{"action":"created","issue":{"url":"https://api.github.com/repos/PacificBiosciences/blasr/issues/245","repository_url":"https://api.github.com/repos/PacificBiosciences/blasr","labels_url":"https://api.github.com/repos/PacificBiosciences/blasr/issues/245/labels{/name}","comments_url":"https://api.github.com/repos/PacificBiosciences/blasr/issues/245/comments","events_url":"https://api.github.com/repos/PacificBiosciences/blasr/issues/245/events","html_url":"https://github.com/PacificBiosciences/blasr/issues/245","id":158052061,"number":245,"title":"Issue with --bam option","user":{"login":"gk7279","id":19700859,"avatar_url":"https://avatars.githubusercontent.com/u/19700859?v=3","gravatar_id":"","url":"https://api.github.com/users/gk7279","html_url":"https://github.com/gk7279","followers_url":"https://api.github.com/users/gk7279/followers","following_url":"https://api.github.com/users/gk7279/following{/other_user}","gists_url":"https://api.github.com/users/gk7279/gists{/gist_id}","starred_url":"https://api.github.com/users/gk7279/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/gk7279/subscriptions","organizations_url":"https://api.github.com/users/gk7279/orgs","repos_url":"https://api.github.com/users/gk7279/repos","events_url":"https://api.github.com/users/gk7279/events{/privacy}","received_events_url":"https://api.github.com/users/gk7279/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":23,"created_at":"2016-06-02T03:24:59Z","updated_at":"2016-06-03T20:59:43Z","closed_at":null,"body":"Hi \r\n\r\nWhen I try to run this command below, it gives me an error saying not a valid option\r\n\r\n/path/to/blasr /path/tomy/rawdata/sample.bas.h5 /refs/rat/rn6.fa  --out /output/dir/rat_alignments.bam --nproc 16 --bam\r\n\r\nFor some reasons, it is not reading the dashes before the bam properly. If I specify ---bam, it calls it --bam. If I do --bam, it calls it -bam. It is missing one dash.\r\n\r\nThanks"},"comment":{"url":"https://api.github.com/repos/PacificBiosciences/blasr/issues/comments/223693154","html_url":"https://github.com/PacificBiosciences/blasr/issues/245#issuecomment-223693154","issue_url":"https://api.github.com/repos/PacificBiosciences/blasr/issues/245","id":223693154,"user":{"login":"mhsieh","id":7217130,"avatar_url":"https://avatars.githubusercontent.com/u/7217130?v=3","gravatar_id":"","url":"https://api.github.com/users/mhsieh","html_url":"https://github.com/mhsieh","followers_url":"https://api.github.com/users/mhsieh/followers","following_url":"https://api.github.com/users/mhsieh/following{/other_user}","gists_url":"https://api.github.com/users/mhsieh/gists{/gist_id}","starred_url":"https://api.github.com/users/mhsieh/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mhsieh/subscriptions","organizations_url":"https://api.github.com/users/mhsieh/orgs","repos_url":"https://api.github.com/users/mhsieh/repos","events_url":"https://api.github.com/users/mhsieh/events{/privacy}","received_events_url":"https://api.github.com/users/mhsieh/received_events","type":"User","site_admin":false},"created_at":"2016-06-03T20:59:43Z","updated_at":"2016-06-03T20:59:43Z","body":"Hi, do you have the metadata.xml file?"}}
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