{"action":"closed","issue":{"url":"https://api.github.com/repos/galaxyproject/tools-devteam/issues/130","labels_url":"https://api.github.com/repos/galaxyproject/tools-devteam/issues/130/labels{/name}","comments_url":"https://api.github.com/repos/galaxyproject/tools-devteam/issues/130/comments","events_url":"https://api.github.com/repos/galaxyproject/tools-devteam/issues/130/events","html_url":"https://github.com/galaxyproject/tools-devteam/issues/130","id":74403578,"number":130,"title":"fastq groomer does not parse sequence ids that contain spaces properly","user":{"login":"lparsons","id":645128,"avatar_url":"https://avatars.githubusercontent.com/u/645128?v=3","gravatar_id":"","url":"https://api.github.com/users/lparsons","html_url":"https://github.com/lparsons","followers_url":"https://api.github.com/users/lparsons/followers","following_url":"https://api.github.com/users/lparsons/following{/other_user}","gists_url":"https://api.github.com/users/lparsons/gists{/gist_id}","starred_url":"https://api.github.com/users/lparsons/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/lparsons/subscriptions","organizations_url":"https://api.github.com/users/lparsons/orgs","repos_url":"https://api.github.com/users/lparsons/repos","events_url":"https://api.github.com/users/lparsons/events{/privacy}","received_events_url":"https://api.github.com/users/lparsons/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"milestone":null,"comments":3,"created_at":"2015-05-08T15:36:44Z","updated_at":"2015-05-08T15:47:35Z","closed_at":"2015-05-08T15:47:35Z","body":"The issue is that the FastqReader class parses the entire \"@\" line as a sequence id. The specification actually allows for an \"optional\" description, similar to FASTA which comes after a space. Some files I have seen (such as those from the iMicrobe Project) contain lines like:\r\n\r\n    @<READID> <DESCRIPTION>\r\n    ATCGGTTTCGTTGTGTTATTCGCGGCCAAGGGTTTTGTCGTCGTTATATT\r\n    +<READID>\r\n    ^__ec\\cccgce]`J[R`[[`ee][ccecag__aafU\\baT_WLY^\\Xac\r\n\r\nThese result in the following error:\r\n\r\n    Exception: Invalid FASTQ file: could not find quality score of sequence identifier @<READID> <DESCRIPTION>.\r\n\r\nI believe this would be a simple fix, however, I'm not actually sure where the code for those utility classes is hosted."}}