{"action":"created","issue":{"url":"https://api.github.com/repos/marcelm/cutadapt/issues/63","labels_url":"https://api.github.com/repos/marcelm/cutadapt/issues/63/labels{/name}","comments_url":"https://api.github.com/repos/marcelm/cutadapt/issues/63/comments","events_url":"https://api.github.com/repos/marcelm/cutadapt/issues/63/events","html_url":"https://github.com/marcelm/cutadapt/issues/63","id":61274432,"number":63,"title":"FastQ conversion solid quality of \".\"-> \" \"","user":{"login":"marcelm","id":724864,"avatar_url":"https://avatars.githubusercontent.com/u/724864?v=3","gravatar_id":"","url":"https://api.github.com/users/marcelm","html_url":"https://github.com/marcelm","followers_url":"https://api.github.com/users/marcelm/followers","following_url":"https://api.github.com/users/marcelm/following{/other_user}","gists_url":"https://api.github.com/users/marcelm/gists{/gist_id}","starred_url":"https://api.github.com/users/marcelm/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/marcelm/subscriptions","organizations_url":"https://api.github.com/users/marcelm/orgs","repos_url":"https://api.github.com/users/marcelm/repos","events_url":"https://api.github.com/users/marcelm/events{/privacy}","received_events_url":"https://api.github.com/users/marcelm/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/marcelm/cutadapt/labels/imported","name":"imported","color":"FFFFFF"},{"url":"https://api.github.com/repos/marcelm/cutadapt/labels/Type-Other","name":"Type-Other","color":"FFFFFF"}],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":3,"created_at":"2015-03-13T22:19:21Z","updated_at":"2015-03-13T22:19:35Z","closed_at":null,"body":"_From [jerpars...@gmail.com](https://code.google.com/u/116119796811296373987/) on October 22, 2012 21:28:36_\n\nWhen reading a solid .qual file, any reads containing no-calls or \".\" (quality score =-1) are given quality codes of space \" \" by cutadapt.  This interferes with downstream programs.\r\n\r\nWhile space is the 'correct' ascii conversion, it seems that quality scores of -1 are not supported in fastq.  Converting to 0 (ascii=!) is how other conversion programs handle the difficulty.\r\n\r\n\r\n(original csfasta)\r\n\\> T222231333010222210330210133311021330211103.1032.211031323112320133330321222\r\n(original qual)\r\n\\> 17 14 26 23 31 14 26 31 14 14 21 26 28 27 14 31 14 14 26 31 17 14 14 13 14 14 17 14 21 17 17 14 27 14 14 21 27 21 14 29 14 14 -1 31 14 14 17 -1 27 14 14 27 14 23 26 14 31 14 21 28 14 14 14 21 21 17 23 14 14 14 14 30 23 17 14 \r\n\r\n(cutadapt output) \"Actual output\"\r\n/;8@/;@//6;=</@//;@2//.//2/622/<//6<6/>// @//2 \\<//</8;/@/6=///6628////\r\n\r\n(galaxy's Convert.py output) \"Expected output\"\r\n/;8@/;@//6;=</@//;@2//.//2/622/<//6<6/>//!@//2!<//</8;/@/6=///6628////\n\n_Original issue: http://code.google.com/p/cutadapt/issues/detail?id=53_"},"comment":{"url":"https://api.github.com/repos/marcelm/cutadapt/issues/comments/79476520","html_url":"https://github.com/marcelm/cutadapt/issues/63#issuecomment-79476520","issue_url":"https://api.github.com/repos/marcelm/cutadapt/issues/63","id":79476520,"user":{"login":"marcelm","id":724864,"avatar_url":"https://avatars.githubusercontent.com/u/724864?v=3","gravatar_id":"","url":"https://api.github.com/users/marcelm","html_url":"https://github.com/marcelm","followers_url":"https://api.github.com/users/marcelm/followers","following_url":"https://api.github.com/users/marcelm/following{/other_user}","gists_url":"https://api.github.com/users/marcelm/gists{/gist_id}","starred_url":"https://api.github.com/users/marcelm/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/marcelm/subscriptions","organizations_url":"https://api.github.com/users/marcelm/orgs","repos_url":"https://api.github.com/users/marcelm/repos","events_url":"https://api.github.com/users/marcelm/events{/privacy}","received_events_url":"https://api.github.com/users/marcelm/received_events","type":"User","site_admin":false},"created_at":"2015-03-13T22:19:35Z","updated_at":"2015-03-13T22:19:35Z","body":"_From [marcel.m...@tu-dortmund.de](https://code.google.com/u/115749445199231802729/) on October 23, 2012 08:19:45_\n\nThanks for the reply. I'll update the documentation such that it explicitly mentions the -z parameter. Perhaps it also makes sense to enable -z by default."}}