Fix the position of first amino acid changed by the frame shift

[nokara26]

I have fixed the position of first amino acid changed by the frame shift.

(require '[varity.vcf-to-hgvs :as v2h])

(v2h/vcf-variant->hgvs
 {:chr "chr17", :pos 31261816, :ref "CC", :alt "C"}
 "path/to/hg38.fa" "path/to/refGene.txt.gz" {:prefer-deletion? true})

• before fix

;;=> ({:coding-dna #clj-hgvs/hgvs "NM_000267:c.4621delC",
;;     :protein #clj-hgvs/hgvs "p.L1541=fs*12"}
;;    {:coding-dna #clj-hgvs/hgvs "NM_001042492:c.4684delC",
;;     :protein #clj-hgvs/hgvs "p.L1562=fs*12"})

• after fix

;;=> ({:coding-dna #clj-hgvs/hgvs "NM_000267:c.4621delC",
;;     :protein #clj-hgvs/hgvs "p.N1542Tfs*11"}
;;    {:coding-dna #clj-hgvs/hgvs "NM_001042492:c.4684delC",
;;     :protein #clj-hgvs/hgvs "p.N1563Tfs*11"})

[codecov]

Codecov Report

Merging #66 (48a7fde) into master (ed13cba) will increase coverage by 0.04%.
The diff coverage is 0.00%.

@@            Coverage Diff             @@
##           master      #66      +/-   ##
==========================================
+ Coverage   45.63%   45.67%   +0.04%     
==========================================
  Files          16       16              
  Lines        1992     1990       -2     
  Branches       63       63              
==========================================
  Hits          909      909              
+ Misses       1020     1018       -2     
  Partials       63       63              

Impacted Files	Coverage Δ
src/varity/vcf_to_hgvs/protein.clj	27.82% <0.00%> (+0.16%)	⬆️

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[totakke]

Thank you for fixing a bug that I missed consideration about trailing alt proteins accidentally corresponded to ref proteins.

Your changed code works correctly, but there is a simpler way; all you have to do is removing (= pref palt) condition on L282. The following code passes the test you added.

  (let [[ppos pref palt] (->> (map vector (:ref-prot-seq seq-info) (:alt-prot-seq seq-info))
                              (drop (dec ppos))
                              (map-indexed vector)
                              (drop-while (fn [[_ [r a]]] (= r a)))
                              first
                              ((fn [[i [r a]]]
                                 [(+ ppos i) (str r) (str a)])))
        [_ _ offset _] (diff-bases pref palt)

[nokara26]

Thank you for your review and comment 🙏🏻
I also think your code is clean and concise. I will fix.

[totakke]

LGTM

[federkasten]

🙆‍♂️