{"action":"closed","issue":{"url":"https://api.github.com/repos/hyattpd/gbproks/issues/1","labels_url":"https://api.github.com/repos/hyattpd/gbproks/issues/1/labels{/name}","comments_url":"https://api.github.com/repos/hyattpd/gbproks/issues/1/comments","events_url":"https://api.github.com/repos/hyattpd/gbproks/issues/1/events","html_url":"https://github.com/hyattpd/gbproks/issues/1","id":62351449,"number":1,"title":"command-line help text still states 'single'/'meta' for mode","user":{"login":"aleimba","id":6207266,"avatar_url":"https://avatars.githubusercontent.com/u/6207266?v=3","gravatar_id":"","url":"https://api.github.com/users/aleimba","html_url":"https://github.com/aleimba","followers_url":"https://api.github.com/users/aleimba/followers","following_url":"https://api.github.com/users/aleimba/following{/other_user}","gists_url":"https://api.github.com/users/aleimba/gists{/gist_id}","starred_url":"https://api.github.com/users/aleimba/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/aleimba/subscriptions","organizations_url":"https://api.github.com/users/aleimba/orgs","repos_url":"https://api.github.com/users/aleimba/repos","events_url":"https://api.github.com/users/aleimba/events{/privacy}","received_events_url":"https://api.github.com/users/aleimba/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"milestone":null,"comments":1,"created_at":"2015-03-17T10:02:31Z","updated_at":"2015-03-17T10:03:28Z","closed_at":"2015-03-17T10:03:28Z","body":"The Prodigal help text needs to be updated to include the newly named 'normal' and 'anon' modes.\r\n```bash\r\n$ prodigal -v\r\nProdigal V2.6.2: January, 2015\r\n```\r\n```\r\n$ prodigal -h\r\nUsage:  prodigal [-a trans_file] [-c] [-d nuc_file] [-f output_type]\r\n                 [-g tr_table] [-h] [-i input_file] [-m] [-n] [-o output_file]\r\n                 [-p mode] [-q] [-s start_file] [-t training_file] [-v]\r\n\r\n         -a:  Write protein translations to the selected file.\r\n         -c:  Closed ends.  Do not allow genes to run off edges.\r\n         -d:  Write nucleotide sequences of genes to the selected file.\r\n         -f:  Select output format (gbk, gff, or sco).  Default is gbk.\r\n         -g:  Specify a translation table to use (default 11).\r\n         -h:  Print help menu and exit.\r\n         -i:  Specify input file (default reads from stdin).\r\n         -m:  Treat runs of n's as masked sequence and do not build genes across \r\n              them.\r\n         -n:  Bypass the Shine-Dalgarno trainer and force the program to scan\r\n              for motifs.\r\n         -o:  Specify output file (default writes to stdout).\r\n         -p:  Select procedure (single or meta).  Default is single.\r\n         -q:  Run quietly (suppress normal stderr output).\r\n         -s:  Write all potential genes (with scores) to the selected file.\r\n         -t:  Write a training file (if none exists); otherwise, read and use\r\n              the specified training file.\r\n         -v:  Print version number and exit.\r\n```"}}