{"action":"created","issue":{"url":"https://api.github.com/repos/pysam-developers/pysam/issues/567","repository_url":"https://api.github.com/repos/pysam-developers/pysam","labels_url":"https://api.github.com/repos/pysam-developers/pysam/issues/567/labels{/name}","comments_url":"https://api.github.com/repos/pysam-developers/pysam/issues/567/comments","events_url":"https://api.github.com/repos/pysam-developers/pysam/issues/567/events","html_url":"https://github.com/pysam-developers/pysam/issues/567","id":272399837,"number":567,"title":"0.13 release - CRAM iteration throws OSError: truncated file","user":{"login":"egafni","id":798987,"avatar_url":"https://avatars2.githubusercontent.com/u/798987?v=4","gravatar_id":"","url":"https://api.github.com/users/egafni","html_url":"https://github.com/egafni","followers_url":"https://api.github.com/users/egafni/followers","following_url":"https://api.github.com/users/egafni/following{/other_user}","gists_url":"https://api.github.com/users/egafni/gists{/gist_id}","starred_url":"https://api.github.com/users/egafni/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/egafni/subscriptions","organizations_url":"https://api.github.com/users/egafni/orgs","repos_url":"https://api.github.com/users/egafni/repos","events_url":"https://api.github.com/users/egafni/events{/privacy}","received_events_url":"https://api.github.com/users/egafni/received_events","type":"User","site_admin":false},"labels":[{"id":773245168,"url":"https://api.github.com/repos/pysam-developers/pysam/labels/SAM/BAM/CRAM","name":"SAM/BAM/CRAM","color":"26b58a","default":false},{"id":753604387,"url":"https://api.github.com/repos/pysam-developers/pysam/labels/upstream","name":"upstream","color":"b60205","default":false}],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":11,"created_at":"2017-11-09T00:32:42Z","updated_at":"2018-02-07T20:43:19Z","closed_at":"2018-02-07T20:43:19Z","author_association":"NONE","body":"Bam works fine using python 0.12.1 but the following fetch generates an error:\r\n\r\nbam = pysam.AlignmentFile ('align.cram')\r\nlen(list(bam.fetch('chr8', 145100000, 145138636)))\r\n  File \"pysam/libcalignmentfile.pyx\", line 1752, in pysam.libcalignmentfile.IteratorRowRegion.__next__\r\nOSError: truncated file\r\n\r\niterating over the file is fine, and most regions are fine, but this one is broken"},"comment":{"url":"https://api.github.com/repos/pysam-developers/pysam/issues/comments/363904098","html_url":"https://github.com/pysam-developers/pysam/issues/567#issuecomment-363904098","issue_url":"https://api.github.com/repos/pysam-developers/pysam/issues/567","id":363904098,"user":{"login":"AndreasHeger","id":4426336,"avatar_url":"https://avatars1.githubusercontent.com/u/4426336?v=4","gravatar_id":"","url":"https://api.github.com/users/AndreasHeger","html_url":"https://github.com/AndreasHeger","followers_url":"https://api.github.com/users/AndreasHeger/followers","following_url":"https://api.github.com/users/AndreasHeger/following{/other_user}","gists_url":"https://api.github.com/users/AndreasHeger/gists{/gist_id}","starred_url":"https://api.github.com/users/AndreasHeger/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/AndreasHeger/subscriptions","organizations_url":"https://api.github.com/users/AndreasHeger/orgs","repos_url":"https://api.github.com/users/AndreasHeger/repos","events_url":"https://api.github.com/users/AndreasHeger/events{/privacy}","received_events_url":"https://api.github.com/users/AndreasHeger/received_events","type":"User","site_admin":false},"created_at":"2018-02-07T20:43:19Z","updated_at":"2018-02-07T20:43:19Z","author_association":"CONTRIBUTOR","body":"Thanks all, the example is now working on the master branch after the upgrade to htslib 1.7.\r\nClosing this issue."}}
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