{"action":"created","issue":{"url":"https://api.github.com/repos/DerrickWood/kraken/issues/85","repository_url":"https://api.github.com/repos/DerrickWood/kraken","labels_url":"https://api.github.com/repos/DerrickWood/kraken/issues/85/labels{/name}","comments_url":"https://api.github.com/repos/DerrickWood/kraken/issues/85/comments","events_url":"https://api.github.com/repos/DerrickWood/kraken/issues/85/events","html_url":"https://github.com/DerrickWood/kraken/pull/85","id":256475759,"number":85,"title":"Easy un-pair","user":{"login":"dfornika","id":145659,"avatar_url":"https://avatars1.githubusercontent.com/u/145659?v=4","gravatar_id":"","url":"https://api.github.com/users/dfornika","html_url":"https://github.com/dfornika","followers_url":"https://api.github.com/users/dfornika/followers","following_url":"https://api.github.com/users/dfornika/following{/other_user}","gists_url":"https://api.github.com/users/dfornika/gists{/gist_id}","starred_url":"https://api.github.com/users/dfornika/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/dfornika/subscriptions","organizations_url":"https://api.github.com/users/dfornika/orgs","repos_url":"https://api.github.com/users/dfornika/repos","events_url":"https://api.github.com/users/dfornika/events{/privacy}","received_events_url":"https://api.github.com/users/dfornika/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":{"login":"jenniferlu717","id":3779419,"avatar_url":"https://avatars2.githubusercontent.com/u/3779419?v=4","gravatar_id":"","url":"https://api.github.com/users/jenniferlu717","html_url":"https://github.com/jenniferlu717","followers_url":"https://api.github.com/users/jenniferlu717/followers","following_url":"https://api.github.com/users/jenniferlu717/following{/other_user}","gists_url":"https://api.github.com/users/jenniferlu717/gists{/gist_id}","starred_url":"https://api.github.com/users/jenniferlu717/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jenniferlu717/subscriptions","organizations_url":"https://api.github.com/users/jenniferlu717/orgs","repos_url":"https://api.github.com/users/jenniferlu717/repos","events_url":"https://api.github.com/users/jenniferlu717/events{/privacy}","received_events_url":"https://api.github.com/users/jenniferlu717/received_events","type":"User","site_admin":false},"assignees":[{"login":"jenniferlu717","id":3779419,"avatar_url":"https://avatars2.githubusercontent.com/u/3779419?v=4","gravatar_id":"","url":"https://api.github.com/users/jenniferlu717","html_url":"https://github.com/jenniferlu717","followers_url":"https://api.github.com/users/jenniferlu717/followers","following_url":"https://api.github.com/users/jenniferlu717/following{/other_user}","gists_url":"https://api.github.com/users/jenniferlu717/gists{/gist_id}","starred_url":"https://api.github.com/users/jenniferlu717/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jenniferlu717/subscriptions","organizations_url":"https://api.github.com/users/jenniferlu717/orgs","repos_url":"https://api.github.com/users/jenniferlu717/repos","events_url":"https://api.github.com/users/jenniferlu717/events{/privacy}","received_events_url":"https://api.github.com/users/jenniferlu717/received_events","type":"User","site_admin":false},{"login":"DerrickWood","id":5395172,"avatar_url":"https://avatars1.githubusercontent.com/u/5395172?v=4","gravatar_id":"","url":"https://api.github.com/users/DerrickWood","html_url":"https://github.com/DerrickWood","followers_url":"https://api.github.com/users/DerrickWood/followers","following_url":"https://api.github.com/users/DerrickWood/following{/other_user}","gists_url":"https://api.github.com/users/DerrickWood/gists{/gist_id}","starred_url":"https://api.github.com/users/DerrickWood/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/DerrickWood/subscriptions","organizations_url":"https://api.github.com/users/DerrickWood/orgs","repos_url":"https://api.github.com/users/DerrickWood/repos","events_url":"https://api.github.com/users/DerrickWood/events{/privacy}","received_events_url":"https://api.github.com/users/DerrickWood/received_events","type":"User","site_admin":false}],"milestone":null,"comments":3,"created_at":"2017-09-10T00:35:51Z","updated_at":"2017-10-30T18:07:08Z","closed_at":"2017-10-30T17:12:13Z","author_association":"CONTRIBUTOR","pull_request":{"url":"https://api.github.com/repos/DerrickWood/kraken/pulls/85","html_url":"https://github.com/DerrickWood/kraken/pull/85","diff_url":"https://github.com/DerrickWood/kraken/pull/85.diff","patch_url":"https://github.com/DerrickWood/kraken/pull/85.patch"},"body":"Addresses #84.\r\n\r\nI preserved default behavior, so `--out-fmt legacy` is the default. It still outputs `N` as the sequence delimiter.\r\n\r\nWhen `--out-fmt paired` is used, then `--classified-out` and `--unclassified-out` are interpreted as prefixes. \r\n\r\nDefault output is fasta, but I've also added a `--fastq-output` flag that will give fastq output. Fastq headers can have one whitespace character, but anything after a second whitespace character would be dropped. `--out-fmt legacy` is incompatible with `--fastq-output`. \r\n\r\nWhen `--out-fmt paired` is used with `--fastq-output` then the output prefixes are appended with `_R1.fastq` and `_R2.fastq`. Otherwise they're appended with `_R1.fa` and `_R2.fa`.\r\n\r\n`--out-fmt interleaved` gives an interleaved file.\r\n\r\nI use `|` as a delimiter internally, but they aren't printed in the output in any setting. \r\n\r\nI've done my best to test out all combinations but I'd suggest testing more before merging into `master`.\r\n\r\nForgive my clumsy C++.\r\n"},"comment":{"url":"https://api.github.com/repos/DerrickWood/kraken/issues/comments/340533878","html_url":"https://github.com/DerrickWood/kraken/pull/85#issuecomment-340533878","issue_url":"https://api.github.com/repos/DerrickWood/kraken/issues/85","id":340533878,"user":{"login":"jenniferlu717","id":3779419,"avatar_url":"https://avatars2.githubusercontent.com/u/3779419?v=4","gravatar_id":"","url":"https://api.github.com/users/jenniferlu717","html_url":"https://github.com/jenniferlu717","followers_url":"https://api.github.com/users/jenniferlu717/followers","following_url":"https://api.github.com/users/jenniferlu717/following{/other_user}","gists_url":"https://api.github.com/users/jenniferlu717/gists{/gist_id}","starred_url":"https://api.github.com/users/jenniferlu717/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jenniferlu717/subscriptions","organizations_url":"https://api.github.com/users/jenniferlu717/orgs","repos_url":"https://api.github.com/users/jenniferlu717/repos","events_url":"https://api.github.com/users/jenniferlu717/events{/privacy}","received_events_url":"https://api.github.com/users/jenniferlu717/received_events","type":"User","site_admin":false},"created_at":"2017-10-30T18:07:08Z","updated_at":"2017-10-30T18:07:08Z","author_association":"COLLABORATOR","body":"Merged the code changes in. This will be version v1.1 probably. I'm updating the manuals before updating the changelog etc. "}}
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