{"action":"created","issue":{"url":"https://api.github.com/repos/ged-lab/khmer/issues/763","labels_url":"https://api.github.com/repos/ged-lab/khmer/issues/763/labels{/name}","comments_url":"https://api.github.com/repos/ged-lab/khmer/issues/763/comments","events_url":"https://api.github.com/repos/ged-lab/khmer/issues/763/events","html_url":"https://github.com/ged-lab/khmer/issues/763","id":57071739,"number":763,"title":"Minor fixes to split-paired-reads.py","user":{"login":"ctb","id":51016,"avatar_url":"https://avatars.githubusercontent.com/u/51016?v=3","gravatar_id":"","url":"https://api.github.com/users/ctb","html_url":"https://github.com/ctb","followers_url":"https://api.github.com/users/ctb/followers","following_url":"https://api.github.com/users/ctb/following{/other_user}","gists_url":"https://api.github.com/users/ctb/gists{/gist_id}","starred_url":"https://api.github.com/users/ctb/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ctb/subscriptions","organizations_url":"https://api.github.com/users/ctb/orgs","repos_url":"https://api.github.com/users/ctb/repos","events_url":"https://api.github.com/users/ctb/events{/privacy}","received_events_url":"https://api.github.com/users/ctb/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/ged-lab/khmer/labels/low-hanging-fruit","name":"low-hanging-fruit","color":"eb6420"}],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":2,"created_at":"2015-02-09T18:43:31Z","updated_at":"2015-02-23T23:58:56Z","closed_at":null,"body":"Once #762 is merged, there are still a few updates to split-paired-reads that could usefully be done.\r\n\r\nFirst, to support https://github.com/ged-lab/khmer/issues/732#issuecomment-71903726 we need to default to stdin.  That can be done by adding ``nargs='?', default='/dev/stdin'`` to line 60, although we also need to require -1 and -2 options in that case.\r\n\r\nSecond, we should switch to using the broken_paired_reader in khmer.utils that #759 will introduce.\r\n\r\nThird, once we can read broken-paired reads, we should allow users to override the requirement that reads be perfectly interleaved. (By default, we should require perfect interleaving, though, because it's the main use case.)"},"comment":{"url":"https://api.github.com/repos/ged-lab/khmer/issues/comments/75666571","html_url":"https://github.com/ged-lab/khmer/issues/763#issuecomment-75666571","issue_url":"https://api.github.com/repos/ged-lab/khmer/issues/763","id":75666571,"user":{"login":"ctb","id":51016,"avatar_url":"https://avatars.githubusercontent.com/u/51016?v=3","gravatar_id":"","url":"https://api.github.com/users/ctb","html_url":"https://github.com/ctb","followers_url":"https://api.github.com/users/ctb/followers","following_url":"https://api.github.com/users/ctb/following{/other_user}","gists_url":"https://api.github.com/users/ctb/gists{/gist_id}","starred_url":"https://api.github.com/users/ctb/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ctb/subscriptions","organizations_url":"https://api.github.com/users/ctb/orgs","repos_url":"https://api.github.com/users/ctb/repos","events_url":"https://api.github.com/users/ctb/events{/privacy}","received_events_url":"https://api.github.com/users/ctb/received_events","type":"User","site_admin":false},"created_at":"2015-02-23T23:58:56Z","updated_at":"2015-02-23T23:58:56Z","body":"Switched to broken_paired_reader & addressed third point in #818.  First point (supporting streaming) still needs to be done."}}