{"action":"created","issue":{"url":"https://api.github.com/repos/GFA-spec/GFA-spec/issues/48","repository_url":"https://api.github.com/repos/GFA-spec/GFA-spec","labels_url":"https://api.github.com/repos/GFA-spec/GFA-spec/issues/48/labels{/name}","comments_url":"https://api.github.com/repos/GFA-spec/GFA-spec/issues/48/comments","events_url":"https://api.github.com/repos/GFA-spec/GFA-spec/issues/48/events","html_url":"https://github.com/GFA-spec/GFA-spec/pull/48","id":178898873,"number":48,"title":"GFA2 Pull Request for 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2.0","creator":{"login":"sjackman","id":291551,"avatar_url":"https://avatars.githubusercontent.com/u/291551?v=3","gravatar_id":"","url":"https://api.github.com/users/sjackman","html_url":"https://github.com/sjackman","followers_url":"https://api.github.com/users/sjackman/followers","following_url":"https://api.github.com/users/sjackman/following{/other_user}","gists_url":"https://api.github.com/users/sjackman/gists{/gist_id}","starred_url":"https://api.github.com/users/sjackman/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/sjackman/subscriptions","organizations_url":"https://api.github.com/users/sjackman/orgs","repos_url":"https://api.github.com/users/sjackman/repos","events_url":"https://api.github.com/users/sjackman/events{/privacy}","received_events_url":"https://api.github.com/users/sjackman/received_events","type":"User","site_admin":false},"open_issues":1,"closed_issues":0,"state":"open","created_at":"2016-09-22T21:01:02Z","updated_at":"2016-09-24T00:30:47Z","due_on":null,"closed_at":null},"comments":61,"created_at":"2016-09-23T14:57:07Z","updated_at":"2016-10-21T22:55:27Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/GFA-spec/GFA-spec/pulls/48","html_url":"https://github.com/GFA-spec/GFA-spec/pull/48","diff_url":"https://github.com/GFA-spec/GFA-spec/pull/48.diff","patch_url":"https://github.com/GFA-spec/GFA-spec/pull/48.patch"},"body":"Here is the long promised pull request for GFA2.\r\n\r\nI've strictly added files to the branch, e.g. GFA2-spec.md, README2.md, etc.\r\n\r\nPlease note carefully that a number of things that were previous optional\r\nSAM-tags are not required field that can be optioned with a * as per the\r\nGFA convention.\r\n\r\nAlso please not carefully the semantics of edges in paths.  The ability to have\r\nedges in paths, implies that orientation signs are not needed."},"comment":{"url":"https://api.github.com/repos/GFA-spec/GFA-spec/issues/comments/255484253","html_url":"https://github.com/GFA-spec/GFA-spec/pull/48#issuecomment-255484253","issue_url":"https://api.github.com/repos/GFA-spec/GFA-spec/issues/48","id":255484253,"user":{"login":"sjackman","id":291551,"avatar_url":"https://avatars.githubusercontent.com/u/291551?v=3","gravatar_id":"","url":"https://api.github.com/users/sjackman","html_url":"https://github.com/sjackman","followers_url":"https://api.github.com/users/sjackman/followers","following_url":"https://api.github.com/users/sjackman/following{/other_user}","gists_url":"https://api.github.com/users/sjackman/gists{/gist_id}","starred_url":"https://api.github.com/users/sjackman/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/sjackman/subscriptions","organizations_url":"https://api.github.com/users/sjackman/orgs","repos_url":"https://api.github.com/users/sjackman/repos","events_url":"https://api.github.com/users/sjackman/events{/privacy}","received_events_url":"https://api.github.com/users/sjackman/received_events","type":"User","site_admin":false},"created_at":"2016-10-21T22:55:27Z","updated_at":"2016-10-21T22:55:27Z","body":"Jason and I met in person and had a chance to discuss the path record. The following graph represents a tandem inverted repeat, which Jason calls a lollipop, because of how they look in long read overlap graphs. (Care to post your example figure of a lollipop, Jason?) In this graph there are two possible paths through the lollipop that visit both of the non-repeat segments, `X` and `Y`.\r\n\r\n1. `X+ A+ R+ A- Y+`\r\n2. `X+ A+ R- A- Y+`\r\n\r\n![lollipop](https://cloud.githubusercontent.com/assets/291551/19613793/d176d83e-97a3-11e6-8a2f-c6e3684e2875.png)\r\n\r\nThe example below shows a path represented as both a sequence of oriented segments and the equivalent sequence of edge IDs.\r\n\r\n# GFA\r\n```\r\nS\tX\t9\tACACCACCC\r\nS\tA\t9\tACCCAACGT\r\nS\tR\t9\tACGTAACGT\r\nS\tY\t9\tGGGTTTTTT\r\nE\t1\tX\t+\tA\t5\t9$\t0\t4\t4M\r\nE\t2\tA\t+\tR\t5\t9$\t0\t4\t4M\r\nE\t3\tA\t-\tR\t5\t9$\t5\t9$\t4M\r\nE\t4\tA\t-\tY\t0\t4\t0\t4\t4M\r\n# A sequence of oriented segments\r\nO\tP1\tX+ A+ R+ A- Y+\r\nO\tP2\tX+ A+ R- A- Y+\r\n# A sequence of edges\r\nO\tP1\t1 2 3 4\r\nO\tP2\t1 3 2 4\r\n```\r\n\r\nA path of oriented segment IDs is sufficient to represent a path in a skew-symmetric graph that does not have multiple parallel edges. A graph that does have multiple parallel edges may use a path of edge IDs. I propose that a GFA path record be a sequence of either\r\n\r\n1. segment IDs\r\n2. oriented segment IDs\r\n3. edge IDs"}}
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