{"action":"created","issue":{"url":"https://api.github.com/repos/bihealth/vcfpy/issues/128","repository_url":"https://api.github.com/repos/bihealth/vcfpy","labels_url":"https://api.github.com/repos/bihealth/vcfpy/issues/128/labels{/name}","comments_url":"https://api.github.com/repos/bihealth/vcfpy/issues/128/comments","events_url":"https://api.github.com/repos/bihealth/vcfpy/issues/128/events","html_url":"https://github.com/bihealth/vcfpy/issues/128","id":350105736,"node_id":"MDU6SXNzdWUzNTAxMDU3MzY=","number":128,"title":"VCF without FORMAT and sample columns causes error","user":{"login":"susannasiebert","id":6617192,"node_id":"MDQ6VXNlcjY2MTcxOTI=","avatar_url":"https://avatars1.githubusercontent.com/u/6617192?v=4","gravatar_id":"","url":"https://api.github.com/users/susannasiebert","html_url":"https://github.com/susannasiebert","followers_url":"https://api.github.com/users/susannasiebert/followers","following_url":"https://api.github.com/users/susannasiebert/following{/other_user}","gists_url":"https://api.github.com/users/susannasiebert/gists{/gist_id}","starred_url":"https://api.github.com/users/susannasiebert/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/susannasiebert/subscriptions","organizations_url":"https://api.github.com/users/susannasiebert/orgs","repos_url":"https://api.github.com/users/susannasiebert/repos","events_url":"https://api.github.com/users/susannasiebert/events{/privacy}","received_events_url":"https://api.github.com/users/susannasiebert/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2018-08-13T16:39:12Z","updated_at":"2018-11-01T17:08:39Z","closed_at":null,"author_association":"NONE","body":"* vcfpy version: 0.11.2\r\n* Python version: 3.5.0\r\n* Operating System: Mac OSX Yosemite 10.10.5\r\n\r\n### Description\r\n\r\nAccording to the VCF specs (https://samtools.github.io/hts-specs/VCFv4.2.pdf) it is valid to have a VCF without a FORMAT and sample columns. However, this causes an error when parsing the individual variant entries.\r\n\r\n### What I Did\r\n\r\n```\r\n$ cat tests/test_data/input.no_sample.vcf \r\n##fileformat=VCFv4.2\r\n#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\r\n22\t18644673\t.\tC\tT\t.\t.\t.\r\n```\r\n```\r\n$python\r\n>>> import vcfpy\r\n>>> vcf_reader = vcfpy.Reader.from_path('tests/test_data/input.no_sample.vcf')\r\n>>> next(vcf_reader)\r\nTraceback (most recent call last):\r\n  File \"<stdin>\", line 1, in <module>\r\n  File \"/Users/ssiebert/miniconda2/envs/pvactools/lib/python3.5/site-packages/vcfpy/reader.py\", line 170, in __next__\r\n    result = self.parser.parse_next_record()\r\n  File \"/Users/ssiebert/miniconda2/envs/pvactools/lib/python3.5/site-packages/vcfpy/parser.py\", line 792, in parse_next_record\r\n    return self.parse_line(self._read_next_line())\r\n  File \"/Users/ssiebert/miniconda2/envs/pvactools/lib/python3.5/site-packages/vcfpy/parser.py\", line 783, in parse_line\r\n    return self._record_parser.parse_line(line)\r\n  File \"/Users/ssiebert/miniconda2/envs/pvactools/lib/python3.5/site-packages/vcfpy/parser.py\", line 457, in parse_line\r\n    format_ = arr[8].split(':')\r\nIndexError: list index out of range\r\n```\r\n\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/bihealth/vcfpy/issues/comments/435112392","html_url":"https://github.com/bihealth/vcfpy/issues/128#issuecomment-435112392","issue_url":"https://api.github.com/repos/bihealth/vcfpy/issues/128","id":435112392,"node_id":"MDEyOklzc3VlQ29tbWVudDQzNTExMjM5Mg==","user":{"login":"ghannum","id":9534138,"node_id":"MDQ6VXNlcjk1MzQxMzg=","avatar_url":"https://avatars2.githubusercontent.com/u/9534138?v=4","gravatar_id":"","url":"https://api.github.com/users/ghannum","html_url":"https://github.com/ghannum","followers_url":"https://api.github.com/users/ghannum/followers","following_url":"https://api.github.com/users/ghannum/following{/other_user}","gists_url":"https://api.github.com/users/ghannum/gists{/gist_id}","starred_url":"https://api.github.com/users/ghannum/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ghannum/subscriptions","organizations_url":"https://api.github.com/users/ghannum/orgs","repos_url":"https://api.github.com/users/ghannum/repos","events_url":"https://api.github.com/users/ghannum/events{/privacy}","received_events_url":"https://api.github.com/users/ghannum/received_events","type":"User","site_admin":false},"created_at":"2018-11-01T17:08:39Z","updated_at":"2018-11-01T17:08:39Z","author_association":"NONE","body":"This is an unfortunate oversight in an otherwise very powerful VCF tool. Is there any timeline when this might be addressed?"}}
{"actor":{"display_login":"ghannum"}}