{"action":"created","issue":{"url":"https://api.github.com/repos/biogo/hts/issues/46","repository_url":"https://api.github.com/repos/biogo/hts","labels_url":"https://api.github.com/repos/biogo/hts/issues/46/labels{/name}","comments_url":"https://api.github.com/repos/biogo/hts/issues/46/comments","events_url":"https://api.github.com/repos/biogo/hts/issues/46/events","html_url":"https://github.com/biogo/hts/pull/46","id":187525109,"number":46,"title":"tabix: change Chunks signature to resemble csi and bam","user":{"login":"kortschak","id":275221,"avatar_url":"https://avatars.githubusercontent.com/u/275221?v=3","gravatar_id":"","url":"https://api.github.com/users/kortschak","html_url":"https://github.com/kortschak","followers_url":"https://api.github.com/users/kortschak/followers","following_url":"https://api.github.com/users/kortschak/following{/other_user}","gists_url":"https://api.github.com/users/kortschak/gists{/gist_id}","starred_url":"https://api.github.com/users/kortschak/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/kortschak/subscriptions","organizations_url":"https://api.github.com/users/kortschak/orgs","repos_url":"https://api.github.com/users/kortschak/repos","events_url":"https://api.github.com/users/kortschak/events{/privacy}","received_events_url":"https://api.github.com/users/kortschak/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":11,"created_at":"2016-11-05T21:43:20Z","updated_at":"2016-11-07T02:42:48Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/biogo/hts/pulls/46","html_url":"https://github.com/biogo/hts/pull/46","diff_url":"https://github.com/biogo/hts/pull/46.diff","patch_url":"https://github.com/biogo/hts/pull/46.patch"},"body":"API-breaking change.\r\n\r\n@brentp Please take a look.\r\n\r\nCloses #44."},"comment":{"url":"https://api.github.com/repos/biogo/hts/issues/comments/258735267","html_url":"https://github.com/biogo/hts/pull/46#issuecomment-258735267","issue_url":"https://api.github.com/repos/biogo/hts/issues/46","id":258735267,"user":{"login":"brentp","id":1739,"avatar_url":"https://avatars.githubusercontent.com/u/1739?v=3","gravatar_id":"","url":"https://api.github.com/users/brentp","html_url":"https://github.com/brentp","followers_url":"https://api.github.com/users/brentp/followers","following_url":"https://api.github.com/users/brentp/following{/other_user}","gists_url":"https://api.github.com/users/brentp/gists{/gist_id}","starred_url":"https://api.github.com/users/brentp/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/brentp/subscriptions","organizations_url":"https://api.github.com/users/brentp/orgs","repos_url":"https://api.github.com/users/brentp/repos","events_url":"https://api.github.com/users/brentp/events{/privacy}","received_events_url":"https://api.github.com/users/brentp/received_events","type":"User","site_admin":false},"created_at":"2016-11-07T02:42:48Z","updated_at":"2016-11-07T02:42:48Z","body":"Looks like, in htslib, they are storing the seqnames in the meta/auxilary of CSI: https://github.com/samtools/htslib/blob/develop/tbx.c#L306\r\nI think it's reading tbx_conf_t as the first 24 bytes which contains\r\n```\r\ntypedef struct {\r\n    int32_t preset;\r\n    int32_t sc, bc, ec; // seq col., beg col. and end col.\r\n    int32_t meta_char, line_skip;\r\n} tbx_conf_t;\r\n```\r\nthen it gets the length of the remaining bytes in the next 4. And then parsing the seq names add adding them to the dict at line 306. I verified that code gets executed when loading a CSI index for a VCF.\r\n\r\nJust like the spec says, ahem."}}
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