{"action":"created","comment":{"url":"https://api.github.com/repos/ga4gh/schemas/pulls/comments/23213421","id":23213421,"diff_hunk":"@@ -94,48 +147,44 @@ record CallSet {\n }\n \n /**\n-A `Call` represents the determination of genotype with respect to a\n-particular variant. It may include associated information such as quality\n-and phasing. For example, a call might assign a probability of 0.32 to\n-the occurrence of a SNP named rs1234 in a call set with the name NA12345.\n+Represents a `Genotype` integrating over the `Call`s belonging to a particular\n+`Variant` in a `CallSet`. Analogous to a `Variant`-level `Call`, as might be\n+found in VCF.\n+\n+Mostly useful for importing VCF annotations, or for giving joint distributions\n+on copy numbers of different `Call`s referencing a `Variant` (like genotype\n+likelihoods).\n */\n-record Call {\n+record Genotype {\n \n   /**\n-  The ID of the call set this variant call belongs to.\n-  If this field is not present, the ordering of the call sets from a\n-  `SearchCallSetsRequest` over this `VariantSet` is guaranteed to match\n-  the ordering of the calls on this `Variant`.\n-  The number of results will also be the same.\n+  The ID of the call set this `Genotype` belongs to. Either this field\n+  or callSetName must be set.\n   */\n   union { null, string } callSetId;\n \n   /**\n-  The name of the call set this variant call belongs to.\n-  If this field is not present, the ordering of the call sets from a\n-  `SearchCallSetsRequest` over this `VariantSet` is guaranteed to match\n-  the ordering of the calls on this `Variant`.\n-  The number of results will also be the same.\n+  The name of the call set this `Genotype` belongs to. Either this\n+  field or callSetId must be set.\n   */\n   union { null, string } callSetName = null;\n \n   /**\n-  The genotype of this variant call. Each value represents either the value\n-  of the referenceBases field or is a 1-based index into alternateBases.\n-  If a variant had a referenceBases field of \"T\", an alternateBases\n-  value of [\"A\", \"C\"], and the genotype was [2, 1], that would mean the call\n-  represented the heterozygous value \"CA\" for this variant. If the genotype\n-  was instead [0, 1] the represented value would be \"TA\". Ordering of the\n-  genotype values is important if the phaseset field is present.\n+  What is the ID of this `Genotype`? Unique within the repository.","path":"src/main/resources/avro/variants.avdl","position":134,"original_position":134,"commit_id":"8864a6dd7db70d727cb2bfaf51572ea82cbbd812","original_commit_id":"8864a6dd7db70d727cb2bfaf51572ea82cbbd812","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":"It would be better to follow the existing pattern for documenting these attributes. i.e. `/** The ID of this Genotype. Unique within the repository. */`. I find it confusing to state the documentation for these attributes in the form of questions. Please rephrase these as declarative statements. (See above the documentation for `Segment.start`)","created_at":"2015-01-20T10:28:16Z","updated_at":"2015-01-20T10:28:16Z","html_url":"https://github.com/ga4gh/schemas/pull/198#discussion_r23213421","pull_request_url":"https://api.github.com/repos/ga4gh/schemas/pulls/198","_links":{"self":{"href":"https://api.github.com/repos/ga4gh/schemas/pulls/comments/23213421"},"html":{"href":"https://github.com/ga4gh/schemas/pull/198#discussion_r23213421"},"pull_request":{"href":"https://api.github.com/repos/ga4gh/schemas/pulls/198"}}},"pull_request":{"url":"https://api.github.com/repos/ga4gh/schemas/pulls/198","id":25464188,"html_url":"https://github.com/ga4gh/schemas/pull/198","diff_url":"https://github.com/ga4gh/schemas/pull/198.diff","patch_url":"https://github.com/ga4gh/schemas/pull/198.patch","issue_url":"https://api.github.com/repos/ga4gh/schemas/issues/198","number":198,"state":"open","locked":false,"title":"Graph Adaptations of Variants, References, and Reads APIs","user":{"login":"adamnovak","id":5062495,"avatar_url":"https://avatars.githubusercontent.com/u/5062495?v=3","gravatar_id":"","url":"https://api.github.com/users/adamnovak","html_url":"https://github.com/adamnovak","followers_url":"https://api.github.com/users/adamnovak/followers","following_url":"https://api.github.com/users/adamnovak/following{/other_user}","gists_url":"https://api.github.com/users/adamnovak/gists{/gist_id}","starred_url":"https://api.github.com/users/adamnovak/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/adamnovak/subscriptions","organizations_url":"https://api.github.com/users/adamnovak/orgs","repos_url":"https://api.github.com/users/adamnovak/repos","events_url":"https://api.github.com/users/adamnovak/events{/privacy}","received_events_url":"https://api.github.com/users/adamnovak/received_events","type":"User","site_admin":false},"body":"This pull request seeks to merge a first shot at adapting the Variants, References, and Reads APIs to a graph reverence into the *`graph` branch*, which is not the main master branch. They will sit there until they are ready to replace the current non-graph-capable API.\r\n\r\nThis PR also includes some commits that have been merged into master since the graph branch was created, but you can ignore those.\r\n\r\nThe biggest changes are in the Variants API, which has been converted to a monoallelic model. Additionally, the References API now has support for `Reference`s branching off of other `Reference`s in the same `ReferenceSet`, and the Reads API has support for reads that are aligned to multiple `Reference`s without being chimeric (because they follow adjacencies in the graph of `Reference`s).\r\n\r\nCloses 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