{"action":"created","issue":{"url":"https://api.github.com/repos/BioJulia/Bio.jl/issues/334","repository_url":"https://api.github.com/repos/BioJulia/Bio.jl","labels_url":"https://api.github.com/repos/BioJulia/Bio.jl/issues/334/labels{/name}","comments_url":"https://api.github.com/repos/BioJulia/Bio.jl/issues/334/comments","events_url":"https://api.github.com/repos/BioJulia/Bio.jl/issues/334/events","html_url":"https://github.com/BioJulia/Bio.jl/pull/334","id":176042111,"number":334,"title":"Performant mutation counting.","user":{"login":"Ward9250","id":3399309,"avatar_url":"https://avatars.githubusercontent.com/u/3399309?v=3","gravatar_id":"","url":"https://api.github.com/users/Ward9250","html_url":"https://github.com/Ward9250","followers_url":"https://api.github.com/users/Ward9250/followers","following_url":"https://api.github.com/users/Ward9250/following{/other_user}","gists_url":"https://api.github.com/users/Ward9250/gists{/gist_id}","starred_url":"https://api.github.com/users/Ward9250/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/Ward9250/subscriptions","organizations_url":"https://api.github.com/users/Ward9250/orgs","repos_url":"https://api.github.com/users/Ward9250/repos","events_url":"https://api.github.com/users/Ward9250/events{/privacy}","received_events_url":"https://api.github.com/users/Ward9250/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/BioJulia/Bio.jl/labels/enhancement","name":"enhancement","color":"84b6eb"},{"url":"https://api.github.com/repos/BioJulia/Bio.jl/labels/performance","name":"performance","color":"0e8a16"},{"url":"https://api.github.com/repos/BioJulia/Bio.jl/labels/priority:%20soon","name":"priority: soon","color":"fef2c0"},{"url":"https://api.github.com/repos/BioJulia/Bio.jl/labels/stage:%20WIP","name":"stage: WIP","color":"d4c5f9"}],"state":"open","locked":false,"assignee":{"login":"Ward9250","id":3399309,"avatar_url":"https://avatars.githubusercontent.com/u/3399309?v=3","gravatar_id":"","url":"https://api.github.com/users/Ward9250","html_url":"https://github.com/Ward9250","followers_url":"https://api.github.com/users/Ward9250/followers","following_url":"https://api.github.com/users/Ward9250/following{/other_user}","gists_url":"https://api.github.com/users/Ward9250/gists{/gist_id}","starred_url":"https://api.github.com/users/Ward9250/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/Ward9250/subscriptions","organizations_url":"https://api.github.com/users/Ward9250/orgs","repos_url":"https://api.github.com/users/Ward9250/repos","events_url":"https://api.github.com/users/Ward9250/events{/privacy}","received_events_url":"https://api.github.com/users/Ward9250/received_events","type":"User","site_admin":false},"assignees":[{"login":"Ward9250","id":3399309,"avatar_url":"https://avatars.githubusercontent.com/u/3399309?v=3","gravatar_id":"","url":"https://api.github.com/users/Ward9250","html_url":"https://github.com/Ward9250","followers_url":"https://api.github.com/users/Ward9250/followers","following_url":"https://api.github.com/users/Ward9250/following{/other_user}","gists_url":"https://api.github.com/users/Ward9250/gists{/gist_id}","starred_url":"https://api.github.com/users/Ward9250/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/Ward9250/subscriptions","organizations_url":"https://api.github.com/users/Ward9250/orgs","repos_url":"https://api.github.com/users/Ward9250/repos","events_url":"https://api.github.com/users/Ward9250/events{/privacy}","received_events_url":"https://api.github.com/users/Ward9250/received_events","type":"User","site_admin":false}],"milestone":null,"comments":12,"created_at":"2016-09-09T15:46:39Z","updated_at":"2016-10-19T03:09:41Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/BioJulia/Bio.jl/pulls/334","html_url":"https://github.com/BioJulia/Bio.jl/pull/334","diff_url":"https://github.com/BioJulia/Bio.jl/pull/334.diff","patch_url":"https://github.com/BioJulia/Bio.jl/pull/334.patch"},"body":"A PR to improve the current mutation counting functionality of `Bio.Var`.\r\n\r\nCurrently such methods require transformation of BioSequences into Nucleotide matrices and looping over the matrices and comparing nucleotides. This is analogous to the strategy used in the 8-bit encoding based C code used by the APE package for R. We can do better than this.\r\n\r\nThis PR will implement bit parallel mutation counting methods that will work on the 2 bit and 4 bit encoded nucleotide sequences in `Bio.Seq`. This will give great speed up as with DNAAlphabet{4}, 16 nucleotides can be considered at once, plus whatever speed up simd will give us looping over each 64bit integer of a biosequence data field. With 2 bit encoded sequences, presumably the speed up will be faster, since A). More nucleotides are considered at once, and B). Masking and checks for ambiguous or gap sites are not nessecery."},"comment":{"url":"https://api.github.com/repos/BioJulia/Bio.jl/issues/comments/254698904","html_url":"https://github.com/BioJulia/Bio.jl/pull/334#issuecomment-254698904","issue_url":"https://api.github.com/repos/BioJulia/Bio.jl/issues/334","id":254698904,"user":{"login":"coveralls","id":2354108,"avatar_url":"https://avatars.githubusercontent.com/u/2354108?v=3","gravatar_id":"","url":"https://api.github.com/users/coveralls","html_url":"https://github.com/coveralls","followers_url":"https://api.github.com/users/coveralls/followers","following_url":"https://api.github.com/users/coveralls/following{/other_user}","gists_url":"https://api.github.com/users/coveralls/gists{/gist_id}","starred_url":"https://api.github.com/users/coveralls/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/coveralls/subscriptions","organizations_url":"https://api.github.com/users/coveralls/orgs","repos_url":"https://api.github.com/users/coveralls/repos","events_url":"https://api.github.com/users/coveralls/events{/privacy}","received_events_url":"https://api.github.com/users/coveralls/received_events","type":"User","site_admin":false},"created_at":"2016-10-19T03:09:41Z","updated_at":"2016-10-19T03:09:41Z","body":"\n[![Coverage Status](https://coveralls.io/builds/8402909/badge)](https://coveralls.io/builds/8402909)\n\nCoverage increased (+11.0%) to 83.881% when pulling **8a973b9e2f5b49affe82a1aa26119e4ff9cf9ea4 on mcount_performance** into **fde871237fcd57bc9f5054bb8c96ba2897ccf956 on master**.\n"}}
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