Copy script to convert vcf to zarr to this repo

[tnguyensanger]

Copy script from https://github.com/malariagen/legacy_pipelines/blob/master/prod-tools/scripts/vcf_to_zarr.py to this repository.

@gbggrant All the legacy scripts used the by vrpipe (the legacy workflow management system) should be found in https://github.com/malariagen/legacy_pipelines in case you want to refer to them.

The legacy vcf_to_zarr.py script needs edits for the new vector pipelines, which we will review in a PR:

• Previous versions of zarr (until at least zarr v2.1.4) set permissions on files underneath a zarr directory to be read-write by user only, regardless of your umask. The newest version of zarr v2.4.0 will obey your umask. The legacy vcf_to_zarr.py script contains code to traverse the directory tree to explicitly set permissions. This code is no longer required.
• the function vcf_to_zarr. zip_zarr() will zip the converted zarr using python package zipfile with zip64 extensions disabled. This was required on legacy machines which used old versions of zip which did not support zip64 extensions. zipfile requires zip64 extensions when the zipped file is > 4GiB (according to v3.8.3 zipfile documentation https://docs.python.org/3/library/zipfile.html). At the time, we were creating small zip files < 4GiB, so it was not an issue. Either we enable zip64 extensions to allow for larger zipfiles, or we should scrap using python package zipfile and just use a recent version of zip directly. Whatever turns out to be easier.