{"action":"opened","issue":{"url":"https://api.github.com/repos/alexdobin/STAR/issues/416","repository_url":"https://api.github.com/repos/alexdobin/STAR","labels_url":"https://api.github.com/repos/alexdobin/STAR/issues/416/labels{/name}","comments_url":"https://api.github.com/repos/alexdobin/STAR/issues/416/comments","events_url":"https://api.github.com/repos/alexdobin/STAR/issues/416/events","html_url":"https://github.com/alexdobin/STAR/issues/416","id":320335094,"number":416,"title":"Documentation issue / bug with SAM input","user":{"login":"jhart99","id":7755604,"avatar_url":"https://avatars0.githubusercontent.com/u/7755604?v=4","gravatar_id":"","url":"https://api.github.com/users/jhart99","html_url":"https://github.com/jhart99","followers_url":"https://api.github.com/users/jhart99/followers","following_url":"https://api.github.com/users/jhart99/following{/other_user}","gists_url":"https://api.github.com/users/jhart99/gists{/gist_id}","starred_url":"https://api.github.com/users/jhart99/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jhart99/subscriptions","organizations_url":"https://api.github.com/users/jhart99/orgs","repos_url":"https://api.github.com/users/jhart99/repos","events_url":"https://api.github.com/users/jhart99/events{/privacy}","received_events_url":"https://api.github.com/users/jhart99/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2018-05-04T16:15:14Z","updated_at":"2018-05-04T16:15:14Z","closed_at":null,"author_association":"NONE","body":"\"--readFilesType SAM PE\" gives unexpected results.  If used with a previously aligned bam file and samtools view, the majority of reads will fail to align as \"Alignment too short\".  \r\n\r\nI think this is a documentation issue and the manual should be updated to reflect that the input file needs to be sorted by read name or unsorted as long as the pairs come out sequentially from samtools view.  If the same alignment is first converted back to FASTQ and aligned there is no problem."}}
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