Fix vcf-to-hgvs protein to handle initiation or stop codon variant more precisely
nokara26 opened this issue · comments
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)
...