{"action":"created","issue":{"url":"https://api.github.com/repos/arq5x/bedtools2/issues/71","labels_url":"https://api.github.com/repos/arq5x/bedtools2/issues/71/labels{/name}","comments_url":"https://api.github.com/repos/arq5x/bedtools2/issues/71/comments","events_url":"https://api.github.com/repos/arq5x/bedtools2/issues/71/events","html_url":"https://github.com/arq5x/bedtools2/issues/71","id":32632465,"number":71,"title":"Question: bedtools genomecov -d output from bam files does not include chromosomes with not coverage","user":{"login":"bchapm5","id":5454129,"avatar_url":"https://avatars.githubusercontent.com/u/5454129?v=3","gravatar_id":"","url":"https://api.github.com/users/bchapm5","html_url":"https://github.com/bchapm5","followers_url":"https://api.github.com/users/bchapm5/followers","following_url":"https://api.github.com/users/bchapm5/following{/other_user}","gists_url":"https://api.github.com/users/bchapm5/gists{/gist_id}","starred_url":"https://api.github.com/users/bchapm5/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/bchapm5/subscriptions","organizations_url":"https://api.github.com/users/bchapm5/orgs","repos_url":"https://api.github.com/users/bchapm5/repos","events_url":"https://api.github.com/users/bchapm5/events{/privacy}","received_events_url":"https://api.github.com/users/bchapm5/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":6,"created_at":"2014-05-01T17:50:02Z","updated_at":"2015-05-06T00:42:05Z","closed_at":null,"body":"after creating a BAM file by aligning RNA sequence to a small file of coding sequences bedtools genomecov -d did not report sequences with zero coverage over the entire length.\r\n\r\nIs this a feature or a bug ?\r\n\r\n$samtools idxstats ARC10_.unique.bam > ARC10_.unique.idxstats # get output of idxstats\r\n$cat ARC10_.unique.idxstats | grep -v \"^\\*\" | wc -l # count the number of entries in idxstats\r\n233\r\n$cat ARC10_.unique.idxstats | cut -f3 | grep -v '^0' | wc -l # count the number of entries in idx stats without zero coverage\r\n158\r\n$./bedtools --versionbedtools v2.19.1-41-g656fd84 # show we are using current version of bedtoos\r\n$ ./bedtools genomecov -dz -ibam ARC10_.unique.bam > ARC10_.unique.depth # output all coverage of bedtools\r\n$ cat ARC10_.unique.depth | cut -f1 | uniq | wc -l # count the number of different sequences in bedtools\r\n158\r\n\r\nI hope to get small example fasta and SAM file together to better demonstrate I hope the above is understandable"},"comment":{"url":"https://api.github.com/repos/arq5x/bedtools2/issues/comments/99275882","html_url":"https://github.com/arq5x/bedtools2/issues/71#issuecomment-99275882","issue_url":"https://api.github.com/repos/arq5x/bedtools2/issues/71","id":99275882,"user":{"login":"arq5x","id":72291,"avatar_url":"https://avatars.githubusercontent.com/u/72291?v=3","gravatar_id":"","url":"https://api.github.com/users/arq5x","html_url":"https://github.com/arq5x","followers_url":"https://api.github.com/users/arq5x/followers","following_url":"https://api.github.com/users/arq5x/following{/other_user}","gists_url":"https://api.github.com/users/arq5x/gists{/gist_id}","starred_url":"https://api.github.com/users/arq5x/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/arq5x/subscriptions","organizations_url":"https://api.github.com/users/arq5x/orgs","repos_url":"https://api.github.com/users/arq5x/repos","events_url":"https://api.github.com/users/arq5x/events{/privacy}","received_events_url":"https://api.github.com/users/arq5x/received_events","type":"User","site_admin":false},"created_at":"2015-05-06T00:42:05Z","updated_at":"2015-05-06T00:42:05Z","body":"Sorry for the delayed response.  I have taken a look at the code and have a plan in mind for addressing this, but I just haven't had a free chunk of time to knock this out yet.  I apologize."}}