{"action":"opened","issue":{"url":"https://api.github.com/repos/yarden/MISO/issues/129","repository_url":"https://api.github.com/repos/yarden/MISO","labels_url":"https://api.github.com/repos/yarden/MISO/issues/129/labels{/name}","comments_url":"https://api.github.com/repos/yarden/MISO/issues/129/comments","events_url":"https://api.github.com/repos/yarden/MISO/issues/129/events","html_url":"https://github.com/yarden/MISO/issues/129","id":391469038,"node_id":"MDU6SXNzdWUzOTE0NjkwMzg=","number":129,"title":"sam_utils.py problem","user":{"login":"obenno","id":6121668,"node_id":"MDQ6VXNlcjYxMjE2Njg=","avatar_url":"https://avatars0.githubusercontent.com/u/6121668?v=4","gravatar_id":"","url":"https://api.github.com/users/obenno","html_url":"https://github.com/obenno","followers_url":"https://api.github.com/users/obenno/followers","following_url":"https://api.github.com/users/obenno/following{/other_user}","gists_url":"https://api.github.com/users/obenno/gists{/gist_id}","starred_url":"https://api.github.com/users/obenno/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/obenno/subscriptions","organizations_url":"https://api.github.com/users/obenno/orgs","repos_url":"https://api.github.com/users/obenno/repos","events_url":"https://api.github.com/users/obenno/events{/privacy}","received_events_url":"https://api.github.com/users/obenno/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2018-12-16T13:46:12Z","updated_at":"2018-12-16T13:46:12Z","closed_at":null,"author_association":"NONE","body":"Hi,\r\n\r\nThanks for the amazing tool. \r\nI found a little problem in misopy/sam_utils.py.\r\nhttps://github.com/yarden/MISO/blob/1ca049faa6f122751db25e8be49f04a695260557/misopy/sam_utils.py#L254\r\n\r\nIf the input bam includes secondary alignment (which is default for many mapping tools), the `len(read)` will has a value larger than 2, yet they were not unpaired, might be properly paired. In the subsequent code they will be discarded, despite whether their first alignment is good.\r\n\r\nhttps://github.com/yarden/MISO/blob/1ca049faa6f122751db25e8be49f04a695260557/misopy/sam_utils.py#L281\r\nIt seems that should be `%(len(to_delete)-num_unpaired)`\r\n\r\nCould you please make the function compatible to bam with secondary alignment or state that secondary alignment should be removed in MISO documentation? Thanks.\r\n\r\nRegards,\r\nobenno"}}
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