Populate ref allele

[khetherin]

Obtains a single base REF allele and populates the VCF file with it. Added option to provide the FASTA assembly file.

[apriltuesday]

You can add this to the requirements file.

Since the requirements file is new in the main branch, you will either need to do it in your next PR, or you can dive into the joys of git rebase/merge to see how to update your branch with the newest changes from the main branch. In theory it's as simple as:

git checkout main
git pull origin main
git checkout populate_ref_allele
git rebase main

In practice there can be merge conflicts you need to resolve, but hopefully in this case there won't be.

[tcezard]

We will address the issue with the requirements in #7 and that should also fix the tests