SACGF / SACGF/variantgrid

SVLEN should probably always be positive

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#1,344 1 comment 0 reactions 1 assignee Claimed by @davmlaw View on GitHub
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Description

Spun out of #1340 - which found we accidentally inserted a DEL with positive SVLEN

This caused duplicate variants as we use SVLEN in unique_together

The other issue will ensure we have consistency and no dupes. Howeve, it highlights how perhaps we should just have SVLEN be always positive

VCF 4.3 defines SVLEN as diff between ref/alt which doesn't really make sense with INV
VCF 4.4+ (current latest version is 4.5) defines SVLEN as always positive

I think we should just make SVLEN always positive.

We should then make a setting for what VCF version to export, and if <= 4.3 then set SVLEN to negative for DELs

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