Fix reference protein seq in fs-ter-substitution

[itoooo]

This PR fixes the assert error that is occured if returning :ref contains stop symbol, '*', at the end.

VCV000965170.1 is a one of example case to cause this.

You can reproduce this problem like below steps:

(require ['varity.hgvs-to-vcf :as 'h2v]
         ['varity.vcf-to-hgvs :as 'v2h]
         ['clj-hgvs.core :as 'clj-hgvs])

(h2v/hgvs->vcf-variants (clj-hgvs/parse "NM_199003.1:c.72-53_*28del") "/path/to/hg38.fa" "/path/to/hg38/20200818015652/refGene.txt.gz")
;; =>
;; ({:chr "chr8",
;;   :pos 42838217,
;;   :ref "GAGATTAACAGGGGTCTGAAGAGGCGGCATTAGTAATCCAATAGCAGCATCAACCTGGGAAACAGGAGGCGGTAAAGGAGGTGGGGGAAGCTGTTCCTGTGGCTCCAGAAGATCTTCTTTCTAAAACAAAAATACAAAGTATGTTTGAATTTAGTAACTAAAAACAGTTTAAA",
;;   :alt "G"})

(v2h/vcf-variant->hgvs (first *1) "/path/to/hg38.fa" "/path/to/hg38/20200818015652/refGene.txt.gz" {:verbose? true})
;;  variant: {:chr "chr8", :pos 42838217, :ref "GAGATTAACAGGGGTCT...", :alt "G"}
;; ref-gene: {:name "NM_199003", :name2 "THAP1", :strand :reverse}
;; 
;;              42838201  42838211  42838221  42838231  42838241  42838251  42838261  42838271  42838281  42838291  42838301  42838311  42838321  42838331  42838341  42838351  42838361  42838371  42838381  42838391  42838401
;;     ref: TTGTGGTCACAGAAAACTGAGAGATTAACAGGGGTCTGAAGAGGCGGCATTAGTAATCCAATAGCAGCATCAACCTGGGAAACAGGAGGCGGTAAAGGAGGTGGGGGAAGCTGTTCCTGTGGCTCCAGAAGATCTTCTTTCTAAAACAAAAATACAAAGTATGTTTGAATTTAGTAACTAAAAACAGTTTAAAAGAATCTGTGGACTGACCAG
;;     alt: TTGTGGTCACAGAAAACTGAG                                                                                                                                                                            AGAATCTGTGGACTGACCAG
;;                              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
;; 
;;                   72-65     72-55     72-45     72-35     72-25     72-15     72-5      77        87        97        107       117       127       137       147       157       *5        *15       *25       *35       *45
;;   c.ref: cctggtcagtccacagattcttttaaactgtttttagttactaaattcaaacatactttgtatttttgttttagAAAGAAGATCTTCTGGAGCCACAGGAACAGCTTCCCCCACCTCCTTTACCGCCTCCTGTTTCCCAGGTTGATGCTGCTATTGGATTACTAATGCCGCCTCTTCAGACCCCTGTTAATCTCTCAGTTTTCTGTGACCACAA
;;   c.alt: cctggtcagtccacagattct                                                                                                                                                                            CTCAGTTTTCTGTGACCACAA
;;                              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
;; 
;;                 11        21        31        41
;;   p.ref: SCSAYGCKNRYDKDKPVSFHKKKIFWSHRNSFPHLLYRLLFPRLMLLLDY*
;;   p.alt: SCSAYGCKNRYDKDKPVSFHK*GPCAPRGAVPPLQTPVNLS
;;                              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
;; Execution error (AssertionError) at clj-hgvs.mutation/protein-substitution (mutation.cljc:1584).
;; Assert failed: (intl/valid? :clj-hgvs.mutation/protein-substitution %)

So I fixed this issue by trimming :ref, that is returned caller, with returning :alt's length. In the above case, "KK" for :ref, "K*" for :alt.

Now, vcf-variant-hgvs should returns following HGVS instances:

({:coding-dna #clj-hgvs/hgvs"NM_199003:c.72-53_*28delTTTAAACTGTTTTTAGTTACTAAATTCAAACATACTTTGTATTTTTGTTTTAGAAAGAAGATCTTCTGGAGCCACAGGAACAGCTTCCCCCACCTCCTTTACCGCCTCCTGTTTCCCAGGTTGATGCTGCTATTGGATTACTAATGCCGCCTCTTCAGACCCCTGTTAATCT",
  :protein #clj-hgvs/hgvs"p.K25*"}
 {:coding-dna #clj-hgvs/hgvs"NM_018105:c.268-53_386delTTTAAACTGTTTTTAGTTACTAAATTCAAACATACTTTGTATTTTTGTTTTAGAAAGAAGATCTTCTGGAGCCACAGGAACAGCTTCCCCCACCTCCTTTACCGCCTCCTGTTTCCCAGGTTGATGCTGCTATTGGATTACTAATGCCGCCTCTTCAGACCCCTGTTAATCT",
  :protein #clj-hgvs/hgvs"p.K90Lfs*5"})

I confirmed lein test :all passed.

[codecov]

Codecov Report

Merging #40 (02c31cc) into master (7f5eb02) will decrease coverage by 0.11%.
The diff coverage is 0.00%.

❗ Current head 02c31cc differs from pull request most recent head 9aaad15. Consider uploading reports for the commit 9aaad15 to get more accurate results

@@            Coverage Diff             @@
##           master      #40      +/-   ##
==========================================
- Coverage   39.06%   38.94%   -0.12%     
==========================================
  Files          15       15              
  Lines        1687     1692       +5     
  Branches       33       33              
==========================================
  Hits          659      659              
- Misses        995     1000       +5     
  Partials       33       33              

Impacted Files	Coverage Δ
src/varity/vcf_to_hgvs/protein.clj	27.94% <0.00%> (-0.42%)	⬇️

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[totakke]

Thank you. Your fix seems to work fine. I have left the only comment at the nonsense code.

[totakke]

(max 0 ...) is nonsense because (inc (- palt-len pref-len)) is at least 0 under (<= pref-len palt-ter-len).

[itoooo]

Oh, exactly, I'm kind of too focused on to keep the original code. I'll fix it!

[itoooo]

Thank you for the review! I fixed the code you pointed to. Could you review that again?

[totakke]

LGTM

[itoooo]

Thanks for the merge! 🙏