Remove chromosome/scaffold name mangling for bed/vcf files

[evancofer]

Reference Issues/PRs

None

What does this implement/fix? Explain your changes.

Selene should no longer automatically add "chr" to the start of the chromosome/scaffold name for every record in a bed/vcf file.

What testing did you do to verify the changes in this PR?

Verified that specified changes did not cause existing prediction and VEP examples to fail.

[kathyxchen]

Thanks @evancofer! Was thinking about whether to remove the chr prepend thing entirely or not.
Could we instead modify to a line that checks if all the chromosomes in reference_sequence.get_chrs() begin with chr and Selene prepends with 'chr' only in those cases? (Maybe set a flag at the beginning check_chr and then if check_chr and 'chr' not in chrom...) I'm sure there are other/better ways to do it, haha.

[evancofer]

@kathyxchen This has been updated to include the suggested changes.

[kathyxchen]

LGTM after 1 adjustment (noted in my review comment) & all changes are tested for standard + nonstandard chromosome FASTA. Thank you!!

[kathyxchen]

update to 'chr' not in chrom and check_chr