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Crazy long VCF lines silently fail #9

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edawson opened this issue Oct 13, 2019 · 0 comments
Open

Crazy long VCF lines silently fail #9

edawson opened this issue Oct 13, 2019 · 0 comments
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@edawson
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edawson commented Oct 13, 2019

Long vcf lines (such as those with the SV sequence in the ref/alt fields) silently fail parsing. This is standard get_line behavior but is a major issue.

Temporarily, I've fixed this by making the maximum line length really large. This is not an efficient solution. I need to think about how to write a better line-by-line or htslib-style parser (or just htslib) for variants.

@edawson edawson added the bug Something isn't working label Oct 13, 2019
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