleleannotations/search  *********************/\n+/** This request maps to the body of `POST /alleleannotations/search` as JSON. */\n+record SearchAlleleAnnotationsRequest {\n+  /** Required. The IDs of the annotation sets to search over. */\n+  array<string> annotationSetIds = [];","path":"src/main/resources/avro/alleleAnnotationmethods.avdl","position":116,"original_position":116,"commit_id":"de0593397edcc4e9e514046b588780c6366030c4","original_commit_id":"de0593397edcc4e9e514046b588780c6366030c4","user":{"login":"calbach","id":822298,"avatar_url":"https://avatars.githubusercontent.com/u/822298?v=3","gravatar_id":"","url":"https://api.github.com/users/calbach","html_url":"https://github.com/calbach","followers_url":"https://api.github.com/users/calbach/followers","following_url":"https://api.github.com/users/calbach/following{/other_user}","gists_url":"https://api.github.com/users/calbach/gists{/gist_id}","starred_url":"https://api.github.com/users/calbach/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/calbach/subscriptions","organizations_url":"https://api.github.com/users/calbach/orgs","repos_url":"https://api.github.com/users/calbach/repos","events_url":"https://api.github.com/users/calbach/events{/privacy}","received_events_url":"https://api.github.com/users/calbach/received_events","type":"User","site_admin":false},"body":"Per #253 this should now *maybe* be singular. Though this one is definitely higher value..","created_at":"2015-05-29T05:13:14Z","updated_at":"2015-05-29T05:13:14Z","html_url":"https://github.com/ga4gh/schemas/pull/302#discussion_r31299580","pull_request_url":"https://api.github.com/repos/ga4gh/schemas/pulls/302","_links":{"self":{"href":"https://api.github.com/repos/ga4gh/schemas/pulls/comments/31299580"},"html":{"href":"https://github.com/ga4gh/schemas/pull/302#discussion_r31299580"},"pull_request":{"href":"https://api.github.com/repos/ga4gh/schemas/pulls/302"}}},"pull_request":{"url":"https://api.github.com/repos/ga4gh/schemas/pulls/302","id":34904254,"html_url":"https://github.com/ga4gh/schemas/pull/302","diff_url":"https://github.com/ga4gh/schemas/pull/302.diff","patch_url":"https://github.com/ga4gh/schemas/pull/302.patch","issue_url":"https://api.github.com/repos/ga4gh/schemas/issues/302","number":302,"state":"open","locked":false,"title":"Variant annotation support","user":{"login":"sarahhunt","id":6123326,"avatar_url":"https://avatars.githubusercontent.com/u/6123326?v=3","gravatar_id":"","url":"https://api.github.com/users/sarahhunt","html_url":"https://github.com/sarahhunt","followers_url":"https://api.github.com/users/sarahhunt/followers","following_url":"https://api.github.com/users/sarahhunt/following{/other_user}","gists_url":"https://api.github.com/users/sarahhunt/gists{/gist_id}","starred_url":"https://api.github.com/users/sarahhunt/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/sarahhunt/subscriptions","organizations_url":"https://api.github.com/users/sarahhunt/orgs","repos_url":"https://api.github.com/users/sarahhunt/repos","events_url":"https://api.github.com/users/sarahhunt/events{/privacy}","received_events_url":"https://api.github.com/users/sarahhunt/received_events","type":"User","site_admin":false},"body":"These three new protocols form an initial proposal for variant annotation support. \r\n\r\nVariantAnnotation and AlleleAnnotation records hold different types of annotation derived by comparing a Variant or Allele to a set of reference data.  AnnotationSets group VariantAnnotation/ AlleleAnnotation records and hold full details of all software and reference data sets used. \r\n\r\nThe effect of alternate alleles on transcript sets is the first type of annotation to be considered in detail.\r\n\r\nTwo methods protocols are proposed. alleleAnnotationmethods.avdl supports the mining of pre-calculated annotation data and annotateAllelemethods.avdl supports annotation as a service. 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