{"action":"opened","issue":{"url":"https://api.github.com/repos/exomiser/Exomiser/issues/171","repository_url":"https://api.github.com/repos/exomiser/Exomiser","labels_url":"https://api.github.com/repos/exomiser/Exomiser/issues/171/labels{/name}","comments_url":"https://api.github.com/repos/exomiser/Exomiser/issues/171/comments","events_url":"https://api.github.com/repos/exomiser/Exomiser/issues/171/events","html_url":"https://github.com/exomiser/Exomiser/issues/171","id":196685424,"number":171,"title":"support bgzip files","user":{"login":"visze","id":9267120,"avatar_url":"https://avatars.githubusercontent.com/u/9267120?v=3","gravatar_id":"","url":"https://api.github.com/users/visze","html_url":"https://github.com/visze","followers_url":"https://api.github.com/users/visze/followers","following_url":"https://api.github.com/users/visze/following{/other_user}","gists_url":"https://api.github.com/users/visze/gists{/gist_id}","starred_url":"https://api.github.com/users/visze/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/visze/subscriptions","organizations_url":"https://api.github.com/users/visze/orgs","repos_url":"https://api.github.com/users/visze/repos","events_url":"https://api.github.com/users/visze/events{/privacy}","received_events_url":"https://api.github.com/users/visze/received_events","type":"User","site_admin":false},"labels":[{"id":144469386,"url":"https://api.github.com/repos/exomiser/Exomiser/labels/bug","name":"bug","color":"fc2929","default":true},{"id":176414518,"url":"https://api.github.com/repos/exomiser/Exomiser/labels/web","name":"web","color":"0052cc","default":false}],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2016-12-20T14:26:27Z","updated_at":"2016-12-20T14:26:27Z","closed_at":null,"body":"I get an error when I used bgzipped files. I think the problem is the following:\r\n\r\na `*.vcf.gz` file is stored in `tmp` as `*.vcf`If htsjdk tries to read this file it thinks the file is uncompressed. Therefore it cannot find the header (see error message). So the easiest was to fix it is to store the vcf.gz file as vcf.gz in the tmp directory after upload\r\n\r\n```\r\n2016-12-20 15:19:21.379 ERROR 27595 --- [nio-8080-exec-5] o.a.c.c.C.[.[.[.[dispatcherServlet]      : Servlet.service() for servlet [dispatcherServlet] in context with path [/exomiser] threw exception [Request processing failed; nested exception is htsjdk.tribble.TribbleException$MalformedFeatureFile: Unable to parse header with error: Your input file has a malformed header: We never saw the required CHROM header line (starting with one #) for the input VCF file, for input source: /tmp/exomiser-1558470031508872380.vcf] with root cause\r\n\r\nhtsjdk.tribble.TribbleException$InvalidHeader: Your input file has a malformed header: We never saw the required CHROM header line (starting with one #) for the input VCF file\r\n\tat htsjdk.variant.vcf.VCFCodec.readActualHeader(VCFCodec.java:115) ~[htsjdk-2.5.0.jar!/:2.5.0]\r\n\tat htsjdk.tribble.AsciiFeatureCodec.readHeader(AsciiFeatureCodec.java:83) ~[htsjdk-2.5.0.jar!/:2.5.0]\r\n\tat htsjdk.tribble.AsciiFeatureCodec.readHeader(AsciiFeatureCodec.java:36) ~[htsjdk-ar!/:2.5.0]\r\n\tat htsjdk.tribble.TribbleIndexedFeatureReader.<init>(TribbleIndexedFeatureReader.java:94) ~[htsjdk-2.5.0.jar!/:2.5.0]\r\n\tat htsjdk.tribble.TribbleIndexedFeatureReader.<init>(TribbleIndexedFeatureReader.java:105) ~[htsjdk-2.5.0.jar!/:2.5.0]\r\n\tat htsjdk.tribble.AbstractFeatureReader.getFeatureReader(AbstractFeatureReader.java:90) ~[htsjdk-2.5.0.jar!/:2.5.0]\r\n\tat htsjdk.tribble.AbstractFeatureReader.getFeatureReader(AbstractFeatureReader.java:67) ~[htsjdk-2.5.0.jar!/:2.5.0]\r\n\tat htsjdk.variant.vcf.VCFFileReader.<init>(VCFFileReader.java:58) ~[htsjdk-2.5.0.jar!/:2.5.0]\r\n\tat org.monarchinitiative.exomiser.core.analysis.AbstractAnalysisRunner.readVcfHeader(AbstractAnalysisRunner.java:279) ~[exomiser-core-7.3.0-SNAPSHOT.jar!/:na]\r\n\r\n\r\n```"}}
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