{"action":"closed","issue":{"url":"https://api.github.com/repos/broadinstitute/hellbender/issues/273","labels_url":"https://api.github.com/repos/broadinstitute/hellbender/issues/273/labels{/name}","comments_url":"https://api.github.com/repos/broadinstitute/hellbender/issues/273/comments","events_url":"https://api.github.com/repos/broadinstitute/hellbender/issues/273/events","html_url":"https://github.com/broadinstitute/hellbender/issues/273","id":60397455,"number":273,"title":"NPE in CreateSequenceDictionary if the user does not indicate a reference.","user":{"login":"vruano","id":791104,"avatar_url":"https://avatars.githubusercontent.com/u/791104?v=3","gravatar_id":"","url":"https://api.github.com/users/vruano","html_url":"https://github.com/vruano","followers_url":"https://api.github.com/users/vruano/followers","following_url":"https://api.github.com/users/vruano/following{/other_user}","gists_url":"https://api.github.com/users/vruano/gists{/gist_id}","starred_url":"https://api.github.com/users/vruano/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/vruano/subscriptions","organizations_url":"https://api.github.com/users/vruano/orgs","repos_url":"https://api.github.com/users/vruano/repos","events_url":"https://api.github.com/users/vruano/events{/privacy}","received_events_url":"https://api.github.com/users/vruano/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/broadinstitute/hellbender/labels/bug","name":"bug","color":"fc2929"},{"url":"https://api.github.com/repos/broadinstitute/hellbender/labels/Help%20Wanted%20(Community)","name":"Help Wanted (Community)","color":"159818"},{"url":"https://api.github.com/repos/broadinstitute/hellbender/labels/Picard","name":"Picard","color":"207de5"},{"url":"https://api.github.com/repos/broadinstitute/hellbender/labels/PRIORITY_HIGH","name":"PRIORITY_HIGH","color":"e11d21"}],"state":"closed","locked":false,"assignee":{"login":"edwardkw","id":10030435,"avatar_url":"https://avatars.githubusercontent.com/u/10030435?v=3","gravatar_id":"","url":"https://api.github.com/users/edwardkw","html_url":"https://github.com/edwardkw","followers_url":"https://api.github.com/users/edwardkw/followers","following_url":"https://api.github.com/users/edwardkw/following{/other_user}","gists_url":"https://api.github.com/users/edwardkw/gists{/gist_id}","starred_url":"https://api.github.com/users/edwardkw/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/edwardkw/subscriptions","organizations_url":"https://api.github.com/users/edwardkw/orgs","repos_url":"https://api.github.com/users/edwardkw/repos","events_url":"https://api.github.com/users/edwardkw/events{/privacy}","received_events_url":"https://api.github.com/users/edwardkw/received_events","type":"User","site_admin":false},"milestone":null,"comments":2,"created_at":"2015-03-09T19:35:59Z","updated_at":"2015-06-30T14:04:13Z","closed_at":"2015-06-30T14:04:13Z","body":"If you don't indicate the reference file with --REFERENCE a NPE is thrown.\r\n\r\nExample:\r\n\r\n$     java -jar ./build/libs/hellbender-all-1.0.jar CreateSequenceDictionary -OUTPUT=/tmp/1.dict\r\n\r\nException in thread \"main\" java.lang.NullPointerException\r\n\tat org.broadinstitute.hellbender.tools.picard.sam.CreateSequenceDictionary.customCommandLineValidation(CreateSequenceDictionary.java:54)\r\n\tat org.broadinstitute.hellbender.cmdline.CommandLineProgram.parseArgs(CommandLineProgram.java:206)\r\n\tat org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:124)\r\n\tat org.broadinstitute.hellbender.cmdline.PicardCommandLineProgram.instanceMain(PicardCommandLineProgram.java:51)\r\n\tat org.broadinstitute.hellbender.Main.instanceMain(Main.java:102)\r\n\tat org.broadinstitute.hellbender.Main.main(Main.java:117)"}}