{"action":"created","comment":{"url":"https://api.github.com/repos/BD2KGenomics/toil-scripts/pulls/comments/57346105","id":57346105,"diff_hunk":"@@ -298,10 +313,12 @@ def parse_config(job, shared_ids, input_args):\n \n     with open(config, 'r') as f_in:\n         for line in f_in:\n-            line = line.strip().split(',')\n-            uuid = line[0]\n-            urls = line[1:]\n-            samples.append((uuid, urls))\n+            if line.strip():\n+                line = line.strip().split(',')\n+                assert len(line) == 3, 'Improper formatting'","path":"src/toil_scripts/batch_alignment/bwa_alignment.py","position":43,"original_position":43,"commit_id":"1759293fbf08d2d4489a6ef18c82d83224166eba","original_commit_id":"1759293fbf08d2d4489a6ef18c82d83224166eba","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},"body":"@hannes-ucsc and I argued a bit about this a while ago, but I prefer raising named exceptions when validating user input (e.g., if a user provides bad arguments, throw a `IllegalArgumentException` as a Java equivalent) and asserts for checking program invariants (i.e., if the assert failed, there is a bug in the code somewhere, not bad user input).\r\n\r\nAlso, I'd prefer a more detailed error message, e.g., `Improper formatting. Expected 3 fields, 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pipeline\r\ns3://cgl-driver-projects/test/variants/DTB-005.tar.gz","created_at":"2016-03-24T16:32:47Z","updated_at":"2016-03-24T16:36:31Z","closed_at":null,"merged_at":null,"merge_commit_sha":"c36b1e0819b610cef9914bfe08df94bac5be72a8","assignee":null,"milestone":null,"commits_url":"https://api.github.com/repos/BD2KGenomics/toil-scripts/pulls/208/commits","review_comments_url":"https://api.github.com/repos/BD2KGenomics/toil-scripts/pulls/208/comments","review_comment_url":"https://api.github.com/repos/BD2KGenomics/toil-scripts/pulls/comments{/number}","comments_url":"https://api.github.com/repos/BD2KGenomics/toil-scripts/issues/208/comments","statuses_url":"https://api.github.com/repos/BD2KGenomics/toil-scripts/statuses/1759293fbf08d2d4489a6ef18c82d83224166eba","head":{"label":"BD2KGenomics:releases/1.0","ref":"releases/1.0","sha":"1759293fbf08d2d4489a6ef18c82d83224166eba","user":{"login":"BD2KGenomics","id":8701293,"avatar_url":"https://avatars.githubusercontent.com/u/8701293?v=3","gravatar_id":"","url":"https://api.github.com/users/BD2KGenomics","html_url":"https://github.com/BD2KGenomics","followers_url":"https://api.github.com/users/BD2KGenomics/followers","following_url":"https://api.github.com/users/BD2KGenomics/following{/other_user}","gists_url":"https://api.github.com/users/BD2KGenomics/gists{/gist_id}","starred_url":"https://api.github.com/users/BD2KGenomics/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/BD2KGenomics/subscriptions","organizations_url":"https://api.github.com/users/BD2KGenomics/orgs","repos_url":"https://api.github.com/users/BD2KGenomics/repos","events_url":"https://api.github.com/users/BD2KGenomics/events{/privacy}","received_events_url":"https://api.github.com/users/BD2KGenomics/received_events","type":"Organization","site_admin":false},"repo":{"id":39923176,"name":"toil-scripts","full_name":"BD2KGenomics/toil-scripts","owner":{"login":"BD2KGenomics","id":8701293,"avatar_url":"https://avatars.githubusercontent.com/u/8701293?v=3","gravatar_id":"","url":"https://api.github.com/users/BD2KGenomics","html_url":"https://github.com/BD2KGenomics","followers_url":"https://api.github.com/users/BD2KGenomics/followers","following_url":"https://api.github.com/users/BD2KGenomics/following{/other_user}","gists_url":"https://api.github.com/users/BD2KGenomics/gists{/gist_id}","starred_url":"https://api.github.com/users/BD2KGenomics/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/BD2KGenomics/subscriptions","organizations_url":"https://api.github.com/users/BD2KGenomics/orgs","repos_url":"https://api.github.com/users/BD2KGenomics/repos","events_url":"https://api.github.com/users/BD2KGenomics/events{/privacy}","received_events_url":"https://api.github.com/users/BD2KGenomics/received_events","type":"Organization","site_admin":false},"private":false,"html_url":"https://github.com/BD2KGenomics/toil-scripts","description":"A 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