{"action":"created","issue":{"url":"https://api.github.com/repos/ekg/freebayes/issues/361","repository_url":"https://api.github.com/repos/ekg/freebayes","labels_url":"https://api.github.com/repos/ekg/freebayes/issues/361/labels{/name}","comments_url":"https://api.github.com/repos/ekg/freebayes/issues/361/comments","events_url":"https://api.github.com/repos/ekg/freebayes/issues/361/events","html_url":"https://github.com/ekg/freebayes/issues/361","id":206300543,"number":361,"title":"New allele qualities not == in length to sequence (core dumped)","user":{"login":"mrtnb","id":471110,"avatar_url":"https://avatars3.githubusercontent.com/u/471110?v=4","gravatar_id":"","url":"https://api.github.com/users/mrtnb","html_url":"https://github.com/mrtnb","followers_url":"https://api.github.com/users/mrtnb/followers","following_url":"https://api.github.com/users/mrtnb/following{/other_user}","gists_url":"https://api.github.com/users/mrtnb/gists{/gist_id}","starred_url":"https://api.github.com/users/mrtnb/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mrtnb/subscriptions","organizations_url":"https://api.github.com/users/mrtnb/orgs","repos_url":"https://api.github.com/users/mrtnb/repos","events_url":"https://api.github.com/users/mrtnb/events{/privacy}","received_events_url":"https://api.github.com/users/mrtnb/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":4,"created_at":"2017-02-08T19:34:00Z","updated_at":"2018-02-28T23:53:42Z","closed_at":null,"author_association":"NONE","body":"Freebayes crashes with error message:\r\n\r\n> new allele qualities not == in length to sequence: Sx8drs-SAMPLE:C38WVACXX_1:8:2116:1266365:0:null:81:81:10267:-:NTNAACNCAAAACCNAATCCAACCCNTNCCCCTCCACNAANNNAANCCCTNCCCNAACCCNAACCCTANGCCNATTCCTAC:10267:81N:-6.4:-6.4\r\nfreebayes: AlleleParser.cpp:1016: void RegisteredAlignment::addAllele(Allele, bool, int, bool): Assertion `false' failed.\r\n/bin/sh: line 1:  7542 Aborted                 (core dumped)\r\n\r\nIt seems to complain about a quality string in the alignment not having the same length as the read. Here is the relevant read pair from the alignment:\r\n\r\n```\r\nC38WVACXX_1:8:2116:1266365:0    99      1       10050   28      14M4D82M4S      =       10349   318     AACCCTAACCCTAAAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCAACCCTAACCCTAACCCTAACCCTAAACCTACCCCTAACCCTCCC    <BBBFFFFFFFFFIIFIFIFFFIIIFIFBBFFIIFFFFIIFIFBFFFFFB<BFIIIIIIFFFFFBFFBBBFFBFB7<B<BBBBFBB'7BBBFBB<BB'77  NM:i:6  MD:Z:14^CCCT67C4A9      AS:i:76 XS:i:73 MC:Z:81S19M     MQ:i:28 RG:Z:SAMPLE.2\r\nC38WVACXX_1:8:2116:1266365:0    147     1       10349   28      81S19M  =       10050   -318    NTNAACNCAAAACCNAATCCAACCCNTNCCCCTCCACNAANNNAANCCCTNCCCNAACCCNAACCCTANGCCNATTCCTACCCCTACCCTAACCCTAACC    !'!'00!'000'0'!'0''''0'00!0!'77'0'''0!00!!!'0!'0''!7''!77<<0!<077''0!'<0!0''<B0''''<'07<<700'7'<'777  NM:i:0  MD:Z:19 AS:i:19 XS:i:21 MC:Z:14M4D82M4S MQ:i:28 RG:Z:SAMPLE.2\r\n```\r\nBoth read string and quality string are of length 100. Note that in the error message above freebayes only displays the first 81 bases from the second read and its CIGAR string starts with 81S.\r\n\r\nFreebayes version:  v1.1.0-4-gb6041c6"},"comment":{"url":"https://api.github.com/repos/ekg/freebayes/issues/comments/369425075","html_url":"https://github.com/ekg/freebayes/issues/361#issuecomment-369425075","issue_url":"https://api.github.com/repos/ekg/freebayes/issues/361","id":369425075,"user":{"login":"ekg","id":145425,"avatar_url":"https://avatars1.githubusercontent.com/u/145425?v=4","gravatar_id":"","url":"https://api.github.com/users/ekg","html_url":"https://github.com/ekg","followers_url":"https://api.github.com/users/ekg/followers","following_url":"https://api.github.com/users/ekg/following{/other_user}","gists_url":"https://api.github.com/users/ekg/gists{/gist_id}","starred_url":"https://api.github.com/users/ekg/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ekg/subscriptions","organizations_url":"https://api.github.com/users/ekg/orgs","repos_url":"https://api.github.com/users/ekg/repos","events_url":"https://api.github.com/users/ekg/events{/privacy}","received_events_url":"https://api.github.com/users/ekg/received_events","type":"User","site_admin":false},"created_at":"2018-02-28T23:53:41Z","updated_at":"2018-02-28T23:53:41Z","author_association":"OWNER","body":"Ok let me try to reproduce with the read listed above.\n\nOn Fri, Jan 26, 2018, 22:39 Johnny Sena <notifications@github.com> wrote:\n\n> Hi ekg,\n> This seems to be an issue with version v1.1.0-4-gb6041c6 .\n> When I run freebayes version v1.0.0 freebayes will run.\n>\n> —\n> You are receiving this because you commented.\n>\n>\n> Reply to this email directly, view it on GitHub\n> <https://github.com/ekg/freebayes/issues/361#issuecomment-360924353>, or mute\n> the thread\n> <https://github.com/notifications/unsubscribe-auth/AAI4ERJadqjWzkeynZJ129vzm7XEmlzrks5tOlQMgaJpZM4L7Qjk>\n> .\n>\n"}}
{"actor":{"display_login":"ekg"}}