{"action":"created","issue":{"url":"https://api.github.com/repos/BioJulia/Bio.jl/issues/303","repository_url":"https://api.github.com/repos/BioJulia/Bio.jl","labels_url":"https://api.github.com/repos/BioJulia/Bio.jl/issues/303/labels{/name}","comments_url":"https://api.github.com/repos/BioJulia/Bio.jl/issues/303/comments","events_url":"https://api.github.com/repos/BioJulia/Bio.jl/issues/303/events","html_url":"https://github.com/BioJulia/Bio.jl/pull/303","id":174707613,"number":303,"title":"Rewrite the FASTQ reader","user":{"login":"bicycle1885","id":905683,"avatar_url":"https://avatars.githubusercontent.com/u/905683?v=3","gravatar_id":"","url":"https://api.github.com/users/bicycle1885","html_url":"https://github.com/bicycle1885","followers_url":"https://api.github.com/users/bicycle1885/followers","following_url":"https://api.github.com/users/bicycle1885/following{/other_user}","gists_url":"https://api.github.com/users/bicycle1885/gists{/gist_id}","starred_url":"https://api.github.com/users/bicycle1885/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/bicycle1885/subscriptions","organizations_url":"https://api.github.com/users/bicycle1885/orgs","repos_url":"https://api.github.com/users/bicycle1885/repos","events_url":"https://api.github.com/users/bicycle1885/events{/privacy}","received_events_url":"https://api.github.com/users/bicycle1885/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/BioJulia/Bio.jl/labels/stage:%20review","name":"stage: review","color":"c2e0c6"}],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":9,"created_at":"2016-09-02T08:32:24Z","updated_at":"2016-09-02T09:32:59Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/BioJulia/Bio.jl/pulls/303","html_url":"https://github.com/BioJulia/Bio.jl/pull/303","diff_url":"https://github.com/BioJulia/Bio.jl/pull/303.diff","patch_url":"https://github.com/BioJulia/Bio.jl/pull/303.patch"},"body":"This giant rewrite will improve the FASTQ reader and clean up quality encoding code.\r\n\r\n* `QualityEnoding` is now a structure type, not bit flag.\r\n* `FASTQReader` and `FASTQWriter` takes an argument `quality_encoding` to determine the encoding.\r\n    * The default value of `quality_ecoding` is `:sanger`.\r\n    * Encoding inference is completely removed.\r\n    * `FASTQReader` checks whether all base qualities are within the range of `quality_encoding`.\r\n* `FASTQReader` supports `fill_ambiguous` argument to fill ambiguous nucleotides with a given nucleotide (say `DNAA`), which will meet @timbitz's request.\r\n* Update docs."},"comment":{"url":"https://api.github.com/repos/BioJulia/Bio.jl/issues/comments/244328982","html_url":"https://github.com/BioJulia/Bio.jl/pull/303#issuecomment-244328982","issue_url":"https://api.github.com/repos/BioJulia/Bio.jl/issues/303","id":244328982,"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":"2016-09-02T09:32:59Z","updated_at":"2016-09-02T09:32:59Z","body":"\n[![Coverage Status](https://coveralls.io/builds/7720671/badge)](https://coveralls.io/builds/7720671)\n\nCoverage increased (+0.3%) to 71.165% when pulling **2b8af6fe6828f1ba3fa36daaedac89d540ac7863 on bicycle1885:fix-fastq** into **0d1e0d784f3e593aae3c96e87ec347b3ab8e05eb on BioJulia:master**.\n"}}
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