SVLEN should probably always be positive
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- Python
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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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