{"action":"created","issue":{"url":"https://api.github.com/repos/samtools/samtools/issues/374","labels_url":"https://api.github.com/repos/samtools/samtools/issues/374/labels{/name}","comments_url":"https://api.github.com/repos/samtools/samtools/issues/374/comments","events_url":"https://api.github.com/repos/samtools/samtools/issues/374/events","html_url":"https://github.com/samtools/samtools/issues/374","id":66243969,"number":374,"title":"samtools depth - output for zero-coverage positions","user":{"login":"tseemann","id":453972,"avatar_url":"https://avatars.githubusercontent.com/u/453972?v=3","gravatar_id":"","url":"https://api.github.com/users/tseemann","html_url":"https://github.com/tseemann","followers_url":"https://api.github.com/users/tseemann/followers","following_url":"https://api.github.com/users/tseemann/following{/other_user}","gists_url":"https://api.github.com/users/tseemann/gists{/gist_id}","starred_url":"https://api.github.com/users/tseemann/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/tseemann/subscriptions","organizations_url":"https://api.github.com/users/tseemann/orgs","repos_url":"https://api.github.com/users/tseemann/repos","events_url":"https://api.github.com/users/tseemann/events{/privacy}","received_events_url":"https://api.github.com/users/tseemann/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":{"login":"jkbonfield","id":2210525,"avatar_url":"https://avatars.githubusercontent.com/u/2210525?v=3","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},"milestone":null,"comments":4,"created_at":"2015-04-03T23:05:29Z","updated_at":"2016-01-08T18:29:57Z","closed_at":"2015-04-14T11:45:28Z","body":"The default behaviour for ```samtools depth``` seems to be to skip over positions that have zero depth in all the provided BAM files.\r\n\r\nWould you consider adding an option ```-a   output all positions``` to output _every_ position in every sequence even if it is zero?\r\n\r\nThis would make it much more straightforward for downstream streaming applications. Currently they need to have more complicated stateful parsers (to keep track of skipped locations) and also they need to the reference FASTA and .fai file to determine if any sequences (or bases at the end of a sequence) were missed."},"comment":{"url":"https://api.github.com/repos/samtools/samtools/issues/comments/170083302","html_url":"https://github.com/samtools/samtools/issues/374#issuecomment-170083302","issue_url":"https://api.github.com/repos/samtools/samtools/issues/374","id":170083302,"user":{"login":"johnmu","id":885356,"avatar_url":"https://avatars.githubusercontent.com/u/885356?v=3","gravatar_id":"","url":"https://api.github.com/users/johnmu","html_url":"https://github.com/johnmu","followers_url":"https://api.github.com/users/johnmu/followers","following_url":"https://api.github.com/users/johnmu/following{/other_user}","gists_url":"https://api.github.com/users/johnmu/gists{/gist_id}","starred_url":"https://api.github.com/users/johnmu/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/johnmu/subscriptions","organizations_url":"https://api.github.com/users/johnmu/orgs","repos_url":"https://api.github.com/users/johnmu/repos","events_url":"https://api.github.com/users/johnmu/events{/privacy}","received_events_url":"https://api.github.com/users/johnmu/received_events","type":"User","site_admin":false},"created_at":"2016-01-08T18:29:57Z","updated_at":"2016-01-08T18:29:57Z","body":"Should the -a option ignore N positions in the reference instead of just ignoring on the end? That is take a reference genome and ignore N positions in the genome when outputting depth. \r\n\r\nMaybe I am missing something, but it seems like -a will ignore the telomere regions in a chromosome but still output zeros in the centromere region or any internal unmappable regions. Is that right?"}}