{"action":"created","issue":{"url":"https://api.github.com/repos/oneillkza/ContiBAIT/issues/17","labels_url":"https://api.github.com/repos/oneillkza/ContiBAIT/issues/17/labels{/name}","comments_url":"https://api.github.com/repos/oneillkza/ContiBAIT/issues/17/comments","events_url":"https://api.github.com/repos/oneillkza/ContiBAIT/issues/17/events","html_url":"https://github.com/oneillkza/ContiBAIT/pull/17","id":125304444,"number":17,"title":"new pull request","user":{"login":"rareaquaticbadger","id":15741733,"avatar_url":"https://avatars.githubusercontent.com/u/15741733?v=3","gravatar_id":"","url":"https://api.github.com/users/rareaquaticbadger","html_url":"https://github.com/rareaquaticbadger","followers_url":"https://api.github.com/users/rareaquaticbadger/followers","following_url":"https://api.github.com/users/rareaquaticbadger/following{/other_user}","gists_url":"https://api.github.com/users/rareaquaticbadger/gists{/gist_id}","starred_url":"https://api.github.com/users/rareaquaticbadger/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/rareaquaticbadger/subscriptions","organizations_url":"https://api.github.com/users/rareaquaticbadger/orgs","repos_url":"https://api.github.com/users/rareaquaticbadger/repos","events_url":"https://api.github.com/users/rareaquaticbadger/events{/privacy}","received_events_url":"https://api.github.com/users/rareaquaticbadger/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":5,"created_at":"2016-01-07T01:49:49Z","updated_at":"2016-01-14T23:38:51Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/oneillkza/ContiBAIT/pulls/17","html_url":"https://github.com/oneillkza/ContiBAIT/pull/17","diff_url":"https://github.com/oneillkza/ContiBAIT/pull/17.diff","patch_url":"https://github.com/oneillkza/ContiBAIT/pull/17.patch"},"body":"Hi,\r\n\r\nI've merged the two reorientation functions now that clusterContigs defaults to taking homozygous vs heterozygous calls.\r\n\r\nNote that rerunning clusterContigs in the reorientation code to find misorientations was very slow and was generating multiple sub-linkage groups.  Instead I opted for a simple hclust with a cutree approach: the fragments have already been clustered (hopefully) correctly, so a less intensive clustering within the linkage groups seemed the best course. It also clustered better from what I could see of intermediate heatmaps that I made to validate.  reorientLinkageGroups now returns a list where the first element is an object of type StrandStateMatrix, and the second element is a data.frame of contigs and orientations."},"comment":{"url":"https://api.github.com/repos/oneillkza/ContiBAIT/issues/comments/171817947","html_url":"https://github.com/oneillkza/ContiBAIT/pull/17#issuecomment-171817947","issue_url":"https://api.github.com/repos/oneillkza/ContiBAIT/issues/17","id":171817947,"user":{"login":"oneillkza","id":3099991,"avatar_url":"https://avatars.githubusercontent.com/u/3099991?v=3","gravatar_id":"","url":"https://api.github.com/users/oneillkza","html_url":"https://github.com/oneillkza","followers_url":"https://api.github.com/users/oneillkza/followers","following_url":"https://api.github.com/users/oneillkza/following{/other_user}","gists_url":"https://api.github.com/users/oneillkza/gists{/gist_id}","starred_url":"https://api.github.com/users/oneillkza/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/oneillkza/subscriptions","organizations_url":"https://api.github.com/users/oneillkza/orgs","repos_url":"https://api.github.com/users/oneillkza/repos","events_url":"https://api.github.com/users/oneillkza/events{/privacy}","received_events_url":"https://api.github.com/users/oneillkza/received_events","type":"User","site_admin":false},"created_at":"2016-01-14T23:38:51Z","updated_at":"2016-01-14T23:38:51Z","body":"Oh, and re:generics, only methods need to have generics. Functions that we don't turn into methods do not need them. I think pretty much everything we export is a method (except for `strandSeqFreqTable` which loads directly from a file).\r\n\r\nHmm ... `preprocessStrandTable` should be a method, actually, since we pass it a `StrandFreqMatrix`."}}