fix: add extension conditional branch to insertion

Author: nokara26

src/varity/vcf_to_hgvs/protein.clj

@@ -464,14 +464,18 @@
               (or (and (zero? nprefo) (zero? npalto))
                   (and (= nprefo 1) (= npalto 1))) :substitution
               (and prefer-deletion? (pos? nprefo) (zero? npalto)) :deletion
-              (and prefer-insertion? (zero? nprefo) (pos? npalto)) :insertion
+              (and prefer-insertion? (zero? nprefo) (pos? npalto)) (if first-diff-aa-is-ter-site
+                                                                     :extension
+                                                                     :insertion)
               (and (some? unit) (= ref-repeat 1) (= alt-repeat 2)) :duplication
               (and (some? unit) (pos? alt-repeat)) :repeated-seqs
               (and (pos? nprefo) (zero? npalto)) :deletion
               (and (pos? nprefo) (pos? npalto)) (if (= base-ppos 1)
                                                   :extension
                                                   :indel)
-              (and (zero? nprefo) (pos? npalto)) :insertion
+              (and (zero? nprefo) (pos? npalto)) (if first-diff-aa-is-ter-site
+                                                   :extension
+                                                   :insertion)
               :else (throw (ex-info "Unsupported variant" {:type ::unsupported-variant})))]
       {:type (if (= t :fs-ter-substitution) :substitution t)
        :pos base-ppos

test/varity/vcf_to_hgvs_test.clj

@@ -344,8 +344,9 @@
         "chr1" 47438996 "T" "TCCGCAC" {:prefer-insertion? false} '("p.P286_H287[5]")
         "chr1" 47438996 "T" "TCCGCAC" {:prefer-insertion? true} '("p.H293_A294insPH")
 
-        ;; prefer-insertion?, not actual example (+)
-        "chr1" 26773690 "C" "CGCAGCA" {:prefer-insertion? true} '("p.Q1334_R1335insQQ")
+        ;; prefer-insertion?
+        "chr1" 26773690 "C" "CGCAGCA" {:prefer-insertion? true} '("p.Q1334_R1335insQQ") ;; not actual example (+)
+        "chr10" 103089678 "T" "TTCC" {:prefer-insertion? true} '("p.*562Eext*1") ;; not actual example (-)
 
         ;; prefer-extension-for-initial-codon-alt?
         "chr10" 121593814 "CCATGGT" "C" {:prefer-extension-for-initial-codon-alt? true} '("p.M1Vext-17") ;; not actual example (-)