{"action":"created","issue":{"url":"https://api.github.com/repos/infphilo/centrifuge/issues/97","repository_url":"https://api.github.com/repos/infphilo/centrifuge","labels_url":"https://api.github.com/repos/infphilo/centrifuge/issues/97/labels{/name}","comments_url":"https://api.github.com/repos/infphilo/centrifuge/issues/97/comments","events_url":"https://api.github.com/repos/infphilo/centrifuge/issues/97/events","html_url":"https://github.com/infphilo/centrifuge/issues/97","id":299786568,"number":97,"title":"Centrifuge misassigns some reads","user":{"login":"jsh58","id":4921955,"avatar_url":"https://avatars3.githubusercontent.com/u/4921955?v=4","gravatar_id":"","url":"https://api.github.com/users/jsh58","html_url":"https://github.com/jsh58","followers_url":"https://api.github.com/users/jsh58/followers","following_url":"https://api.github.com/users/jsh58/following{/other_user}","gists_url":"https://api.github.com/users/jsh58/gists{/gist_id}","starred_url":"https://api.github.com/users/jsh58/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jsh58/subscriptions","organizations_url":"https://api.github.com/users/jsh58/orgs","repos_url":"https://api.github.com/users/jsh58/repos","events_url":"https://api.github.com/users/jsh58/events{/privacy}","received_events_url":"https://api.github.com/users/jsh58/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":7,"created_at":"2018-02-23T17:19:06Z","updated_at":"2018-03-06T15:19:02Z","closed_at":null,"author_association":"NONE","body":"Centrifuge misassigns some reads that align near the beginning of one reference sequence.  The incorrect assignment is to the previous reference sequence in the database.\r\n\r\nI have observed this with the nt database, but I will illustrate here with a toy example:\r\n\r\n##### reference database:\r\n```\r\n>seq_A\r\nAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\r\n>seq_B\r\nGCGTAGCCAGTAGCAGGACTTTACCGTGCGGTACAAGCCTACAGACCGATTA\r\n```\r\n##### query sequences (each 25-mer of `seq_B`, from \"qseq0\" to \"qseq27\"):\r\n```\r\n@qseq0\r\nGCGTAGCCAGTAGCAGGACTTTACC\r\n+\r\nIIIIIIIIIIIIIIIIIIIIIIIII\r\n@qseq1\r\nCGTAGCCAGTAGCAGGACTTTACCG\r\n+\r\nIIIIIIIIIIIIIIIIIIIIIIIII\r\n[...]\r\n@qseq27\r\nGCGGTACAAGCCTACAGACCGATTA\r\n+\r\nIIIIIIIIIIIIIIIIIIIIIIIII\r\n```\r\n\r\n#### results:\r\nCentrifuge incorrectly assigns the first 15 reads to `seq_A`.  Here is the output:\r\n```\r\nreadID\tseqID\ttaxID\tscore\t2ndBestScore\thitLength\tqueryLength\tnumMatches\r\nqseq0\tseq_A\t0\t100\t0\t25\t25\t1\r\nqseq1\tseq_A\t0\t100\t0\t25\t25\t1\r\nqseq2\tseq_A\t0\t100\t0\t25\t25\t1\r\nqseq3\tseq_A\t0\t100\t0\t25\t25\t1\r\nqseq4\tseq_A\t0\t100\t0\t25\t25\t1\r\nqseq5\tseq_A\t0\t100\t0\t25\t25\t1\r\nqseq6\tseq_A\t0\t100\t0\t25\t25\t1\r\nqseq7\tseq_A\t0\t100\t0\t25\t25\t1\r\nqseq8\tseq_A\t0\t100\t0\t25\t25\t1\r\nqseq9\tseq_A\t0\t100\t0\t25\t25\t1\r\nqseq10\tseq_A\t0\t100\t0\t25\t25\t1\r\nqseq11\tseq_A\t0\t100\t0\t25\t25\t1\r\nqseq12\tseq_A\t0\t100\t0\t25\t25\t1\r\nqseq13\tseq_A\t0\t100\t0\t25\t25\t1\r\nqseq14\tseq_A\t0\t100\t0\t25\t25\t1\r\nqseq15\tseq_B\t0\t100\t0\t25\t25\t1\r\nqseq16\tseq_B\t0\t100\t0\t25\t25\t1\r\nqseq17\tseq_B\t0\t100\t0\t25\t25\t1\r\nqseq18\tseq_B\t0\t100\t0\t25\t25\t1\r\nqseq19\tseq_B\t0\t100\t0\t25\t25\t1\r\nqseq20\tseq_B\t0\t100\t0\t25\t25\t1\r\nqseq21\tseq_B\t0\t100\t0\t25\t25\t1\r\nqseq22\tseq_B\t0\t100\t0\t25\t25\t1\r\nqseq23\tseq_B\t0\t100\t0\t25\t25\t1\r\nqseq24\tseq_B\t0\t100\t0\t25\t25\t1\r\nqseq25\tseq_B\t0\t100\t0\t25\t25\t1\r\nqseq26\tseq_B\t0\t100\t0\t25\t25\t1\r\nqseq27\tseq_B\t0\t100\t0\t25\t25\t1\r\n```\r\nAll 28 reads should have been assigned to `seq_B`."},"comment":{"url":"https://api.github.com/repos/infphilo/centrifuge/issues/comments/370815441","html_url":"https://github.com/infphilo/centrifuge/issues/97#issuecomment-370815441","issue_url":"https://api.github.com/repos/infphilo/centrifuge/issues/97","id":370815441,"user":{"login":"jsh58","id":4921955,"avatar_url":"https://avatars3.githubusercontent.com/u/4921955?v=4","gravatar_id":"","url":"https://api.github.com/users/jsh58","html_url":"https://github.com/jsh58","followers_url":"https://api.github.com/users/jsh58/followers","following_url":"https://api.github.com/users/jsh58/following{/other_user}","gists_url":"https://api.github.com/users/jsh58/gists{/gist_id}","starred_url":"https://api.github.com/users/jsh58/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jsh58/subscriptions","organizations_url":"https://api.github.com/users/jsh58/orgs","repos_url":"https://api.github.com/users/jsh58/repos","events_url":"https://api.github.com/users/jsh58/events{/privacy}","received_events_url":"https://api.github.com/users/jsh58/received_events","type":"User","site_admin":false},"created_at":"2018-03-06T15:19:02Z","updated_at":"2018-03-06T15:19:02Z","author_association":"NONE","body":"@mourisl \r\nOK, I understand.  Any chance of incorporating the code changes into a new release/version in the main branch?"}}
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