fix: fix changed amino acid in extension

chrovis · Dec 22, 2023 · 146ed99 · 146ed99
1 parent 367a363
commit 146ed99
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Showing 2 changed files with 4 additions and 2 deletions.
diff --git a/src/varity/vcf_to_hgvs/protein.clj b/src/varity/vcf_to_hgvs/protein.clj
@@ -438,7 +438,9 @@
         ter-site (some-> (string/index-of rest-seq (if (= ppos 1) "M" "*")) inc)]
     (mut/protein-extension (if (= ppos 1) "Met" "Ter")
                            (coord/protein-coordinate (if (= ppos 1) 1 (+ ppos offset)))
-                           (mut/->long-amino-acid (last ins))
+                           (mut/->long-amino-acid (if (= ppos 1)
+                                                    (last ins)
+                                                    (or (last ins) (first rest-seq))))
                            (if (= ppos 1) :upstream :downstream)
                            (if ter-site
                              (coord/protein-coordinate ter-site)

diff --git a/test/varity/vcf_to_hgvs_test.clj b/test/varity/vcf_to_hgvs_test.clj
@@ -244,7 +244,7 @@
         ;; NOTE: There are very few correct examples...
 
         ;; Extension without termination site
-        "chr17" 81537077 "CT" "C" '("p.*517ext*?" "p.*493ext*?") ; not actual example (+)
+        "chr17" 81537077 "CT" "C" '("p.*517Eext*?" "p.*493Eext*?") ; not actual example (+)
         "chr17" 9771487 "GT" "G" '("p.*312Yext*?" "p.*313Yext*?") ; not actual example (-)
 
         ;; no effect