{"action":"created","issue":{"url":"https://api.github.com/repos/FRED-2/OptiType/issues/20","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":"open","locked":false,"assignee":null,"milestone":null,"comments":0,"created_at":"2016-01-26T16:53:41Z","updated_at":"2016-01-26T17:09:53Z","closed_at":null,"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/175121471","html_url":"https://github.com/FRED-2/OptiType/issues/20#issuecomment-175121471","issue_url":"https://api.github.com/repos/FRED-2/OptiType/issues/20","id":175121471,"user":{"login":"andras86","id":3963729,"avatar_url":"https://avatars.githubusercontent.com/u/3963729?v=3","gravatar_id":"","url":"https://api.github.com/users/andras86","html_url":"https://github.com/andras86","followers_url":"https://api.github.com/users/andras86/followers","following_url":"https://api.github.com/users/andras86/following{/other_user}","gists_url":"https://api.github.com/users/andras86/gists{/gist_id}","starred_url":"https://api.github.com/users/andras86/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/andras86/subscriptions","organizations_url":"https://api.github.com/users/andras86/orgs","repos_url":"https://api.github.com/users/andras86/repos","events_url":"https://api.github.com/users/andras86/events{/privacy}","received_events_url":"https://api.github.com/users/andras86/received_events","type":"User","site_admin":false},"created_at":"2016-01-26T17:09:53Z","updated_at":"2016-01-26T17:09:53Z","body":"Hi Alvin,\r\n\r\nYes, we're aware and we'll switch to Yara (developed by the same guy) soon. You'll need a small workaround then: you can feed OT the all-mapped bam files instead of the fastq files. So index hla_reference_(dna|rna).fasta first with yara_indexer. Then use the following call:\r\n\r\n`yara_mapper -e 3 -f bam -u -os /path/to/ref path/to/reads_1.fastq.gz | samtools view -h -F 4 -b1 - > mapped_1.bam`\r\n\r\n...and the same for the second end. Avoid multithreading with yara for now. Then call OT with the two bam files instead of fastq files."}}