{"action":"created","issue":{"url":"https://api.github.com/repos/PacificBiosciences/SMRT-Link/issues/39","repository_url":"https://api.github.com/repos/PacificBiosciences/SMRT-Link","labels_url":"https://api.github.com/repos/PacificBiosciences/SMRT-Link/issues/39/labels{/name}","comments_url":"https://api.github.com/repos/PacificBiosciences/SMRT-Link/issues/39/comments","events_url":"https://api.github.com/repos/PacificBiosciences/SMRT-Link/issues/39/events","html_url":"https://github.com/PacificBiosciences/SMRT-Link/issues/39","id":172760731,"number":39,"title":"'bam2fastx --split-barcodes'  fails on command line v3.1.1","user":{"login":"jrharting","id":3595985,"avatar_url":"https://avatars.githubusercontent.com/u/3595985?v=3","gravatar_id":"","url":"https://api.github.com/users/jrharting","html_url":"https://github.com/jrharting","followers_url":"https://api.github.com/users/jrharting/followers","following_url":"https://api.github.com/users/jrharting/following{/other_user}","gists_url":"https://api.github.com/users/jrharting/gists{/gist_id}","starred_url":"https://api.github.com/users/jrharting/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jrharting/subscriptions","organizations_url":"https://api.github.com/users/jrharting/orgs","repos_url":"https://api.github.com/users/jrharting/repos","events_url":"https://api.github.com/users/jrharting/events{/privacy}","received_events_url":"https://api.github.com/users/jrharting/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/PacificBiosciences/SMRT-Link/labels/bug","name":"bug","color":"fc2929"},{"url":"https://api.github.com/repos/PacificBiosciences/SMRT-Link/labels/Known%20Issue","name":"Known Issue","color":"fbca04"},{"url":"https://api.github.com/repos/PacificBiosciences/SMRT-Link/labels/workaround","name":"workaround","color":"5319e7"}],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":{"url":"https://api.github.com/repos/PacificBiosciences/SMRT-Link/milestones/10","html_url":"https://github.com/PacificBiosciences/SMRT-Link/milestones/3.2.0","labels_url":"https://api.github.com/repos/PacificBiosciences/SMRT-Link/milestones/10/labels","id":1814524,"number":10,"title":"3.2.0","description":"","creator":{"login":"jkaralius","id":274860,"avatar_url":"https://avatars.githubusercontent.com/u/274860?v=3","gravatar_id":"","url":"https://api.github.com/users/jkaralius","html_url":"https://github.com/jkaralius","followers_url":"https://api.github.com/users/jkaralius/followers","following_url":"https://api.github.com/users/jkaralius/following{/other_user}","gists_url":"https://api.github.com/users/jkaralius/gists{/gist_id}","starred_url":"https://api.github.com/users/jkaralius/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jkaralius/subscriptions","organizations_url":"https://api.github.com/users/jkaralius/orgs","repos_url":"https://api.github.com/users/jkaralius/repos","events_url":"https://api.github.com/users/jkaralius/events{/privacy}","received_events_url":"https://api.github.com/users/jkaralius/received_events","type":"User","site_admin":false},"open_issues":3,"closed_issues":2,"state":"open","created_at":"2016-06-07T22:41:16Z","updated_at":"2016-09-30T19:20:12Z","due_on":null,"closed_at":null},"comments":16,"created_at":"2016-08-23T17:38:08Z","updated_at":"2016-10-17T19:30:08Z","closed_at":null,"body":"Demultiplexing bam files on the command line is not working due to a bug.  The bug does show up in smrtlink-beta running 3.1.1.  \r\n\r\n    $ readlink -f $(which bam2fastq)\r\n    /pbi/dept/secondary/builds/3.1.1/smrttools/fromsrc/linux/x86-64/libc-2.5/gcc-4.8.4/ubuntu-1404/182868/smrttools-fromsrc_3.1.1.182868.installdir/private/pacbio/bam2fastx/binwrap/bam2fastq\r\n    $ bam2fastq --split-barcodes -o testOut/b2fq test.bam\r\n    terminate called after throwing an instance of 'std::runtime_error'\r\n      what():  barcode tag (bc) was requested but is missing\r\n    Aborted (core dumped)\r\n\r\nA workaround is vailable via a python script using pbcore.\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/PacificBiosciences/SMRT-Link/issues/comments/254308534","html_url":"https://github.com/PacificBiosciences/SMRT-Link/issues/39#issuecomment-254308534","issue_url":"https://api.github.com/repos/PacificBiosciences/SMRT-Link/issues/39","id":254308534,"user":{"login":"jrharting","id":3595985,"avatar_url":"https://avatars.githubusercontent.com/u/3595985?v=3","gravatar_id":"","url":"https://api.github.com/users/jrharting","html_url":"https://github.com/jrharting","followers_url":"https://api.github.com/users/jrharting/followers","following_url":"https://api.github.com/users/jrharting/following{/other_user}","gists_url":"https://api.github.com/users/jrharting/gists{/gist_id}","starred_url":"https://api.github.com/users/jrharting/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jrharting/subscriptions","organizations_url":"https://api.github.com/users/jrharting/orgs","repos_url":"https://api.github.com/users/jrharting/repos","events_url":"https://api.github.com/users/jrharting/events{/privacy}","received_events_url":"https://api.github.com/users/jrharting/received_events","type":"User","site_admin":false},"created_at":"2016-10-17T19:30:08Z","updated_at":"2016-10-17T19:30:08Z","body":"@AfterRain You're welcome :).  The Arrow model is much improved over Quiver, and a lot of work by our statisticians has gone into improving it.  Additionally, it is easier to train, so that future improvements in terms of chemistry and other primary factors can be included in the model more easily.  Here is a link with some information:\r\nhttps://github.com/PacificBiosciences/GenomicConsensus/blob/master/doc/FAQ.rst\r\n Also here is more info about the overall PB consensus design   (some focus on CCS, but the model is essentially the same in LAA)\r\nhttps://github.com/PacificBiosciences/unanimity/blob/master/doc/PBCCS.md\r\n "}}
{"actor":{"display_login":"jrharting"}}