{"action":"created","issue":{"url":"https://api.github.com/repos/BioJulia/Bio.jl/issues/436","repository_url":"https://api.github.com/repos/BioJulia/Bio.jl","labels_url":"https://api.github.com/repos/BioJulia/Bio.jl/issues/436/labels{/name}","comments_url":"https://api.github.com/repos/BioJulia/Bio.jl/issues/436/comments","events_url":"https://api.github.com/repos/BioJulia/Bio.jl/issues/436/events","html_url":"https://github.com/BioJulia/Bio.jl/pull/436","id":217936811,"number":436,"title":"Site counting framework completion","user":{"login":"Ward9250","id":3399309,"avatar_url":"https://avatars2.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":[{"id":245663806,"url":"https://api.github.com/repos/BioJulia/Bio.jl/labels/stage:%20WIP","name":"stage: WIP","color":"d4c5f9","default":false}],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":1,"created_at":"2017-03-29T16:40:30Z","updated_at":"2017-04-18T14:05:42Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/BioJulia/Bio.jl/pulls/436","html_url":"https://github.com/BioJulia/Bio.jl/pull/436","diff_url":"https://github.com/BioJulia/Bio.jl/pull/436.diff","patch_url":"https://github.com/BioJulia/Bio.jl/pull/436.patch"},"body":"This completes a site counting framework for Seq which has both naive methods and faster bit-flipping data-parallel methods. And is extended by Var for sites that constitute mutations.\r\n\r\nThis will clean up and finish work done in #334 and previous PR's that deal with counting sequence sites.\r\n\r\nThis should be finished and merged before Bio.jl decomposition occurs - or at least before Seq and Var are decomposed."},"comment":{"url":"https://api.github.com/repos/BioJulia/Bio.jl/issues/comments/294855227","html_url":"https://github.com/BioJulia/Bio.jl/pull/436#issuecomment-294855227","issue_url":"https://api.github.com/repos/BioJulia/Bio.jl/issues/436","id":294855227,"user":{"login":"codecov-io","id":8655789,"avatar_url":"https://avatars3.githubusercontent.com/u/8655789?v=3","gravatar_id":"","url":"https://api.github.com/users/codecov-io","html_url":"https://github.com/codecov-io","followers_url":"https://api.github.com/users/codecov-io/followers","following_url":"https://api.github.com/users/codecov-io/following{/other_user}","gists_url":"https://api.github.com/users/codecov-io/gists{/gist_id}","starred_url":"https://api.github.com/users/codecov-io/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/codecov-io/subscriptions","organizations_url":"https://api.github.com/users/codecov-io/orgs","repos_url":"https://api.github.com/users/codecov-io/repos","events_url":"https://api.github.com/users/codecov-io/events{/privacy}","received_events_url":"https://api.github.com/users/codecov-io/received_events","type":"User","site_admin":false},"created_at":"2017-04-18T14:05:42Z","updated_at":"2017-04-18T14:05:42Z","body":"# [Codecov](https://codecov.io/gh/BioJulia/Bio.jl/pull/436?src=pr&el=h1) Report\n> Merging [#436](https://codecov.io/gh/BioJulia/Bio.jl/pull/436?src=pr&el=desc) into [master](https://codecov.io/gh/BioJulia/Bio.jl/commit/48f297c507ceb787a7720f6ce918e1599ee401fa?src=pr&el=desc) will **increase** coverage by `0.39%`.\n> The diff coverage is `45.11%`.\n\n[![Impacted file tree graph](https://codecov.io/gh/BioJulia/Bio.jl/pull/436/graphs/tree.svg?token=sjVCESM655&src=pr&height=150&width=650)](https://codecov.io/gh/BioJulia/Bio.jl/pull/436?src=pr&el=tree)\n\n```diff\n@@            Coverage Diff             @@\n##           master     #436      +/-   ##\n==========================================\n+ Coverage   70.76%   71.15%   +0.39%     \n==========================================\n  Files         142      152      +10     \n  Lines       10440    10329     -111     \n==========================================\n- Hits         7388     7350      -38     \n+ Misses       3052     2979      -73\n```\n\n\n| [Impacted Files](https://codecov.io/gh/BioJulia/Bio.jl/pull/436?src=pr&el=tree) | Coverage Δ | |\n|---|---|---|\n| [src/seq/Seq.jl](https://codecov.io/gh/BioJulia/Bio.jl/pull/436?src=pr&el=tree#diff-c3JjL3NlcS9TZXEuamw=) | `0% <ø> (ø)` | :arrow_up: |\n| [src/var/distances/dist.jl](https://codecov.io/gh/BioJulia/Bio.jl/pull/436?src=pr&el=tree#diff-c3JjL3Zhci9kaXN0YW5jZXMvZGlzdC5qbA==) | `0% <0%> (ø)` | |\n| [src/var/site\\_counting/bitpar/count\\_nibbles.jl](https://codecov.io/gh/BioJulia/Bio.jl/pull/436?src=pr&el=tree#diff-c3JjL3Zhci9zaXRlX2NvdW50aW5nL2JpdHBhci9jb3VudF9uaWJibGVzLmps) | `0% <0%> (ø)` | |\n| [src/var/distances/distance\\_types.jl](https://codecov.io/gh/BioJulia/Bio.jl/pull/436?src=pr&el=tree#diff-c3JjL3Zhci9kaXN0YW5jZXMvZGlzdGFuY2VfdHlwZXMuamw=) | `0% <0%> (ø)` | |\n| [src/var/site\\_counting/site\\_types/conserved.jl](https://codecov.io/gh/BioJulia/Bio.jl/pull/436?src=pr&el=tree#diff-c3JjL3Zhci9zaXRlX2NvdW50aW5nL3NpdGVfdHlwZXMvY29uc2VydmVkLmps) | `100% <100%> (ø)` | |\n| [src/seq/bioseq/operators.jl](https://codecov.io/gh/BioJulia/Bio.jl/pull/436?src=pr&el=tree#diff-c3JjL3NlcS9iaW9zZXEvb3BlcmF0b3JzLmps) | `66.91% <100%> (-25%)` | :arrow_down: |\n| [src/seq/bioseq/site\\_counting/count\\_sites\\_naive.jl](https://codecov.io/gh/BioJulia/Bio.jl/pull/436?src=pr&el=tree#diff-c3JjL3NlcS9iaW9zZXEvc2l0ZV9jb3VudGluZy9jb3VudF9zaXRlc19uYWl2ZS5qbA==) | `100% <100%> (ø)` | |\n| [src/var/site\\_counting/site\\_types/mutated.jl](https://codecov.io/gh/BioJulia/Bio.jl/pull/436?src=pr&el=tree#diff-c3JjL3Zhci9zaXRlX2NvdW50aW5nL3NpdGVfdHlwZXMvbXV0YXRlZC5qbA==) | `100% <100%> (ø)` | |\n| [src/var/site\\_counting/site\\_types/transition.jl](https://codecov.io/gh/BioJulia/Bio.jl/pull/436?src=pr&el=tree#diff-c3JjL3Zhci9zaXRlX2NvdW50aW5nL3NpdGVfdHlwZXMvdHJhbnNpdGlvbi5qbA==) | `100% <100%> (ø)` | |\n| [src/var/site\\_counting/site\\_types/transversion.jl](https://codecov.io/gh/BioJulia/Bio.jl/pull/436?src=pr&el=tree#diff-c3JjL3Zhci9zaXRlX2NvdW50aW5nL3NpdGVfdHlwZXMvdHJhbnN2ZXJzaW9uLmps) | `100% <100%> (ø)` | |\n| ... and [45 more](https://codecov.io/gh/BioJulia/Bio.jl/pull/436?src=pr&el=tree-more) | |\n\n------\n\n[Continue to review full report at Codecov](https://codecov.io/gh/BioJulia/Bio.jl/pull/436?src=pr&el=continue).\n> **Legend** - [Click here to learn more](https://docs.codecov.io/docs/codecov-delta)\n> `Δ = absolute <relative> (impact)`, `ø = not affected`, `? = missing data`\n> Powered by [Codecov](https://codecov.io/gh/BioJulia/Bio.jl/pull/436?src=pr&el=footer). Last update [48f297c...ba007b6](https://codecov.io/gh/BioJulia/Bio.jl/pull/436?src=pr&el=lastupdated). Read the [comment docs](https://docs.codecov.io/docs/pull-request-comments).\n"}}
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