Move gimbleprep away from textfile based inputs

[GertjanBisschop]

Ideally, gimbleprep would perform all required preprocessing steps on an array containing all variants. This can be done using sgkit. This is compatible with zarr. This would simplify the workflow a lot.

[GertjanBisschop]

see for example #18

[GertjanBisschop]

see bio2zarr for a great library to parse a vcf and convert it to zarr.