{"action":"created","issue":{"url":"https://api.github.com/repos/broadinstitute/hellbender/issues/755","labels_url":"https://api.github.com/repos/broadinstitute/hellbender/issues/755/labels{/name}","comments_url":"https://api.github.com/repos/broadinstitute/hellbender/issues/755/comments","events_url":"https://api.github.com/repos/broadinstitute/hellbender/issues/755/events","html_url":"https://github.com/broadinstitute/hellbender/issues/755","id":97508498,"number":755,"title":"Read CRAM spec to answer important questions","user":{"login":"droazen","id":798637,"avatar_url":"https://avatars.githubusercontent.com/u/798637?v=3","gravatar_id":"","url":"https://api.github.com/users/droazen","html_url":"https://github.com/droazen","followers_url":"https://api.github.com/users/droazen/followers","following_url":"https://api.github.com/users/droazen/following{/other_user}","gists_url":"https://api.github.com/users/droazen/gists{/gist_id}","starred_url":"https://api.github.com/users/droazen/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/droazen/subscriptions","organizations_url":"https://api.github.com/users/droazen/orgs","repos_url":"https://api.github.com/users/droazen/repos","events_url":"https://api.github.com/users/droazen/events{/privacy}","received_events_url":"https://api.github.com/users/droazen/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/broadinstitute/hellbender/labels/question","name":"question","color":"cc317c"}],"state":"open","locked":false,"assignee":{"login":"edwardkw","id":10030435,"avatar_url":"https://avatars.githubusercontent.com/u/10030435?v=3","gravatar_id":"","url":"https://api.github.com/users/edwardkw","html_url":"https://github.com/edwardkw","followers_url":"https://api.github.com/users/edwardkw/followers","following_url":"https://api.github.com/users/edwardkw/following{/other_user}","gists_url":"https://api.github.com/users/edwardkw/gists{/gist_id}","starred_url":"https://api.github.com/users/edwardkw/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/edwardkw/subscriptions","organizations_url":"https://api.github.com/users/edwardkw/orgs","repos_url":"https://api.github.com/users/edwardkw/repos","events_url":"https://api.github.com/users/edwardkw/events{/privacy}","received_events_url":"https://api.github.com/users/edwardkw/received_events","type":"User","site_admin":false},"milestone":{"url":"https://api.github.com/repos/broadinstitute/hellbender/milestones/5","html_url":"https://github.com/broadinstitute/hellbender/milestones/alpha","labels_url":"https://api.github.com/repos/broadinstitute/hellbender/milestones/5/labels","id":1220227,"number":5,"title":"alpha","description":"","creator":{"login":"akiezun","id":1993519,"avatar_url":"https://avatars.githubusercontent.com/u/1993519?v=3","gravatar_id":"","url":"https://api.github.com/users/akiezun","html_url":"https://github.com/akiezun","followers_url":"https://api.github.com/users/akiezun/followers","following_url":"https://api.github.com/users/akiezun/following{/other_user}","gists_url":"https://api.github.com/users/akiezun/gists{/gist_id}","starred_url":"https://api.github.com/users/akiezun/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/akiezun/subscriptions","organizations_url":"https://api.github.com/users/akiezun/orgs","repos_url":"https://api.github.com/users/akiezun/repos","events_url":"https://api.github.com/users/akiezun/events{/privacy}","received_events_url":"https://api.github.com/users/akiezun/received_events","type":"User","site_admin":false},"open_issues":84,"closed_issues":10,"state":"open","created_at":"2015-07-22T13:37:37Z","updated_at":"2015-07-27T22:46:20Z","due_on":"2015-10-31T04:00:00Z","closed_at":null},"comments":3,"created_at":"2015-07-27T16:59:28Z","updated_at":"2015-07-28T16:58:09Z","closed_at":null,"body":"We should read the CRAM spec (http://samtools.github.io/hts-specs/CRAMv3.pdf) to find out:\r\n\r\n1. Whether CRAM files **always** require a reference, or only sometimes based on the compression used (needed for https://github.com/broadinstitute/hellbender/issues/673)\r\n\r\n2. When CRAM compression is lossy vs. lossless (we need to understand this so that when we write the tests for https://github.com/broadinstitute/hellbender/issues/590, we can convert our existing BAMs to CRAM without losing any information)."},"comment":{"url":"https://api.github.com/repos/broadinstitute/hellbender/issues/comments/125678829","html_url":"https://github.com/broadinstitute/hellbender/issues/755#issuecomment-125678829","issue_url":"https://api.github.com/repos/broadinstitute/hellbender/issues/755","id":125678829,"user":{"login":"edwardkw","id":10030435,"avatar_url":"https://avatars.githubusercontent.com/u/10030435?v=3","gravatar_id":"","url":"https://api.github.com/users/edwardkw","html_url":"https://github.com/edwardkw","followers_url":"https://api.github.com/users/edwardkw/followers","following_url":"https://api.github.com/users/edwardkw/following{/other_user}","gists_url":"https://api.github.com/users/edwardkw/gists{/gist_id}","starred_url":"https://api.github.com/users/edwardkw/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/edwardkw/subscriptions","organizations_url":"https://api.github.com/users/edwardkw/orgs","repos_url":"https://api.github.com/users/edwardkw/repos","events_url":"https://api.github.com/users/edwardkw/events{/privacy}","received_events_url":"https://api.github.com/users/edwardkw/received_events","type":"User","site_admin":false},"created_at":"2015-07-28T16:58:08Z","updated_at":"2015-07-28T16:58:08Z","body":"1. There aren't differences between the two specs, with regards to references. Generally, it seems that reference sequences are often used but not always required. As best I can tell, reference isn't needed for unsorted or unmapped reads. I can't tell about different kinds of compression.\r\n\r\n2. There are both kinds of CRAM compression; a wide range of lossy and lossless compression methods exist for CRAM."}}