Variants in overlapping SYNALs break downstream tools

[lrauschning]

Making this issue here to track the behaviour matt reported in schneebergerlab/msyd#18.
SYNALs can overlap, and when the overlap contains variants at the same position, these will be emitted to the VCF and break some downstream tools.
This seems to be particularly an issue when merging multiple syri VCFs with msyd, but could in principle happen in a single output VCF as well, I think.

[mparker2]

Thanks Leon. to add to this - I don't think that overlapping variants are a problem per se, if they have a record of which alignment they come from. The problem as I see it is that variants only have a record of the parent SYN, not of the SYNAL, resulting in ambiguity in these overlap regions as to which SYNAL the variant originates from. Presumably the same thing could be true for other record types like INV, DUP etc that are made up of multiple, possibly overlapping INVAL and DUPAL records, although I have not seen an example of this yet.