{"action":"created","issue":{"url":"https://api.github.com/repos/broadinstitute/picard/issues/329","labels_url":"https://api.github.com/repos/broadinstitute/picard/issues/329/labels{/name}","comments_url":"https://api.github.com/repos/broadinstitute/picard/issues/329/comments","events_url":"https://api.github.com/repos/broadinstitute/picard/issues/329/events","html_url":"https://github.com/broadinstitute/picard/pull/329","id":115515447,"number":329,"title":"Allow molecular barcode reads","user":{"login":"yfarjoun","id":2745554,"avatar_url":"https://avatars.githubusercontent.com/u/2745554?v=3","gravatar_id":"","url":"https://api.github.com/users/yfarjoun","html_url":"https://github.com/yfarjoun","followers_url":"https://api.github.com/users/yfarjoun/followers","following_url":"https://api.github.com/users/yfarjoun/following{/other_user}","gists_url":"https://api.github.com/users/yfarjoun/gists{/gist_id}","starred_url":"https://api.github.com/users/yfarjoun/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/yfarjoun/subscriptions","organizations_url":"https://api.github.com/users/yfarjoun/orgs","repos_url":"https://api.github.com/users/yfarjoun/repos","events_url":"https://api.github.com/users/yfarjoun/events{/privacy}","received_events_url":"https://api.github.com/users/yfarjoun/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/broadinstitute/picard/labels/2%20-%20Working","name":"2 - Working","color":"CCCCCC"}],"state":"open","locked":false,"assignee":{"login":"yfarjoun","id":2745554,"avatar_url":"https://avatars.githubusercontent.com/u/2745554?v=3","gravatar_id":"","url":"https://api.github.com/users/yfarjoun","html_url":"https://github.com/yfarjoun","followers_url":"https://api.github.com/users/yfarjoun/followers","following_url":"https://api.github.com/users/yfarjoun/following{/other_user}","gists_url":"https://api.github.com/users/yfarjoun/gists{/gist_id}","starred_url":"https://api.github.com/users/yfarjoun/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/yfarjoun/subscriptions","organizations_url":"https://api.github.com/users/yfarjoun/orgs","repos_url":"https://api.github.com/users/yfarjoun/repos","events_url":"https://api.github.com/users/yfarjoun/events{/privacy}","received_events_url":"https://api.github.com/users/yfarjoun/received_events","type":"User","site_admin":false},"milestone":null,"comments":6,"created_at":"2015-11-06T14:32:57Z","updated_at":"2015-11-15T01:47:21Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/broadinstitute/picard/pulls/329","html_url":"https://github.com/broadinstitute/picard/pull/329","diff_url":"https://github.com/broadinstitute/picard/pull/329.diff","patch_url":"https://github.com/broadinstitute/picard/pull/329.patch"},"body":"This modification to IlluminaBasecallsTo* and friends allows the inclusion of \"M\" operators in the ReadStructure string. The M operator stands for \"MolecularIndex\" and is supposed to identify the original molecule from which the read(s) was/were derived. This can be useful in two currently identified scenarios:\r\n\r\n1. Adding a short UMI to reads prior to PCR which would allow MarkDuplicate to consider reads from different molecules as _not_ duplicates even if the have the same start+stop+orientation+library. The relevant changes to MarkDuplicates are already in place #285.\r\n2. Extracting a molecular barcode that can be used to identify the haplotype from which many read-pairs have been created (a-la 10X)\r\n\r\nThere is no index-checking included here as it seem to be an inappropriate place for it, if there is a white-list of barcodes, a different program should be written and run on the data. if we want error correction in mark-duplicates, a modification to the current implementation is required (currently the code hashes all the information together, so it's impossible to know how different the indices are)\r\n\r\nGiven the importance of the correction of these I am looking for multiple reviews...if possible"},"comment":{"url":"https://api.github.com/repos/broadinstitute/picard/issues/comments/156769705","html_url":"https://github.com/broadinstitute/picard/pull/329#issuecomment-156769705","issue_url":"https://api.github.com/repos/broadinstitute/picard/issues/329","id":156769705,"user":{"login":"yfarjoun","id":2745554,"avatar_url":"https://avatars.githubusercontent.com/u/2745554?v=3","gravatar_id":"","url":"https://api.github.com/users/yfarjoun","html_url":"https://github.com/yfarjoun","followers_url":"https://api.github.com/users/yfarjoun/followers","following_url":"https://api.github.com/users/yfarjoun/following{/other_user}","gists_url":"https://api.github.com/users/yfarjoun/gists{/gist_id}","starred_url":"https://api.github.com/users/yfarjoun/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/yfarjoun/subscriptions","organizations_url":"https://api.github.com/users/yfarjoun/orgs","repos_url":"https://api.github.com/users/yfarjoun/repos","events_url":"https://api.github.com/users/yfarjoun/events{/privacy}","received_events_url":"https://api.github.com/users/yfarjoun/received_events","type":"User","site_admin":false},"created_at":"2015-11-15T01:47:21Z","updated_at":"2015-11-15T01:47:21Z","body":"@mattsooknah and @nh13 I'd be honored if you take a look.\r\n\r\n@nh13 at this point I didn't change SamToFastq and vice-versa since I am not sure of the desired behavior, in particular regarding how to deal with more than one molecular bar-code per insert. I suggest that we address this issue in a few weeks/months when the use-cases will become more clear."}}