{"action":"closed","issue":{"url":"https://api.github.com/repos/mossmatters/HybPiper/issues/13","repository_url":"https://api.github.com/repos/mossmatters/HybPiper","labels_url":"https://api.github.com/repos/mossmatters/HybPiper/issues/13/labels{/name}","comments_url":"https://api.github.com/repos/mossmatters/HybPiper/issues/13/comments","events_url":"https://api.github.com/repos/mossmatters/HybPiper/issues/13/events","html_url":"https://github.com/mossmatters/HybPiper/issues/13","id":182303228,"number":13,"title":"Legacy Illumina FASTQ Header Parsing","user":{"login":"mossmatters","id":1557809,"avatar_url":"https://avatars.githubusercontent.com/u/1557809?v=3","gravatar_id":"","url":"https://api.github.com/users/mossmatters","html_url":"https://github.com/mossmatters","followers_url":"https://api.github.com/users/mossmatters/followers","following_url":"https://api.github.com/users/mossmatters/following{/other_user}","gists_url":"https://api.github.com/users/mossmatters/gists{/gist_id}","starred_url":"https://api.github.com/users/mossmatters/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mossmatters/subscriptions","organizations_url":"https://api.github.com/users/mossmatters/orgs","repos_url":"https://api.github.com/users/mossmatters/repos","events_url":"https://api.github.com/users/mossmatters/events{/privacy}","received_events_url":"https://api.github.com/users/mossmatters/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/mossmatters/HybPiper/labels/bug","name":"bug","color":"fc2929"}],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":{"url":"https://api.github.com/repos/mossmatters/HybPiper/milestones/2","html_url":"https://github.com/mossmatters/HybPiper/milestones/1.1.1","labels_url":"https://api.github.com/repos/mossmatters/HybPiper/milestones/2/labels","id":2089851,"number":2,"title":"1.1.1","description":null,"creator":{"login":"mossmatters","id":1557809,"avatar_url":"https://avatars.githubusercontent.com/u/1557809?v=3","gravatar_id":"","url":"https://api.github.com/users/mossmatters","html_url":"https://github.com/mossmatters","followers_url":"https://api.github.com/users/mossmatters/followers","following_url":"https://api.github.com/users/mossmatters/following{/other_user}","gists_url":"https://api.github.com/users/mossmatters/gists{/gist_id}","starred_url":"https://api.github.com/users/mossmatters/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mossmatters/subscriptions","organizations_url":"https://api.github.com/users/mossmatters/orgs","repos_url":"https://api.github.com/users/mossmatters/repos","events_url":"https://api.github.com/users/mossmatters/events{/privacy}","received_events_url":"https://api.github.com/users/mossmatters/received_events","type":"User","site_admin":false},"open_issues":0,"closed_issues":2,"state":"open","created_at":"2016-10-24T16:37:10Z","updated_at":"2016-10-24T20:52:39Z","due_on":null,"closed_at":null},"comments":4,"created_at":"2016-10-11T15:54:08Z","updated_at":"2016-10-24T20:52:39Z","closed_at":"2016-10-24T20:52:39Z","body":"With the Cassava 1.8 chemistry, Illumina changed the way the headers are generated for FASTQ files:\r\n\r\nhttps://en.wikipedia.org/wiki/FASTQ_format\r\n\r\nWhen parsing reads, both BWA and BLAST take only the first part of the header, until the first whitespace character. Using the more recent Illumina format:\r\n\r\n`@EAS139:136:FC706VJ:2:2104:15343:197393 1:Y:18:ATCACG`\r\n\r\nAppears in the BAM files as:\r\n\r\n`@EAS139:136:FC706VJ:2:2104:15343:197393`\r\n\r\nThe read pairing data is thus lost. However, this is fine in HybPiper because the reads are also parsed in the same way in `distribute_reads.py` and `distribute_reads_bwa.py`\r\n\r\nHowever, the previous Solexa FASTQ format breaks the distribution scripts:\r\n\r\n`@HWUSI-EAS100R:6:73:941:1973#0/1`\r\n\r\nIs listed as `@HWUSI-EAS100R:6:73:941:1973#0` in the BAM output. The read distribution scripts therefore never identify any reads, resulting in the following HybPiper error:\r\n\r\n`ERROR: No genes with BLAST hits! Exiting!`\r\n"}}
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