{"action":"created","issue":{"url":"https://api.github.com/repos/jwalabroad/VariantBam/issues/4","labels_url":"https://api.github.com/repos/jwalabroad/VariantBam/issues/4/labels{/name}","comments_url":"https://api.github.com/repos/jwalabroad/VariantBam/issues/4/comments","events_url":"https://api.github.com/repos/jwalabroad/VariantBam/issues/4/events","html_url":"https://github.com/jwalabroad/VariantBam/issues/4","id":124366686,"number":4,"title":"Referring to target sequences","user":{"login":"maplesond","id":3940628,"avatar_url":"https://avatars.githubusercontent.com/u/3940628?v=3","gravatar_id":"","url":"https://api.github.com/users/maplesond","html_url":"https://github.com/maplesond","followers_url":"https://api.github.com/users/maplesond/followers","following_url":"https://api.github.com/users/maplesond/following{/other_user}","gists_url":"https://api.github.com/users/maplesond/gists{/gist_id}","starred_url":"https://api.github.com/users/maplesond/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/maplesond/subscriptions","organizations_url":"https://api.github.com/users/maplesond/orgs","repos_url":"https://api.github.com/users/maplesond/repos","events_url":"https://api.github.com/users/maplesond/events{/privacy}","received_events_url":"https://api.github.com/users/maplesond/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":1,"created_at":"2015-12-30T16:08:13Z","updated_at":"2016-01-02T23:32:48Z","closed_at":null,"body":"In the quickstart guide it suggests putting in a user BAM and isolating a region with -g 1:100,000,000-100,001,000.  For some BAMs the target sequence name contains long complex strings, which can still work but require that they are wrapped in quotes: e.g: \"variant bowtie2.sorted.bam -g 'gi|253972022|gb|CP000819.1|':1-1000000 -r mapq[20,30] -c counts.tsv -o mini.bam -v\".  This should be made clear in the quickstart guide and in the general documentation.  For the quickstart guide you would work around this by providing a real (small) BAM file in your examples directory.\r\n\r\nAlso it would be nice if we could use the reference id, as well as the reference name to refer to a reference sequence, although care would need to be taken to avoid conflicts in the case where reference names are numeric."},"comment":{"url":"https://api.github.com/repos/jwalabroad/VariantBam/issues/comments/168438518","html_url":"https://github.com/jwalabroad/VariantBam/issues/4#issuecomment-168438518","issue_url":"https://api.github.com/repos/jwalabroad/VariantBam/issues/4","id":168438518,"user":{"login":"jwalabroad","id":6922120,"avatar_url":"https://avatars.githubusercontent.com/u/6922120?v=3","gravatar_id":"","url":"https://api.github.com/users/jwalabroad","html_url":"https://github.com/jwalabroad","followers_url":"https://api.github.com/users/jwalabroad/followers","following_url":"https://api.github.com/users/jwalabroad/following{/other_user}","gists_url":"https://api.github.com/users/jwalabroad/gists{/gist_id}","starred_url":"https://api.github.com/users/jwalabroad/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jwalabroad/subscriptions","organizations_url":"https://api.github.com/users/jwalabroad/orgs","repos_url":"https://api.github.com/users/jwalabroad/repos","events_url":"https://api.github.com/users/jwalabroad/events{/privacy}","received_events_url":"https://api.github.com/users/jwalabroad/received_events","type":"User","site_admin":false},"created_at":"2016-01-02T23:32:48Z","updated_at":"2016-01-02T23:32:48Z","body":"Thanks Daniel, good suggestions on all accounts. I'm modifying the documentation as suggested and adding a small example BAM (with non-protected data). Thanks for a careful look at the docs.\r\n-Jeremiah"}}