{"action":"created","issue":{"url":"https://api.github.com/repos/rdemolgen/SavvySuite/issues/3","repository_url":"https://api.github.com/repos/rdemolgen/SavvySuite","labels_url":"https://api.github.com/repos/rdemolgen/SavvySuite/issues/3/labels{/name}","comments_url":"https://api.github.com/repos/rdemolgen/SavvySuite/issues/3/comments","events_url":"https://api.github.com/repos/rdemolgen/SavvySuite/issues/3/events","html_url":"https://github.com/rdemolgen/SavvySuite/issues/3","id":271548207,"number":3,"title":"Exception when MAPQ unmapped read != 0","user":{"login":"ryanlayer","id":607057,"avatar_url":"https://avatars2.githubusercontent.com/u/607057?v=4","gravatar_id":"","url":"https://api.github.com/users/ryanlayer","html_url":"https://github.com/ryanlayer","followers_url":"https://api.github.com/users/ryanlayer/followers","following_url":"https://api.github.com/users/ryanlayer/following{/other_user}","gists_url":"https://api.github.com/users/ryanlayer/gists{/gist_id}","starred_url":"https://api.github.com/users/ryanlayer/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ryanlayer/subscriptions","organizations_url":"https://api.github.com/users/ryanlayer/orgs","repos_url":"https://api.github.com/users/ryanlayer/repos","events_url":"https://api.github.com/users/ryanlayer/events{/privacy}","received_events_url":"https://api.github.com/users/ryanlayer/received_events","type":"User","site_admin":false},"labels":[{"id":712469778,"url":"https://api.github.com/repos/rdemolgen/SavvySuite/labels/enhancement","name":"enhancement","color":"84b6eb","default":true}],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":1,"created_at":"2017-11-06T17:01:54Z","updated_at":"2017-11-07T20:36:35Z","closed_at":"2017-11-07T11:53:32Z","author_association":"NONE","body":"While this should be true, in the set of bams I have it is not. Can you catch this exception so that I do not have to fix the bams?\r\n\r\nThanks! \r\n\r\nException in thread \"main\" htsjdk.samtools.SAMFormatException: SAM validation error: ERROR: Record 52890647, Read name JDQNNM1:113:D0VJBACXX:1:1311:14032:7891, MAPQ should be 0 for unmapped read.\r\n        at htsjdk.samtools.SAMUtils.processValidationErrors(SAMUtils.java:451)\r\n        at htsjdk.samtools.BAMFileReader$BAMFileIterator.advance(BAMFileReader.java:812)\r\n        at htsjdk.samtools.BAMFileReader$BAMFileIterator.next(BAMFileReader.java:797)\r\n        at htsjdk.samtools.BAMFileReader$BAMFileIterator.next(BAMFileReader.java:765)\r\n        at htsjdk.samtools.SamReader$AssertingIterator.next(SamReader.java:576)\r\n        at htsjdk.samtools.SamReader$AssertingIterator.next(SamReader.java:548)\r\n        at CoverageBinner.main(CoverageBinner.java:25)\r\n"},"comment":{"url":"https://api.github.com/repos/rdemolgen/SavvySuite/issues/comments/342614089","html_url":"https://github.com/rdemolgen/SavvySuite/issues/3#issuecomment-342614089","issue_url":"https://api.github.com/repos/rdemolgen/SavvySuite/issues/3","id":342614089,"user":{"login":"ryanlayer","id":607057,"avatar_url":"https://avatars2.githubusercontent.com/u/607057?v=4","gravatar_id":"","url":"https://api.github.com/users/ryanlayer","html_url":"https://github.com/ryanlayer","followers_url":"https://api.github.com/users/ryanlayer/followers","following_url":"https://api.github.com/users/ryanlayer/following{/other_user}","gists_url":"https://api.github.com/users/ryanlayer/gists{/gist_id}","starred_url":"https://api.github.com/users/ryanlayer/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ryanlayer/subscriptions","organizations_url":"https://api.github.com/users/ryanlayer/orgs","repos_url":"https://api.github.com/users/ryanlayer/repos","events_url":"https://api.github.com/users/ryanlayer/events{/privacy}","received_events_url":"https://api.github.com/users/ryanlayer/received_events","type":"User","site_admin":false},"created_at":"2017-11-07T20:36:35Z","updated_at":"2017-11-07T20:36:35Z","author_association":"NONE","body":"Ignoring SAM validation error: ERROR: Record 15390807, Read name JDQNNM1:123:D1HCGACXX:5:1209:6625:68819, MAPQ should be 0 for unmapped read.\r\n\r\nLooks great. Thanks"}}
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