fix: fix termination codon position in extension

Author: nokara26

src/varity/vcf_to_hgvs/protein.clj

@@ -590,7 +590,7 @@
       (mut/protein-unknown-mutation)
 
       :else
-      (let [[_ ins offset _] (diff-bases (or pref "") (or palt ""))
+      (let [[_ ins _ _] (diff-bases (or pref "") (or palt ""))
             ini-site ((comp str first) ref-prot-seq)
             first-diff-aa-info (if (= ppos 1)
                                  {:ppos 1
@@ -612,7 +612,7 @@
         (if (and (= ppos 1) (= alt-aa "Ter"))
           (mut/protein-unknown-mutation)
           (mut/protein-extension (if (= ppos 1) (mut/->long-amino-acid ini-site) "Ter")
-                                 (coord/protein-coordinate (if (= ppos 1) 1 (+ ppos offset)))
+                                 (coord/protein-coordinate (if (= ppos 1) 1 (:ppos first-diff-aa-info)))
                                  alt-aa
                                  (if (= ppos 1) :upstream :downstream)
                                  (if new-aa-pos

test/varity/vcf_to_hgvs_test.clj

@@ -283,6 +283,7 @@
         "chr10" 87965468 "TC" "T" '("p.*404Eext*11" "p.*577Eext*11" "p.*207Eext*11") ; not actual example (+)
         "chrX" 15823239 "ATAA" "A" '("p.*483Text*?") ; not actual example (+)
         "chr13" 24421118 "CTTA" "C" '("p.*1725Vext*2") ; not actual example (-)
+        "chrX" 15823235 "CCAAA" "C" '("p.*483Lext*?") ; not actual example (+)
         ;; NOTE: There are very few correct examples...
 
         ;; Extension without termination site