In VCF files, I am told that the labels for chromosome ids (the first column of the calls) is often a fairly long string identifying contigs and such. SLiM tries to match up those chromosome ids to the chromosome symbols it uses, but SLiM limits chromosome symbols to 1-3 characters in length (for display purposes in SLiMgui, mostly). So there's a problem there. Of course people can rename the values in the chromosome id column of their VCF to match the symbols they choose to use in SLiM, so this is not an insurmountable problem; but it's an annoyance. Maybe there need to be a distinction between the chromosome identifier that SLiM uses to match the VCF, versus the chromosome symbol that SLiM displays in SLiMgui. But I'll need to think about how to handle this in a backward-compatible way.
In VCF files, I am told that the labels for chromosome ids (the first column of the calls) is often a fairly long string identifying contigs and such. SLiM tries to match up those chromosome ids to the chromosome symbols it uses, but SLiM limits chromosome symbols to 1-3 characters in length (for display purposes in SLiMgui, mostly). So there's a problem there. Of course people can rename the values in the chromosome id column of their VCF to match the symbols they choose to use in SLiM, so this is not an insurmountable problem; but it's an annoyance. Maybe there need to be a distinction between the chromosome identifier that SLiM uses to match the VCF, versus the chromosome symbol that SLiM displays in SLiMgui. But I'll need to think about how to handle this in a backward-compatible way.