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iobio / vcf.iobio.io

MIT License
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Local file problems #39

Open AlistairNWard opened 7 years ago

AlistairNWard commented 7 years ago

vcf.iobio can run with this url:

https://s3.amazonaws.com/iobio/samples/test_files/Horizon-HD728_Panel1385_Hyb11_HFW2KBBXX.union.vcf.gz

But if you run it from the file locally, it fails. The local file opens fine in gene.

tonydisera commented 7 years ago

Thank you for trying in gene.iobio and showing that the local file worked. This gave me the clue I needed to troubleshoot it! It turns out that I had to fix a problem with local file code in Jon Anthony's vcf local file parsing javascript library. This new library was pushed to production for gene.iobio. Once I brought over the new library, vcf.iobio started working with this local file.

It turns out that a super big header in a vcf was hitting the bug where the records were being truncated before the end-of-line.

I will commit this fix to production right now. I've also bumped up the upper threshold of quality scores to 1000. Let me know if you would like to see this a bit lower.