From 2c0c0343de35097201fffb2fe82f4b9d250248da Mon Sep 17 00:00:00 2001 From: Nobuaki Karasawa Date: Tue, 15 Oct 2024 07:42:35 +0900 Subject: [PATCH] fix: return unknown when last codon is not stop codon --- src/varity/vcf_to_hgvs/protein.clj | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/src/varity/vcf_to_hgvs/protein.clj b/src/varity/vcf_to_hgvs/protein.clj index c4f7347..87066ca 100644 --- a/src/varity/vcf_to_hgvs/protein.clj +++ b/src/varity/vcf_to_hgvs/protein.clj @@ -333,6 +333,11 @@ (count ref-exon-seq) (:name rg) (:name2 rg)) {:type :unknown, :pos nil, :ref nil, :alt nil}) + (not= (last ref-prot-seq) \*) + (do (log/warnf "Last codon is not stop codon: %s (%s, %s)" + (str (last ref-prot-seq)) (:name rg) (:name2 rg)) + {:type :unknown, :pos nil, :ref nil, :alt nil}) + :else (let [alt-prot-seq* (format-alt-prot-seq seq-info) ppos (protein-position pos rg)