{"action":"opened","issue":{"url":"https://api.github.com/repos/iqbal-lab/gramtools/issues/24","repository_url":"https://api.github.com/repos/iqbal-lab/gramtools","labels_url":"https://api.github.com/repos/iqbal-lab/gramtools/issues/24/labels{/name}","comments_url":"https://api.github.com/repos/iqbal-lab/gramtools/issues/24/comments","events_url":"https://api.github.com/repos/iqbal-lab/gramtools/issues/24/events","html_url":"https://github.com/iqbal-lab/gramtools/issues/24","id":167982611,"number":24,"title":"False interval added in precalc","user":{"login":"iqbal-lab","id":6476513,"avatar_url":"https://avatars.githubusercontent.com/u/6476513?v=3","gravatar_id":"","url":"https://api.github.com/users/iqbal-lab","html_url":"https://github.com/iqbal-lab","followers_url":"https://api.github.com/users/iqbal-lab/followers","following_url":"https://api.github.com/users/iqbal-lab/following{/other_user}","gists_url":"https://api.github.com/users/iqbal-lab/gists{/gist_id}","starred_url":"https://api.github.com/users/iqbal-lab/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/iqbal-lab/subscriptions","organizations_url":"https://api.github.com/users/iqbal-lab/orgs","repos_url":"https://api.github.com/users/iqbal-lab/repos","events_url":"https://api.github.com/users/iqbal-lab/events{/privacy}","received_events_url":"https://api.github.com/users/iqbal-lab/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2016-07-27T23:47:55Z","updated_at":"2016-07-27T23:47:55Z","closed_at":null,"body":"PRG\r\nATCGCT5CCGCCGGCGA6G5TTTTT\r\n\r\n perl ~/dev/git/pg/ben_langmead_materials/integer_bwt.pl ATCGCT5CCGCCGGCGA6G5TTTTT\r\nbwm of 1423245223223323163544444$ is\r\n$1423245223223323163544444\r\n1423245223223323163544444$\r\n163544444$1423245223223323\r\n223223323163544444$1423245\r\n223323163544444$1423245223\r\n23163544444$14232452232233\r\n23223323163544444$14232452\r\n23245223223323163544444$14\r\n23323163544444$14232452232\r\n245223223323163544444$1423\r\n3163544444$142324522322332\r\n3223323163544444$142324522\r\n323163544444$1423245223223\r\n3245223223323163544444$142\r\n3323163544444$142324522322\r\n3544444$142324522322332316\r\n4$142324522322332316354444\r\n423245223223323163544444$1\r\n44$14232452232233231635444\r\n444$1423245223223323163544   index 19\r\n4444$142324522322332316354\r\n44444$14232452232233231635\r\n45223223323163544444$14232    index 22\r\n5223223323163544444$142324   index 23\r\n544444$1423245223223323163\r\n63544444$14232452232233231\r\n\r\nThis is what the kmer precalc file looks like for TTT\r\n\r\n4 4 4 |1|19 22 22 23 |18 24 25 27 ||5 @|   <<<<< look at this, says intervals [19,22) and [22,23) \r\n\r\n[19,22) is correct.\r\n[22,23) is wrong, corresponds to a TTT crossing and ignoring both alleles\r\nATCGC**T**5CCGCCGGCGA6G5**TT**TTT\r\n\r\nSorina knows about this, just logging this here so we don't forget.\r\n\r\n"}}
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