{"action":"closed","issue":{"url":"https://api.github.com/repos/gt1/biobambam2/issues/34","repository_url":"https://api.github.com/repos/gt1/biobambam2","labels_url":"https://api.github.com/repos/gt1/biobambam2/issues/34/labels{/name}","comments_url":"https://api.github.com/repos/gt1/biobambam2/issues/34/comments","events_url":"https://api.github.com/repos/gt1/biobambam2/issues/34/events","html_url":"https://github.com/gt1/biobambam2/issues/34","id":186327170,"number":34,"title":"Empty MC:Z tags from bamsormadup in 2.0.57","user":{"login":"chapmanb","id":39391,"avatar_url":"https://avatars.githubusercontent.com/u/39391?v=3","gravatar_id":"","url":"https://api.github.com/users/chapmanb","html_url":"https://github.com/chapmanb","followers_url":"https://api.github.com/users/chapmanb/followers","following_url":"https://api.github.com/users/chapmanb/following{/other_user}","gists_url":"https://api.github.com/users/chapmanb/gists{/gist_id}","starred_url":"https://api.github.com/users/chapmanb/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/chapmanb/subscriptions","organizations_url":"https://api.github.com/users/chapmanb/orgs","repos_url":"https://api.github.com/users/chapmanb/repos","events_url":"https://api.github.com/users/chapmanb/events{/privacy}","received_events_url":"https://api.github.com/users/chapmanb/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":2,"created_at":"2016-10-31T16:16:39Z","updated_at":"2016-11-01T14:49:14Z","closed_at":"2016-11-01T14:49:14Z","body":"German;\r\nI'm running into the same issue as reported in #24 in the latest release and will get empty MC:Z tags from bamsormadup:\r\n```\r\nHWI-EAS264:7:101:6410:6415#0    121     chrM    389     60      76M     =       389     0       CAGATTTCAAATTTTATCTTTTGGCGGTATGCACTTTTAACAGTCACCCCCCAACTAACACATTATTTTCCCCTCC    BA?BABDBBDDBBBBDADCDDCDCBDCCCCCDCCCDDCCDCCC@@BCCCCCCCCCCCCCDCB@CCCCC@BCCCCCC    NM:i:1  MD:Z:21A54      AS:i:71 XS:i:0  RG:Z:Test1      ms:i:179        mc:i:388        MC:Z:\r\nHWI-EAS264:7:101:6410:6415#0    181     chrM    389     0       *       =       389     0       GTTGGGGTTTTTGTTTTTGGGGGTTGGGAGGGGTGGGGTTAAGGGGTTGGGGCAGGAGGGGGGGGGGGGGGGGGGG    ######################################################################A=A==@    AS:i:0  XS:i:0  RG:Z:Test1      MQ:i:60 ms:i:2563       mc:i:464\r\n```\r\nI put together a small test case that demonstrates the problem:\r\n```\r\nwget http://s3.amazonaws.com/chapmanb/testcases/biobambam_empty_mc.tar.gz\r\n```\r\nThanks so much for the help and let me know if I can provide any other information."}}
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