{"action":"opened","issue":{"url":"https://api.github.com/repos/lomereiter/sambamba/issues/134","labels_url":"https://api.github.com/repos/lomereiter/sambamba/issues/134/labels{/name}","comments_url":"https://api.github.com/repos/lomereiter/sambamba/issues/134/comments","events_url":"https://api.github.com/repos/lomereiter/sambamba/issues/134/events","html_url":"https://github.com/lomereiter/sambamba/issues/134","id":68208547,"number":134,"title":"Cram Issues","user":{"login":"ACEnglish","id":2422579,"avatar_url":"https://avatars.githubusercontent.com/u/2422579?v=3","gravatar_id":"","url":"https://api.github.com/users/ACEnglish","html_url":"https://github.com/ACEnglish","followers_url":"https://api.github.com/users/ACEnglish/followers","following_url":"https://api.github.com/users/ACEnglish/following{/other_user}","gists_url":"https://api.github.com/users/ACEnglish/gists{/gist_id}","starred_url":"https://api.github.com/users/ACEnglish/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ACEnglish/subscriptions","organizations_url":"https://api.github.com/users/ACEnglish/orgs","repos_url":"https://api.github.com/users/ACEnglish/repos","events_url":"https://api.github.com/users/ACEnglish/events{/privacy}","received_events_url":"https://api.github.com/users/ACEnglish/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":0,"created_at":"2015-04-13T22:31:30Z","updated_at":"2015-04-13T22:31:30Z","closed_at":null,"body":"Is it possible to merge on cram files? I'm currently getting the error:\r\n\r\n**sambamba-merge: Error reading BGZF block starting from offset 0: wrong BGZF magic**\r\n\r\nAlso, I'm seeing an error when trying to use view -f cram:\r\n\r\n**[fai_build] fail to write FASTA index original/hg19.fa.fai\r\nFailed to populate reference for id 0\r\nsambamba-view: Failed to write SAM header**\r\n\r\nI don't have write permissions in this original/ directory, but original/hg19.fa.fai already exists\r\nWhenever I soft-link orginal/hg19.fa to a directory in which I have write permissions, hg19.fa.fai is created, however I'm still getting the error:\r\n\r\n**sambamba-view: Failed to write SAM header**\r\n\r\n"}}