{"action":"created","issue":{"url":"https://api.github.com/repos/jts/nanopolish/issues/355","repository_url":"https://api.github.com/repos/jts/nanopolish","labels_url":"https://api.github.com/repos/jts/nanopolish/issues/355/labels{/name}","comments_url":"https://api.github.com/repos/jts/nanopolish/issues/355/comments","events_url":"https://api.github.com/repos/jts/nanopolish/issues/355/events","html_url":"https://github.com/jts/nanopolish/issues/355","id":304839340,"number":355,"title":"phase-reads - explanation?","user":{"login":"colindaven","id":6094884,"avatar_url":"https://avatars3.githubusercontent.com/u/6094884?v=4","gravatar_id":"","url":"https://api.github.com/users/colindaven","html_url":"https://github.com/colindaven","followers_url":"https://api.github.com/users/colindaven/followers","following_url":"https://api.github.com/users/colindaven/following{/other_user}","gists_url":"https://api.github.com/users/colindaven/gists{/gist_id}","starred_url":"https://api.github.com/users/colindaven/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/colindaven/subscriptions","organizations_url":"https://api.github.com/users/colindaven/orgs","repos_url":"https://api.github.com/users/colindaven/repos","events_url":"https://api.github.com/users/colindaven/events{/privacy}","received_events_url":"https://api.github.com/users/colindaven/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":1,"created_at":"2018-03-13T16:28:39Z","updated_at":"2018-03-13T16:41:40Z","closed_at":null,"author_association":"CONTRIBUTOR","body":"Hi Jared,\r\n\r\nI have successfully used `phase-reads` with nanopolish 0.9.0 - the new index seems to work well, thanks.\r\n\r\nI haven't so far found documentation of the phase. I can find the following in the output file:\r\n```\r\n??`?   -  does this mean unphased?\r\n???P?  - phased VCF SNP?\r\n??W?  - unknown\r\n\r\n```\r\n\r\nSometimes P occurs before ` and sometimes its the other way around.\r\n\r\nI've looked in the code but didn't get far. Are there docs for this -apologies if I've missed them ?\r\n\r\nIt might be also useful to point out you need to run `nanopolish variants` to call SNVs which are then input into the phase-reads pipeline.  Perhaps I can mock up a bit of initial documentation when I get through this ?\r\n\r\ncheers,\r\nColin"},"comment":{"url":"https://api.github.com/repos/jts/nanopolish/issues/comments/372733312","html_url":"https://github.com/jts/nanopolish/issues/355#issuecomment-372733312","issue_url":"https://api.github.com/repos/jts/nanopolish/issues/355","id":372733312,"user":{"login":"colindaven","id":6094884,"avatar_url":"https://avatars3.githubusercontent.com/u/6094884?v=4","gravatar_id":"","url":"https://api.github.com/users/colindaven","html_url":"https://github.com/colindaven","followers_url":"https://api.github.com/users/colindaven/followers","following_url":"https://api.github.com/users/colindaven/following{/other_user}","gists_url":"https://api.github.com/users/colindaven/gists{/gist_id}","starred_url":"https://api.github.com/users/colindaven/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/colindaven/subscriptions","organizations_url":"https://api.github.com/users/colindaven/orgs","repos_url":"https://api.github.com/users/colindaven/repos","events_url":"https://api.github.com/users/colindaven/events{/privacy}","received_events_url":"https://api.github.com/users/colindaven/received_events","type":"User","site_admin":false},"created_at":"2018-03-13T16:41:40Z","updated_at":"2018-03-13T16:41:40Z","author_association":"CONTRIBUTOR","body":"```\r\nfd16f0cc-eb81-4087-bce4-c94652489d98    0       chr18   21118411        60      1301M   *       0       0       TTCCCATGCAACTGTCTTAGCCCAGTCCTCTCCTAGTTTTCTACTGCAAATTAAAGTTGCAGTGGATGCTTATCTGCAATGGCAGCAGCACTTACCCTTTGCCACACTTGGGGTTAGGGTTATCCGAAAGGAACATGGGCAGGAATCTCATGAAGTCTCCCCCCTGAGGCCTCTGTTTGCCTTCCGGAGTCAGAGGCCTGCAGCGAACGCAGGCAGGGTCAACCACTGGCGGAGACATGCAGGGAGGACTGTTAGAAGAATAGGTCTCCAGATTTTTTGTAAAACATTTTAAAATACTGACAGTGAGGGGCATTACTTTCTTCTCTATCGATTACTTTCCTTACTAGTGAGGGATAATCTTTCCCCTTATCTAAAAGCTTCAGCCACATGTCACTTTCACAGTTTAATGAATCTGAAATACCATTTTCATCTTAGGCATACTATGCATCATTTTCTGCCCTGAAGTAGATCTCCTCCTTCAAGTATGGCCTTGACTGGTCAGAGCCCGGGGCTTCTATGTTTTTATTAAGAAAATTCCAGGGCAACCTCGACGCTCCTACAAAACCACAGGGTAAAGTGATAAAGAAAAGCCCTCCTCTGAGAAGCTAAGGCCAGATACCAATCCTGAGAGGCAATCGCTGGAGTTAGAACAGGATGAGAAACCTTATGTGGAAACCACACTCCGAACATGTGGACCTTGTTCAGCTTGCAGCCCCGAGGGTGGCTGTCTGAGCCAGGAACAACATGACAATTTCAGAATGAATGACTGAGGAAAGGAATGATGACACAGGGAGACCCAGCTTTGATATACAAATAGGTATAAACTGAGGCACGATGCAAATGATTTTTAAATGATAATTTGAAAATTTTTCAGCAAAACAGGAAAGATTTGGTAAAGGAGAAGGTACCTGAAGCATTGCAGAACTGGTCAGTGATATTGTCCACTCGACAGCAAGACGACTGTGGCTTCACCCAGTCGAAATAATCGTCGATCCAGGACGAGGGGGCGAAGCCTATTCGGGTACTAGAGAGGACAGACAGGGTTACTGACCTGCTCCACAGGGAGGAAGTCTTTAGTTTCAGTACTTTTTCTTAAAACCTAACTTCCTTTTCTACGTTTTATACTGCTAACAGTCAAAAGAAAAACTACATGAGCACTTAATGAAAAAAGCCTTCAAAGTATTAGGTGGTAAATTAGTCCTTTCAAAGGTTTTTTAAGGTAAAGCCAGATTTAACATACATTTTGCATAAAAACAACTTTTCCAAGAAAGTCTATTTTCAGTGAGACATTTCAGGCCTGA   ???????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????P?????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????\r\n```"}}
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