{"action":"created","issue":{"url":"https://api.github.com/repos/zyxue/kleat/issues/10","repository_url":"https://api.github.com/repos/zyxue/kleat","labels_url":"https://api.github.com/repos/zyxue/kleat/issues/10/labels{/name}","comments_url":"https://api.github.com/repos/zyxue/kleat/issues/10/comments","events_url":"https://api.github.com/repos/zyxue/kleat/issues/10/events","html_url":"https://github.com/zyxue/kleat/issues/10","id":341268916,"node_id":"MDU6SXNzdWUzNDEyNjg5MTY=","number":10,"title":"ctg_hex_pos and ctg_hex_dist is buggy when the contig has indels","user":{"login":"zyxue","id":527862,"node_id":"MDQ6VXNlcjUyNzg2Mg==","avatar_url":"https://avatars2.githubusercontent.com/u/527862?v=4","gravatar_id":"","url":"https://api.github.com/users/zyxue","html_url":"https://github.com/zyxue","followers_url":"https://api.github.com/users/zyxue/followers","following_url":"https://api.github.com/users/zyxue/following{/other_user}","gists_url":"https://api.github.com/users/zyxue/gists{/gist_id}","starred_url":"https://api.github.com/users/zyxue/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/zyxue/subscriptions","organizations_url":"https://api.github.com/users/zyxue/orgs","repos_url":"https://api.github.com/users/zyxue/repos","events_url":"https://api.github.com/users/zyxue/events{/privacy}","received_events_url":"https://api.github.com/users/zyxue/received_events","type":"User","site_admin":false},"labels":[{"id":971832609,"node_id":"MDU6TGFiZWw5NzE4MzI2MDk=","url":"https://api.github.com/repos/zyxue/kleat/labels/bug","name":"bug","color":"d73a4a","default":true},{"id":993911015,"node_id":"MDU6TGFiZWw5OTM5MTEwMTU=","url":"https://api.github.com/repos/zyxue/kleat/labels/high%20priority","name":"high priority","color":"ff3247","default":false}],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":1,"created_at":"2018-07-14T21:21:05Z","updated_at":"2018-07-15T19:21:15Z","closed_at":null,"author_association":"OWNER","body":"This is because the coordinate information is currently lost when the sequence is extracted from contig.\r\n\r\nCurrently, this search function is used to search for hexamer in the contig, it only takes into account the extracted sequence with cigar information missing.\r\n\r\nhttps://github.com/zyxue/kleat/blob/933e2401f8353848e6a1e420aef05d48a8564eb3/kleat/hexamer/search.py#L66\r\n\r\nMaybe it's easier to define the searching window (e.g. 50bp) wst. to the reference, the actual sequence length wst. contig could be a few bp more or less than 50bp.\r\n"},"comment":{"url":"https://api.github.com/repos/zyxue/kleat/issues/comments/405112040","html_url":"https://github.com/zyxue/kleat/issues/10#issuecomment-405112040","issue_url":"https://api.github.com/repos/zyxue/kleat/issues/10","id":405112040,"node_id":"MDEyOklzc3VlQ29tbWVudDQwNTExMjA0MA==","user":{"login":"zyxue","id":527862,"node_id":"MDQ6VXNlcjUyNzg2Mg==","avatar_url":"https://avatars2.githubusercontent.com/u/527862?v=4","gravatar_id":"","url":"https://api.github.com/users/zyxue","html_url":"https://github.com/zyxue","followers_url":"https://api.github.com/users/zyxue/followers","following_url":"https://api.github.com/users/zyxue/following{/other_user}","gists_url":"https://api.github.com/users/zyxue/gists{/gist_id}","starred_url":"https://api.github.com/users/zyxue/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/zyxue/subscriptions","organizations_url":"https://api.github.com/users/zyxue/orgs","repos_url":"https://api.github.com/users/zyxue/repos","events_url":"https://api.github.com/users/zyxue/events{/privacy}","received_events_url":"https://api.github.com/users/zyxue/received_events","type":"User","site_admin":false},"created_at":"2018-07-15T19:21:15Z","updated_at":"2018-07-15T19:21:15Z","author_association":"OWNER","body":"Actually, ctg_hex_dist could be correct, it's just the ctg_hex_pos is not consistent with genomics coordinates and should be dropped."}}
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