{"action":"created","comment":{"url":"https://api.github.com/repos/ga4gh/schemas/pulls/comments/48972733","id":48972733,"diff_hunk":"@@ -0,0 +1,205 @@\n+@namespace(\"org.ga4gh.methods\")\n+protocol AlleleAnnotationMethods {\n+\n+/*\n+This protocol defines methods use to mine pre-calculated variant allele\n+annotations.\n+*/\n+\n+import idl \"methods.avdl\";\n+import idl \"variants.avdl\";\n+import idl \"alleleAnnotations.avdl\";\n+import idl \"metadata.avdl\";\n+/*\n+variantannotations/search returns annotation for the alleles of Variants\n+\n+This allows the mining of allele-specific annotations on a VariantSet by\n+either a region or by a set of genomic features. Where a region is supplied\n+annotation of all alleles vs all features in the region is returned. Where a\n+set of features is supplied, only annotations against these features (matching\n+on featuretype and id) are returned and other overlapping features are ignored.\n+\n+variantannotationsets/search returns information on the input to the\n+annotation. This will be a VariantSet and the reference data and software\n+versions used in calculating the annotation.\n+It is essential this information is exhaustive.\n+*/\n+\n+/******************  /variantannotations/search  *********************/\n+/** \n+This request maps to the body of `POST /variantannotations/search` as JSON\n+*/\n+record SearchVariantAnnotationsRequest {\n+  /** Required. The ID of the variant annotation set to search over. */\n+  string variantAnnotationSetId;\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\n+  name. 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\n+  ID. One 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","path":"src/main/resources/avro/alleleAnnotationmethods.avdl","position":57,"original_position":57,"commit_id":"f31f51a8a1a6f009e1a9baff174121dda7277675","original_commit_id":"f31f51a8a1a6f009e1a9baff174121dda7277675","user":{"login":"jeromekelleher","id":2664569,"avatar_url":"https://avatars.githubusercontent.com/u/2664569?v=3","gravatar_id":"","url":"https://api.github.com/users/jeromekelleher","html_url":"https://github.com/jeromekelleher","followers_url":"https://api.github.com/users/jeromekelleher/followers","following_url":"https://api.github.com/users/jeromekelleher/following{/other_user}","gists_url":"https://api.github.com/users/jeromekelleher/gists{/gist_id}","starred_url":"https://api.github.com/users/jeromekelleher/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jeromekelleher/subscriptions","organizations_url":"https://api.github.com/users/jeromekelleher/orgs","repos_url":"https://api.github.com/users/jeromekelleher/repos","events_url":"https://api.github.com/users/jeromekelleher/events{/privacy}","received_events_url":"https://api.github.com/users/jeromekelleher/received_events","type":"User","site_admin":false},"body":"Shouldn't this be always required (like SearchVariantsRequest)?","created_at":"2016-01-06T16:02:51Z","updated_at":"2016-01-06T16:02:51Z","html_url":"https://github.com/ga4gh/schemas/pull/519#discussion_r48972733","pull_request_url":"https://api.github.com/repos/ga4gh/schemas/pulls/519","_links":{"self":{"href":"https://api.github.com/repos/ga4gh/schemas/pulls/comments/48972733"},"html":{"href":"https://github.com/ga4gh/schemas/pull/519#discussion_r48972733"},"pull_request":{"href":"https://api.github.com/repos/ga4gh/schemas/pulls/519"}}},"pull_request":{"url":"https://api.github.com/repos/ga4gh/schemas/pulls/519","id":54185594,"html_url":"https://github.com/ga4gh/schemas/pull/519","diff_url":"https://github.com/ga4gh/schemas/pull/519.diff","patch_url":"https://github.com/ga4gh/schemas/pull/519.patch","issue_url":"https://api.github.com/repos/ga4gh/schemas/issues/519","number":519,"state":"open","locked":false,"title":"Variant Annotation re-merge","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":"This PR re-merges the Variant Annotation API first discussed in #302, now with additional documentation, a reference server implementation and compliance tests.\r\n\r\nMajor new developments have been avoided. The differences are:\r\n- removal of all graph-related functionality\r\n- rename AnnotationSet to VariantAnnotationSet for clarity\r\n- a VariantAnnotationSet is now derived from a specific VariantSet, rather than a Dataset\r\n- AlleleLocation overlapEnd can be null\r\n- SearchVariantAnnotationsRequest feature_ids key renamed to featureIds to match the standard\r\n- avro corrections - addition of missing null values 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