{"action":"created","issue":{"url":"https://api.github.com/repos/samtools/samtools/issues/619","repository_url":"https://api.github.com/repos/samtools/samtools","labels_url":"https://api.github.com/repos/samtools/samtools/issues/619/labels{/name}","comments_url":"https://api.github.com/repos/samtools/samtools/issues/619/comments","events_url":"https://api.github.com/repos/samtools/samtools/issues/619/events","html_url":"https://github.com/samtools/samtools/issues/619","id":184529636,"node_id":"MDU6SXNzdWUxODQ1Mjk2MzY=","number":619,"title":"samtools mpileup gives inconsistent results with different depth limits","user":{"login":"rvalieris","id":6310472,"node_id":"MDQ6VXNlcjYzMTA0NzI=","avatar_url":"https://avatars3.githubusercontent.com/u/6310472?v=4","gravatar_id":"","url":"https://api.github.com/users/rvalieris","html_url":"https://github.com/rvalieris","followers_url":"https://api.github.com/users/rvalieris/followers","following_url":"https://api.github.com/users/rvalieris/following{/other_user}","gists_url":"https://api.github.com/users/rvalieris/gists{/gist_id}","starred_url":"https://api.github.com/users/rvalieris/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/rvalieris/subscriptions","organizations_url":"https://api.github.com/users/rvalieris/orgs","repos_url":"https://api.github.com/users/rvalieris/repos","events_url":"https://api.github.com/users/rvalieris/events{/privacy}","received_events_url":"https://api.github.com/users/rvalieris/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":4,"created_at":"2016-10-21T16:54:47Z","updated_at":"2018-08-31T14:17:11Z","closed_at":null,"author_association":"NONE","body":"It seems mpileup gives inconsistent results when the bam has too much coverage (more than the default depth limit), see this example:\r\n\r\n```\r\n$ samtools --version\r\nsamtools 1.3.1\r\nUsing htslib 1.3.1\r\n\r\n$ samtools mpileup a.bam -l a.pos -d1000000 -f hg19.fasta| cut -f1-4\r\n[mpileup] 1 samples in 1 input files\r\nchr12   49424640        G       23900\r\nchr12   49424671        G       15642\r\nchr12   49424672        T       15477\r\nchr12   49424673        C       15712\r\nchr12   49424674        A       15340\r\n\r\n$ samtools mpileup a.bam -l a.pos -f hg19.fasta| cut -f1-4\r\n[mpileup] 1 samples in 1 input files\r\n<mpileup> Set max per-file depth to 8000\r\nchr12   49424640        G       8009\r\nchr12   49424671        G       9\r\nchr12   49424672        T       9\r\nchr12   49424673        C       9\r\nchr12   49424674        A       9\r\n```\r\n\r\nThe problem is on the second call, I would have expected that all positions would have at least 8000 reads.\r\n\r\nI uploaded this example bam here: https://drive.google.com/open?id=0B6BiieozRPi9ZzluMDJHbWNjV2M\r\n"},"comment":{"url":"https://api.github.com/repos/samtools/samtools/issues/comments/417678245","html_url":"https://github.com/samtools/samtools/issues/619#issuecomment-417678245","issue_url":"https://api.github.com/repos/samtools/samtools/issues/619","id":417678245,"node_id":"MDEyOklzc3VlQ29tbWVudDQxNzY3ODI0NQ==","user":{"login":"jkbonfield","id":2210525,"node_id":"MDQ6VXNlcjIyMTA1MjU=","avatar_url":"https://avatars0.githubusercontent.com/u/2210525?v=4","gravatar_id":"","url":"https://api.github.com/users/jkbonfield","html_url":"https://github.com/jkbonfield","followers_url":"https://api.github.com/users/jkbonfield/followers","following_url":"https://api.github.com/users/jkbonfield/following{/other_user}","gists_url":"https://api.github.com/users/jkbonfield/gists{/gist_id}","starred_url":"https://api.github.com/users/jkbonfield/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jkbonfield/subscriptions","organizations_url":"https://api.github.com/users/jkbonfield/orgs","repos_url":"https://api.github.com/users/jkbonfield/repos","events_url":"https://api.github.com/users/jkbonfield/events{/privacy}","received_events_url":"https://api.github.com/users/jkbonfield/received_events","type":"User","site_admin":false},"created_at":"2018-08-31T14:17:11Z","updated_at":"2018-08-31T14:17:11Z","author_association":"CONTRIBUTOR","body":"This latter error message is reported by something else as \"Pileup::setn()\" is not our code.  \r\nIt appears to be claiming that you had no data in one pileup line.  Can you save the pileup and try some binary searching to figure out which line is actually responsible?\r\n\r\nIf I recall there are cases where mpileup can produce zero depth regions legitimately, but I believe it normally has \"*\" shown in the sequence column.  Eg covered by one read, but some bases in that read have quality too low.\r\n\r\nNote this isn't the original bug either, which is something different."}}
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