{"action":"created","issue":{"url":"https://api.github.com/repos/seqan/seqan/issues/2298","repository_url":"https://api.github.com/repos/seqan/seqan","labels_url":"https://api.github.com/repos/seqan/seqan/issues/2298/labels{/name}","comments_url":"https://api.github.com/repos/seqan/seqan/issues/2298/comments","events_url":"https://api.github.com/repos/seqan/seqan/issues/2298/events","html_url":"https://github.com/seqan/seqan/pull/2298","id":306951207,"number":2298,"title":"[FIX] Fixes crash when pattern is larger than contig seq for omp-enabled","user":{"login":"s22chan","id":32464643,"avatar_url":"https://avatars3.githubusercontent.com/u/32464643?v=4","gravatar_id":"","url":"https://api.github.com/users/s22chan","html_url":"https://github.com/s22chan","followers_url":"https://api.github.com/users/s22chan/followers","following_url":"https://api.github.com/users/s22chan/following{/other_user}","gists_url":"https://api.github.com/users/s22chan/gists{/gist_id}","starred_url":"https://api.github.com/users/s22chan/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/s22chan/subscriptions","organizations_url":"https://api.github.com/users/s22chan/orgs","repos_url":"https://api.github.com/users/s22chan/repos","events_url":"https://api.github.com/users/s22chan/events{/privacy}","received_events_url":"https://api.github.com/users/s22chan/received_events","type":"User","site_admin":false},"labels":[{"id":17442902,"url":"https://api.github.com/repos/seqan/seqan/labels/bug","name":"bug","color":"fc2929","default":true}],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":{"url":"https://api.github.com/repos/seqan/seqan/milestones/17","html_url":"https://github.com/seqan/seqan/milestone/17","labels_url":"https://api.github.com/repos/seqan/seqan/milestones/17/labels","id":2777647,"number":17,"title":"Release 2.4.1","description":"","creator":{"login":"rrahn","id":1529364,"avatar_url":"https://avatars2.githubusercontent.com/u/1529364?v=4","gravatar_id":"","url":"https://api.github.com/users/rrahn","html_url":"https://github.com/rrahn","followers_url":"https://api.github.com/users/rrahn/followers","following_url":"https://api.github.com/users/rrahn/following{/other_user}","gists_url":"https://api.github.com/users/rrahn/gists{/gist_id}","starred_url":"https://api.github.com/users/rrahn/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/rrahn/subscriptions","organizations_url":"https://api.github.com/users/rrahn/orgs","repos_url":"https://api.github.com/users/rrahn/repos","events_url":"https://api.github.com/users/rrahn/events{/privacy}","received_events_url":"https://api.github.com/users/rrahn/received_events","type":"User","site_admin":false},"open_issues":31,"closed_issues":3,"state":"open","created_at":"2017-09-19T13:23:25Z","updated_at":"2018-03-28T15:39:52Z","due_on":"2017-12-15T08:00:00Z","closed_at":null},"comments":1,"created_at":"2018-03-20T16:51:42Z","updated_at":"2018-03-28T15:57:46Z","closed_at":null,"author_association":"NONE","pull_request":{"url":"https://api.github.com/repos/seqan/seqan/pulls/2298","html_url":"https://github.com/seqan/seqan/pull/2298","diff_url":"https://github.com/seqan/seqan/pull/2298.diff","patch_url":"https://github.com/seqan/seqan/pull/2298.patch"},"body":"This fixes the crash where the region end index underflows and the child fork thinks there's still more results to report back in https://github.com/seqan/seqan/blob/584ae4fbff8312cfe31b3e0aea651edfb1b580ef/apps/razers3/razers_parallel.h#L736-L738\r\n\r\nnow it will err log \r\n```\r\nERROR: windowFindBegin() failed in thread 0\r\n```\r\nand report no hits. The logic can probably be further simplified for https://github.com/seqan/seqan/blob/584ae4fbff8312cfe31b3e0aea651edfb1b580ef/apps/razers3/razers_parallel.h#L664-L667\r\n\r\nto have\r\n```cpp\r\nhasMore = windowFindBegin(...);\r\nwindowsDone += hasMore ? 0 : 1;\r\n```\r\n\r\nbut I'm unsure as to whether the err has utility.\r\n"},"comment":{"url":"https://api.github.com/repos/seqan/seqan/issues/comments/376939527","html_url":"https://github.com/seqan/seqan/pull/2298#issuecomment-376939527","issue_url":"https://api.github.com/repos/seqan/seqan/issues/2298","id":376939527,"user":{"login":"marehr","id":103778,"avatar_url":"https://avatars1.githubusercontent.com/u/103778?v=4","gravatar_id":"","url":"https://api.github.com/users/marehr","html_url":"https://github.com/marehr","followers_url":"https://api.github.com/users/marehr/followers","following_url":"https://api.github.com/users/marehr/following{/other_user}","gists_url":"https://api.github.com/users/marehr/gists{/gist_id}","starred_url":"https://api.github.com/users/marehr/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/marehr/subscriptions","organizations_url":"https://api.github.com/users/marehr/orgs","repos_url":"https://api.github.com/users/marehr/repos","events_url":"https://api.github.com/users/marehr/events{/privacy}","received_events_url":"https://api.github.com/users/marehr/received_events","type":"User","site_admin":false},"created_at":"2018-03-28T15:57:46Z","updated_at":"2018-03-28T15:57:46Z","author_association":"CONTRIBUTOR","body":"@s22chan Thank you for your pull request.\r\n\r\nRazers3 is currently unmaintained and we have to figure out what the underlying issue is here.\r\n\r\nDo you know how a non-parallel execution differs in this aspect? You changed one file that seems to be unrelated to a parallel invocation, does that mean that this bug is also available in a sequential run? \r\n\r\nI'm not from the domain, but is it a valid use case to have shorter contig sequences than the pattern? It seems to me that the author did not take this use case into consideration and that there might be more affected places that might fail.\r\n\r\nWould it be okay to filter-out contig sequences that are shorter than the pattern in a preprocess step? How would this change the output? Sorry again, I have no experience with razers3."}}
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