{"action":"created","issue":{"url":"https://api.github.com/repos/bigdatagenomics/utils/issues/52","labels_url":"https://api.github.com/repos/bigdatagenomics/utils/issues/52/labels{/name}","comments_url":"https://api.github.com/repos/bigdatagenomics/utils/issues/52/comments","events_url":"https://api.github.com/repos/bigdatagenomics/utils/issues/52/events","html_url":"https://github.com/bigdatagenomics/utils/pull/52","id":101527754,"number":52,"title":"Remove help processing shortcut","user":{"login":"heuermh","id":35293,"avatar_url":"https://avatars.githubusercontent.com/u/35293?v=3","gravatar_id":"","url":"https://api.github.com/users/heuermh","html_url":"https://github.com/heuermh","followers_url":"https://api.github.com/users/heuermh/followers","following_url":"https://api.github.com/users/heuermh/following{/other_user}","gists_url":"https://api.github.com/users/heuermh/gists{/gist_id}","starred_url":"https://api.github.com/users/heuermh/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/heuermh/subscriptions","organizations_url":"https://api.github.com/users/heuermh/orgs","repos_url":"https://api.github.com/users/heuermh/repos","events_url":"https://api.github.com/users/heuermh/events{/privacy}","received_events_url":"https://api.github.com/users/heuermh/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"milestone":null,"comments":5,"created_at":"2015-08-17T23:02:36Z","updated_at":"2015-08-18T17:13:58Z","closed_at":"2015-08-18T17:13:58Z","pull_request":{"url":"https://api.github.com/repos/bigdatagenomics/utils/pulls/52","html_url":"https://github.com/bigdatagenomics/utils/pull/52","diff_url":"https://github.com/bigdatagenomics/utils/pull/52.diff","patch_url":"https://github.com/bigdatagenomics/utils/pull/52.patch"},"body":"Possible fix for https://github.com/bigdatagenomics/adam/issues/755\r\n\r\nThese cover the changed lines of code completely\r\n```bash\r\n$ ./bin/adam-submit\r\n15/08/17 17:56:13 INFO ADAMMain: ADAM invoked with args: \r\n\r\n     e            888~-_              e                 e    e\r\n    d8b           888   \\            d8b               d8b  d8b\r\n   /Y88b          888    |          /Y88b             d888bdY88b\r\n  /  Y88b         888    |         /  Y88b           / Y88Y Y888b\r\n /____Y88b        888   /         /____Y88b         /   YY   Y888b\r\n/      Y88b       888_-~         /      Y88b       /          Y888b\r\n\r\nUsage: adam-submit [<spark-args> --] <adam-args>\r\n...\r\n\r\n$ ./bin/adam-submit -h\r\n15/08/17 17:56:15 INFO ADAMMain: ADAM invoked with args: \"-h\"\r\n\r\n     e            888~-_              e                 e    e\r\n    d8b           888   \\            d8b               d8b  d8b\r\n   /Y88b          888    |          /Y88b             d888bdY88b\r\n  /  Y88b         888    |         /  Y88b           / Y88Y Y888b\r\n /____Y88b        888   /         /____Y88b         /   YY   Y888b\r\n/      Y88b       888_-~         /      Y88b       /          Y888b\r\n\r\nUsage: adam-submit [<spark-args> --] <adam-args>\r\n...\r\n\r\n$ ./bin/adam-submit depth \r\n15/08/17 17:57:52 INFO ADAMMain: ADAM invoked with args: \"depth\"\r\nArgument \"ADAM\" is required\r\n ADAM                                                            : The Read file to use to calculate depths\r\n VCF                                                             : The VCF containing the sites at which to calculate depths\r\n -cartesian                                                      : Use a cartesian join, then filter\r\n -h (-help, --help, -?)                                          : Print help\r\n -parquet_block_size N                                           : Parquet block size (default = 128mb)\r\n -parquet_compression_codec [UNCOMPRESSED | SNAPPY | GZIP | LZO] : Parquet compression codec\r\n -parquet_disable_dictionary                                     : Disable dictionary encoding\r\n -parquet_logging_level VAL                                      : Parquet logging level (default = severe)\r\n -parquet_page_size N                                            : Parquet page size (default = 1mb)\r\n -print_metrics                                                  : Print metrics to the log on completion\r\n\r\n$ ./bin/adam-submit depth -h\r\n15/08/17 17:57:55 INFO ADAMMain: ADAM invoked with args: \"depth\" \"-h\"\r\n ADAM                                                            : The Read file to use to calculate depths\r\n VCF                                                             : The VCF containing the sites at which to calculate depths\r\n -cartesian                                                      : Use a cartesian join, then filter\r\n -h (-help, --help, -?)                                          : Print help\r\n -parquet_block_size N                                           : Parquet block size (default = 128mb)\r\n -parquet_compression_codec [UNCOMPRESSED | SNAPPY | GZIP | LZO] : Parquet compression codec\r\n -parquet_disable_dictionary                                     : Disable dictionary encoding\r\n -parquet_logging_level VAL                                      : Parquet logging level (default = severe)\r\n -parquet_page_size N                                            : Parquet page size (default = 1mb)\r\n -print_metrics                                                  : Print metrics to the log on completion\r\n\r\n$ ./bin/adam-submit depth -cartesian -h\r\n15/08/17 17:58:01 INFO ADAMMain: ADAM invoked with args: \"depth\" \"-cartesian\" \"-h\"\r\n ADAM                                                            : The Read file to use to calculate depths\r\n VCF                                                             : The VCF containing the sites at which to calculate depths\r\n -cartesian                                                      : Use a cartesian join, then filter\r\n -h (-help, --help, -?)                                          : Print help\r\n -parquet_block_size N                                           : Parquet block size (default = 128mb)\r\n -parquet_compression_codec [UNCOMPRESSED | SNAPPY | GZIP | LZO] : Parquet compression codec\r\n -parquet_disable_dictionary                                     : Disable dictionary encoding\r\n -parquet_logging_level VAL                                      : Parquet logging level (default = severe)\r\n -parquet_page_size N                                            : Parquet page size (default = 1mb)\r\n -print_metrics                                                  : Print metrics to the log on completion\r\n\r\n$ ./bin/adam-submit wigfix2bed -h\r\n15/08/17 17:58:19 INFO ADAMMain: ADAM invoked with args: \"wigfix2bed\" \"-h\"\r\n -bed VAL               : Location to write BED data (leave out for stdout)\r\n -h (-help, --help, -?) : Print help\r\n -print_metrics         : Print metrics to the log on completion\r\n -wig VAL               : The wig file to convert (leave out for stdin)\r\n```\r\n\r\nI'm not a fan of ```ignoreCmdLineExceptions``` nor of boolean flags generally; please feel free to make other suggestions."},"comment":{"url":"https://api.github.com/repos/bigdatagenomics/utils/issues/comments/132283269","html_url":"https://github.com/bigdatagenomics/utils/pull/52#issuecomment-132283269","issue_url":"https://api.github.com/repos/bigdatagenomics/utils/issues/52","id":132283269,"user":{"login":"fnothaft","id":3752466,"avatar_url":"https://avatars.githubusercontent.com/u/3752466?v=3","gravatar_id":"","url":"https://api.github.com/users/fnothaft","html_url":"https://github.com/fnothaft","followers_url":"https://api.github.com/users/fnothaft/followers","following_url":"https://api.github.com/users/fnothaft/following{/other_user}","gists_url":"https://api.github.com/users/fnothaft/gists{/gist_id}","starred_url":"https://api.github.com/users/fnothaft/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/fnothaft/subscriptions","organizations_url":"https://api.github.com/users/fnothaft/orgs","repos_url":"https://api.github.com/users/fnothaft/repos","events_url":"https://api.github.com/users/fnothaft/events{/privacy}","received_events_url":"https://api.github.com/users/fnothaft/received_events","type":"User","site_admin":false},"created_at":"2015-08-18T17:13:58Z","updated_at":"2015-08-18T17:13:58Z","body":"Thanks @heuermh. Manually merged via https://github.com/bigdatagenomics/utils/commit/5f9290dc2036c24a1115d1536f6f2e042163d44d."}}