{"action":"created","issue":{"url":"https://api.github.com/repos/samtools/htslib/issues/306","labels_url":"https://api.github.com/repos/samtools/htslib/issues/306/labels{/name}","comments_url":"https://api.github.com/repos/samtools/htslib/issues/306/comments","events_url":"https://api.github.com/repos/samtools/htslib/issues/306/events","html_url":"https://github.com/samtools/htslib/issues/306","id":119657792,"number":306,"title":"samtools: mpileup -r <regionspec> includes wrong areas","user":{"login":"jblachly","id":5987153,"avatar_url":"https://avatars.githubusercontent.com/u/5987153?v=3","gravatar_id":"","url":"https://api.github.com/users/jblachly","html_url":"https://github.com/jblachly","followers_url":"https://api.github.com/users/jblachly/followers","following_url":"https://api.github.com/users/jblachly/following{/other_user}","gists_url":"https://api.github.com/users/jblachly/gists{/gist_id}","starred_url":"https://api.github.com/users/jblachly/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jblachly/subscriptions","organizations_url":"https://api.github.com/users/jblachly/orgs","repos_url":"https://api.github.com/users/jblachly/repos","events_url":"https://api.github.com/users/jblachly/events{/privacy}","received_events_url":"https://api.github.com/users/jblachly/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/samtools/htslib/labels/needs-feedback","name":"needs-feedback","color":"bfdadc"}],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":9,"created_at":"2015-12-01T07:13:29Z","updated_at":"2015-12-17T16:47:18Z","closed_at":null,"body":"`samtools mpileup -r chrA:nnn-mmm` includes region `chrA:nnn-mmm` correctly, but for some combinations of BAM files it also returns pileups from the same coordinates on other contigs, for example `chrF:nnn-mmm` and `chrQ:nnn-mmm`\r\n\r\nIt is not yet clear to me under what circumstances this behaviour is triggered. I have only experienced this when passing a list of bamfiles with `-b`, and notably when passing the following\r\n`-b <(head bamfiles.txt | tail -n [1..x])`\r\nto narrow down to a specific file that could trigger it, I triggered the behaviour at `tail -n 4`. However, passing the 4th bamfile ALONE does not trigger the error.\r\n\r\nI previously entered this as issue #305 but it was closed in error."},"comment":{"url":"https://api.github.com/repos/samtools/htslib/issues/comments/165506393","html_url":"https://github.com/samtools/htslib/issues/306#issuecomment-165506393","issue_url":"https://api.github.com/repos/samtools/htslib/issues/306","id":165506393,"user":{"login":"jblachly","id":5987153,"avatar_url":"https://avatars.githubusercontent.com/u/5987153?v=3","gravatar_id":"","url":"https://api.github.com/users/jblachly","html_url":"https://github.com/jblachly","followers_url":"https://api.github.com/users/jblachly/followers","following_url":"https://api.github.com/users/jblachly/following{/other_user}","gists_url":"https://api.github.com/users/jblachly/gists{/gist_id}","starred_url":"https://api.github.com/users/jblachly/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jblachly/subscriptions","organizations_url":"https://api.github.com/users/jblachly/orgs","repos_url":"https://api.github.com/users/jblachly/repos","events_url":"https://api.github.com/users/jblachly/events{/privacy}","received_events_url":"https://api.github.com/users/jblachly/received_events","type":"User","site_admin":false},"created_at":"2015-12-17T16:47:18Z","updated_at":"2015-12-17T16:47:18Z","body":"James - the \"older than\" warnings are just a byproduct of the way the files are downloaded from TCGA. The genetorrent software does not preserve timestamps; the index is often transferred mere seconds before the BAM file. Both are timestamped with creation time on the local system."}}