{"action":"created","issue":{"url":"https://api.github.com/repos/samtools/htsjdk/issues/515","repository_url":"https://api.github.com/repos/samtools/htsjdk","labels_url":"https://api.github.com/repos/samtools/htsjdk/issues/515/labels{/name}","comments_url":"https://api.github.com/repos/samtools/htsjdk/issues/515/comments","events_url":"https://api.github.com/repos/samtools/htsjdk/issues/515/events","html_url":"https://github.com/samtools/htsjdk/pull/515","id":139111255,"number":515,"title":"Fast BAM compression with igzip integrated as part of IntelDeflater","user":{"login":"mishalinaik","id":6305541,"avatar_url":"https://avatars.githubusercontent.com/u/6305541?v=3","gravatar_id":"","url":"https://api.github.com/users/mishalinaik","html_url":"https://github.com/mishalinaik","followers_url":"https://api.github.com/users/mishalinaik/followers","following_url":"https://api.github.com/users/mishalinaik/following{/other_user}","gists_url":"https://api.github.com/users/mishalinaik/gists{/gist_id}","starred_url":"https://api.github.com/users/mishalinaik/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mishalinaik/subscriptions","organizations_url":"https://api.github.com/users/mishalinaik/orgs","repos_url":"https://api.github.com/users/mishalinaik/repos","events_url":"https://api.github.com/users/mishalinaik/events{/privacy}","received_events_url":"https://api.github.com/users/mishalinaik/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":{"login":"akiezun","id":1993519,"avatar_url":"https://avatars.githubusercontent.com/u/1993519?v=3","gravatar_id":"","url":"https://api.github.com/users/akiezun","html_url":"https://github.com/akiezun","followers_url":"https://api.github.com/users/akiezun/followers","following_url":"https://api.github.com/users/akiezun/following{/other_user}","gists_url":"https://api.github.com/users/akiezun/gists{/gist_id}","starred_url":"https://api.github.com/users/akiezun/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/akiezun/subscriptions","organizations_url":"https://api.github.com/users/akiezun/orgs","repos_url":"https://api.github.com/users/akiezun/repos","events_url":"https://api.github.com/users/akiezun/events{/privacy}","received_events_url":"https://api.github.com/users/akiezun/received_events","type":"User","site_admin":false},"milestone":null,"comments":9,"created_at":"2016-03-07T22:15:43Z","updated_at":"2016-03-10T03:33:43Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/samtools/htsjdk/pulls/515","html_url":"https://github.com/samtools/htsjdk/pull/515","diff_url":"https://github.com/samtools/htsjdk/pull/515.diff","patch_url":"https://github.com/samtools/htsjdk/pull/515.patch"},"body":"### Description\r\nigzip provides fast BAM compression at level 1. This PR attempts to integrate igzip fast BAM compression as part of IntelDeflater to enable low latency BAM compression in htsjdk. PR can be summarized as follows:\r\n\r\n1)\tModified IntelDeflater.c to add support for igzip API\r\n2)     Added headers required by.igzip under src/c/inteldeflater\r\n2)\tUpdated src/c/scripts/build_intel_deflater.sh to build libIntelDeflater.so with igzip.\r\n\r\n\r\n\r\n\r\n\r\n### Checklist\r\n\r\n- Code compiles correctly\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/samtools/htsjdk/issues/comments/194644174","html_url":"https://github.com/samtools/htsjdk/pull/515#issuecomment-194644174","issue_url":"https://api.github.com/repos/samtools/htsjdk/issues/515","id":194644174,"user":{"login":"akiezun","id":1993519,"avatar_url":"https://avatars.githubusercontent.com/u/1993519?v=3","gravatar_id":"","url":"https://api.github.com/users/akiezun","html_url":"https://github.com/akiezun","followers_url":"https://api.github.com/users/akiezun/followers","following_url":"https://api.github.com/users/akiezun/following{/other_user}","gists_url":"https://api.github.com/users/akiezun/gists{/gist_id}","starred_url":"https://api.github.com/users/akiezun/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/akiezun/subscriptions","organizations_url":"https://api.github.com/users/akiezun/orgs","repos_url":"https://api.github.com/users/akiezun/repos","events_url":"https://api.github.com/users/akiezun/events{/privacy}","received_events_url":"https://api.github.com/users/akiezun/received_events","type":"User","site_admin":false},"created_at":"2016-03-10T03:33:43Z","updated_at":"2016-03-10T03:33:43Z","body":"I can confirm that this change speeds up compression at level 1 (but not at level 5)\r\n\r\nI'm running this on a file ~800MB \r\n\r\n(compression level 5):\r\n```\r\nnew IntelDeflater   73, 66, 64, 61, 65 seconds. Median 65\r\nold IntelDeflater   62, 62, 70, 64, 62 seconds. Median 62 \r\nJdkDeflater         79, 79, 81, 80, 80 seconds. Median 80\r\n```\r\n\r\n(compression level 1)\r\n```\r\nnew IntelDeflater   43, 35, 31, 37, 44 seconds Median 37 \r\nold IntelDeflater   54, 50, 49, 42, 48 seconds Median 49\r\nJdkDeflater         49, 49, 51, 51, 58 seconds Median 51  \r\n```\r\n\r\nThese numbers are certainly impressive. \r\n"}}