Fix vcf-to-hgvs protein to handle initiation or stop codon variant more precisely

[nokara26]

I encountered a failure while converting with vcf-to-hgvs for the variant below.

These are stop codon deletion variant.

We couldn't handle precisely these variants.
So we need to add conceivable cases which affect initiation or stop codon and implement more precisely.

error case 1

{:chr "chr3" :pos 41239336 :ref "CCTGTAAATCATCCTT" :alt "C"}

message

Cannot invoke "Object.getClass()" because "x" is null

...
varity.vcf-to-hgvs.protein/alt-exon-ranges (protein.clj:60)
...
varity.vcf-to-hgvs.protein/alt-exon-ranges (protein.clj:49)
varity.vcf-to-hgvs.protein/alt-exon-ranges (protein.clj:35)
varity.vcf-to-hgvs.protein/apply-offset (protein.clj:183)
varity.vcf-to-hgvs.protein/apply-offset (protein.clj:185)
varity.vcf-to-hgvs.protein/apply-offset (protein.clj:189)
varity.vcf-to-hgvs.protein/apply-offset (protein.clj:180)

error case 2

{:chr "chr3" :pos 41239336 :ref "CCTGTAAATC" :alt "C"}

message

Range [779, 713) out of bounds for length 783

...
varity.vcf-to-hgvs.protein/->protein-variant (protein.clj:306)
varity.vcf-to-hgvs.protein/->protein-variant (protein.clj:278)
varity.vcf-to-hgvs.protein/mutation (protein.clj:510)
varity.vcf-to-hgvs.protein/mutation (protein.clj:507)
varity.vcf-to-hgvs.protein/->hgvs (protein.clj:532)
varity.vcf-to-hgvs.protein/->hgvs (protein.clj:528)
...