{"action":"created","issue":{"url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1321","repository_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen","labels_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1321/labels{/name}","comments_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1321/comments","events_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1321/events","html_url":"https://github.com/chapmanb/bcbio-nextgen/issues/1321","id":147434343,"number":1321,"title":"Revert to cramtools 2.1","user":{"login":"schelhorn","id":5024959,"avatar_url":"https://avatars.githubusercontent.com/u/5024959?v=3","gravatar_id":"","url":"https://api.github.com/users/schelhorn","html_url":"https://github.com/schelhorn","followers_url":"https://api.github.com/users/schelhorn/followers","following_url":"https://api.github.com/users/schelhorn/following{/other_user}","gists_url":"https://api.github.com/users/schelhorn/gists{/gist_id}","starred_url":"https://api.github.com/users/schelhorn/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/schelhorn/subscriptions","organizations_url":"https://api.github.com/users/schelhorn/orgs","repos_url":"https://api.github.com/users/schelhorn/repos","events_url":"https://api.github.com/users/schelhorn/events{/privacy}","received_events_url":"https://api.github.com/users/schelhorn/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":4,"created_at":"2016-04-11T13:42:48Z","updated_at":"2016-04-12T08:56:24Z","closed_at":null,"body":"I am using the `cram` compression option in bcbio for archival of the alignment. Using `cramtools 2.1` this goes smoothly; however, bcbio now seems to install `cramtools 3.0-b47`, which fails with `Unknown read or base category: i` error when running the bcbio builtin conversion. This `cramtools 3` seems to have other issues as well, for instance here https://github.com/enasequence/cramtools/issues/48 where it forces one to retain read names even if it is specified to omit them. The `cramtools` people are working on it, but the issue is still open. I therefore suggest to revert to the working `cramtools 2.1` version that is in homebrew until all issues are fixed. "},"comment":{"url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/comments/208800378","html_url":"https://github.com/chapmanb/bcbio-nextgen/issues/1321#issuecomment-208800378","issue_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1321","id":208800378,"user":{"login":"schelhorn","id":5024959,"avatar_url":"https://avatars.githubusercontent.com/u/5024959?v=3","gravatar_id":"","url":"https://api.github.com/users/schelhorn","html_url":"https://github.com/schelhorn","followers_url":"https://api.github.com/users/schelhorn/followers","following_url":"https://api.github.com/users/schelhorn/following{/other_user}","gists_url":"https://api.github.com/users/schelhorn/gists{/gist_id}","starred_url":"https://api.github.com/users/schelhorn/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/schelhorn/subscriptions","organizations_url":"https://api.github.com/users/schelhorn/orgs","repos_url":"https://api.github.com/users/schelhorn/repos","events_url":"https://api.github.com/users/schelhorn/events{/privacy}","received_events_url":"https://api.github.com/users/schelhorn/received_events","type":"User","site_admin":false},"created_at":"2016-04-12T08:56:24Z","updated_at":"2016-04-12T08:56:24Z","body":"So the new cramtools version seems to require Java 8 (Java error is `unsupported major.minor version 52.0`). Bcbio comes with Java 7. I'll stick with cramtools 2x for now but I'm fine with monkey patching that in myself if need be. "}}