deconstruct/call can write giant VCF lines. This happens in, say, large svs with lots of samples that each get their own allele due to nested variation (hopefully deconstruct -L can mitigate this via merging). Giant AT fields for each allele don't help. bcf apparently has a 2 gig line limit, and there's a case of deconstruct seemingly truncating large records. vg deconstruct / call are now modified to drop (with a warning) any lines >2Gb to avoid these issues.
Changelog Entry
To be copied to the draft changelog by merger:
deconstruct/callcan write giant VCF lines. This happens in, say, large svs with lots of samples that each get their own allele due to nested variation (hopefullydeconstruct -Lcan mitigate this via merging). GiantATfields for each allele don't help. bcf apparently has a 2 gig line limit, and there's a case ofdeconstructseemingly truncating large records.vg deconstruct / callare now modified to drop (with a warning) any lines>2Gbto avoid these issues.Description