{"action":"created","issue":{"url":"https://api.github.com/repos/PROSIC/libprosic/issues/54","repository_url":"https://api.github.com/repos/PROSIC/libprosic","labels_url":"https://api.github.com/repos/PROSIC/libprosic/issues/54/labels{/name}","comments_url":"https://api.github.com/repos/PROSIC/libprosic/issues/54/comments","events_url":"https://api.github.com/repos/PROSIC/libprosic/issues/54/events","html_url":"https://github.com/PROSIC/libprosic/pull/54","id":383139188,"node_id":"MDExOlB1bGxSZXF1ZXN0MjMyNjgwMjUw","number":54,"title":"PairHMM optimizations","user":{"login":"johanneskoester","id":1858646,"node_id":"MDQ6VXNlcjE4NTg2NDY=","avatar_url":"https://avatars1.githubusercontent.com/u/1858646?v=4","gravatar_id":"","url":"https://api.github.com/users/johanneskoester","html_url":"https://github.com/johanneskoester","followers_url":"https://api.github.com/users/johanneskoester/followers","following_url":"https://api.github.com/users/johanneskoester/following{/other_user}","gists_url":"https://api.github.com/users/johanneskoester/gists{/gist_id}","starred_url":"https://api.github.com/users/johanneskoester/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/johanneskoester/subscriptions","organizations_url":"https://api.github.com/users/johanneskoester/orgs","repos_url":"https://api.github.com/users/johanneskoester/repos","events_url":"https://api.github.com/users/johanneskoester/events{/privacy}","received_events_url":"https://api.github.com/users/johanneskoester/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":10,"created_at":"2018-11-21T14:19:51Z","updated_at":"2018-11-23T10:33:07Z","closed_at":null,"author_association":"CONTRIBUTOR","pull_request":{"url":"https://api.github.com/repos/PROSIC/libprosic/pulls/54","html_url":"https://github.com/PROSIC/libprosic/pull/54","diff_url":"https://github.com/PROSIC/libprosic/pull/54.diff","patch_url":"https://github.com/PROSIC/libprosic/pull/54.patch"},"body":"@dlaehnemann this is another round of optimizations in Rust-Bio. Again this PR includes the changes from #51 and #53. May I ask you for another flamegraph?\r\n\r\nThanks!\r\n\r\n# Summary of overall optimizations\r\n* Omit lower left and upper right triangle in pairHMM dynamic programming matrix if gap extension probability is zero. (#54)\r\n* Try to skip as many LogProb operations as possible in pairHMM code. (#54)\r\n* Use fast approximation of exp (#53).\r\n* Use precomputed per-base match, mismatch and indel probabilities (#51)."},"comment":{"url":"https://api.github.com/repos/PROSIC/libprosic/issues/comments/441205619","html_url":"https://github.com/PROSIC/libprosic/pull/54#issuecomment-441205619","issue_url":"https://api.github.com/repos/PROSIC/libprosic/issues/54","id":441205619,"node_id":"MDEyOklzc3VlQ29tbWVudDQ0MTIwNTYxOQ==","user":{"login":"dlaehnemann","id":1379875,"node_id":"MDQ6VXNlcjEzNzk4NzU=","avatar_url":"https://avatars1.githubusercontent.com/u/1379875?v=4","gravatar_id":"","url":"https://api.github.com/users/dlaehnemann","html_url":"https://github.com/dlaehnemann","followers_url":"https://api.github.com/users/dlaehnemann/followers","following_url":"https://api.github.com/users/dlaehnemann/following{/other_user}","gists_url":"https://api.github.com/users/dlaehnemann/gists{/gist_id}","starred_url":"https://api.github.com/users/dlaehnemann/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/dlaehnemann/subscriptions","organizations_url":"https://api.github.com/users/dlaehnemann/orgs","repos_url":"https://api.github.com/users/dlaehnemann/repos","events_url":"https://api.github.com/users/dlaehnemann/events{/privacy}","received_events_url":"https://api.github.com/users/dlaehnemann/received_events","type":"User","site_admin":false},"created_at":"2018-11-23T10:33:07Z","updated_at":"2018-11-23T10:33:07Z","author_association":"MEMBER","body":"Once again, an updated flamegraph -- now really produced on the same desktop machine (to improve the documentation for me, I used the binary `target/release/deps/lib-bd13d8378779c7b3`):\r\n\r\n<https://gist.github.com/dlaehnemann/250cabbf940cee7087ce7e4d7ee4e497>\r\n(to view the interactive and searchable SVG, right-click the preview in the gist and select View Image)\r\n\r\nAnd here goes the `time`ing on that machine, which is even better:\r\n\r\n```\r\nuser\t0m0,567s\r\nuser\t0m0,548s\r\nuser\t0m0,553s\r\n```"}}
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