{"action":"created","issue":{"url":"https://api.github.com/repos/GregoryFaust/samblaster/issues/13","labels_url":"https://api.github.com/repos/GregoryFaust/samblaster/issues/13/labels{/name}","comments_url":"https://api.github.com/repos/GregoryFaust/samblaster/issues/13/comments","events_url":"https://api.github.com/repos/GregoryFaust/samblaster/issues/13/events","html_url":"https://github.com/GregoryFaust/samblaster/pull/13","id":72783437,"number":13,"title":"Avoid buffer length issues when marking long SAM lines","user":{"login":"chapmanb","id":39391,"avatar_url":"https://avatars.githubusercontent.com/u/39391?v=3","gravatar_id":"","url":"https://api.github.com/users/chapmanb","html_url":"https://github.com/chapmanb","followers_url":"https://api.github.com/users/chapmanb/followers","following_url":"https://api.github.com/users/chapmanb/following{/other_user}","gists_url":"https://api.github.com/users/chapmanb/gists{/gist_id}","starred_url":"https://api.github.com/users/chapmanb/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/chapmanb/subscriptions","organizations_url":"https://api.github.com/users/chapmanb/orgs","repos_url":"https://api.github.com/users/chapmanb/repos","events_url":"https://api.github.com/users/chapmanb/events{/privacy}","received_events_url":"https://api.github.com/users/chapmanb/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"milestone":null,"comments":2,"created_at":"2015-05-03T10:14:30Z","updated_at":"2015-06-18T23:34:45Z","closed_at":"2015-06-18T20:58:30Z","pull_request":{"url":"https://api.github.com/repos/GregoryFaust/samblaster/pulls/13","html_url":"https://github.com/GregoryFaust/samblaster/pull/13","diff_url":"https://github.com/GregoryFaust/samblaster/pull/13.diff","patch_url":"https://github.com/GregoryFaust/samblaster/pull/13.patch"},"body":"While testing with hg38, samblaster dies on very long SAM lines from HLA matches with a larger number of alternative matches:\r\n```\r\nsamblaster: New buffer length exceeds maximum while changing field value\r\n```\r\nThis is a small test case which reproduces the issue (although confusingly, it fails consistently on CentOS 6.6 but not at all on Ubuntu 14.04, both with gcc 4.8.2):\r\n\r\nhttps://s3.amazonaws.com/chapmanb/samblaster/samblaster_hg38_linelength.tar.gz\r\n\r\nThis fix avoid the issue by increasing the maximum buffer length of the line to accommodate these. My C/C++ is terrible so happy for a review on how this affected memory usage or why it behaves differently on Ubuntu/CentOS."},"comment":{"url":"https://api.github.com/repos/GregoryFaust/samblaster/issues/comments/113318804","html_url":"https://github.com/GregoryFaust/samblaster/pull/13#issuecomment-113318804","issue_url":"https://api.github.com/repos/GregoryFaust/samblaster/issues/13","id":113318804,"user":{"login":"chapmanb","id":39391,"avatar_url":"https://avatars.githubusercontent.com/u/39391?v=3","gravatar_id":"","url":"https://api.github.com/users/chapmanb","html_url":"https://github.com/chapmanb","followers_url":"https://api.github.com/users/chapmanb/followers","following_url":"https://api.github.com/users/chapmanb/following{/other_user}","gists_url":"https://api.github.com/users/chapmanb/gists{/gist_id}","starred_url":"https://api.github.com/users/chapmanb/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/chapmanb/subscriptions","organizations_url":"https://api.github.com/users/chapmanb/orgs","repos_url":"https://api.github.com/users/chapmanb/repos","events_url":"https://api.github.com/users/chapmanb/events{/privacy}","received_events_url":"https://api.github.com/users/chapmanb/received_events","type":"User","site_admin":false},"created_at":"2015-06-18T23:34:45Z","updated_at":"2015-06-18T23:34:45Z","body":"Brilliant, thanks much for the better fix and update."}}