{"action":"created","issue":{"url":"https://api.github.com/repos/FRED-2/OptiType/issues/20","repository_url":"https://api.github.com/repos/FRED-2/OptiType","labels_url":"https://api.github.com/repos/FRED-2/OptiType/issues/20/labels{/name}","comments_url":"https://api.github.com/repos/FRED-2/OptiType/issues/20/comments","events_url":"https://api.github.com/repos/FRED-2/OptiType/issues/20/events","html_url":"https://github.com/FRED-2/OptiType/issues/20","id":128877113,"number":20,"title":"Optitype error with gzipped fastqs","user":{"login":"alvinwt","id":3662163,"avatar_url":"https://avatars.githubusercontent.com/u/3662163?v=3","gravatar_id":"","url":"https://api.github.com/users/alvinwt","html_url":"https://github.com/alvinwt","followers_url":"https://api.github.com/users/alvinwt/followers","following_url":"https://api.github.com/users/alvinwt/following{/other_user}","gists_url":"https://api.github.com/users/alvinwt/gists{/gist_id}","starred_url":"https://api.github.com/users/alvinwt/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/alvinwt/subscriptions","organizations_url":"https://api.github.com/users/alvinwt/orgs","repos_url":"https://api.github.com/users/alvinwt/repos","events_url":"https://api.github.com/users/alvinwt/events{/privacy}","received_events_url":"https://api.github.com/users/alvinwt/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"milestone":null,"comments":5,"created_at":"2016-01-26T16:53:41Z","updated_at":"2016-02-10T13:15:48Z","closed_at":"2016-02-10T07:27:05Z","body":"Hi @andras86, \r\n\r\nI realized that razers3.4 has issues with gzipped fastqs due to seqan mentioned in [#987](https://github.com/seqan/seqan/issues/987). Is there other alignments that I can use in place of razers for optitype? It seems like razers3 is not maintained anymore. "},"comment":{"url":"https://api.github.com/repos/FRED-2/OptiType/issues/comments/182368855","html_url":"https://github.com/FRED-2/OptiType/issues/20#issuecomment-182368855","issue_url":"https://api.github.com/repos/FRED-2/OptiType/issues/20","id":182368855,"user":{"login":"alvinwt","id":3662163,"avatar_url":"https://avatars.githubusercontent.com/u/3662163?v=3","gravatar_id":"","url":"https://api.github.com/users/alvinwt","html_url":"https://github.com/alvinwt","followers_url":"https://api.github.com/users/alvinwt/followers","following_url":"https://api.github.com/users/alvinwt/following{/other_user}","gists_url":"https://api.github.com/users/alvinwt/gists{/gist_id}","starred_url":"https://api.github.com/users/alvinwt/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/alvinwt/subscriptions","organizations_url":"https://api.github.com/users/alvinwt/orgs","repos_url":"https://api.github.com/users/alvinwt/repos","events_url":"https://api.github.com/users/alvinwt/events{/privacy}","received_events_url":"https://api.github.com/users/alvinwt/received_events","type":"User","site_admin":false},"created_at":"2016-02-10T13:15:48Z","updated_at":"2016-02-10T13:15:48Z","body":"Thanks @andras86, I'm  getting \r\n````\r\n[bam_header_read] invalid BAM binary header (this is not a BAM file).\r\n````\r\n\r\nas the error message. \r\n\r\nThe command I ran was \r\n````\r\nyara_mapper -e 3 -f bam -u -t 4 -os hla_reference_dna 108T_JH_1.fastq.gz | samtools view -h -F 4 -b1 - > mapped_1.bam\r\n````\r\n\r\nAny clue how to get around this problem?"}}