From 15f033332c2cc255bb0230c9b098e9c9a5a8c19f Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric.coissac@metabarcoding.org>
Date: Tue, 20 Nov 2018 17:39:38 +0100
Subject: [PATCH] Patch a bug leading to a double pseudogene tagging

Former-commit-id: 35e27b66dc2f350b72544626da12a758b40da071
Former-commit-id: d01e79b8e7450e4aa734a8d04e81573602a58fec
---
 detectors/cds/lib/toEmbl.awk | 13 ++++++++-----
 1 file changed, 8 insertions(+), 5 deletions(-)

diff --git a/detectors/cds/lib/toEmbl.awk b/detectors/cds/lib/toEmbl.awk
index a75b3df..3484699 100644
--- a/detectors/cds/lib/toEmbl.awk
+++ b/detectors/cds/lib/toEmbl.awk
@@ -181,12 +181,15 @@ function Unk(s) {
 	QQualifier("product", Product)
 	QQualifier("inference", "similar to DNA sequence:" Simil)
 	QQualifier("inference", "org.annot -- detect pass:" PassType ":" PassInfo)
-	if (match(Translat,/\*/)>0) {
-		QQualifier("pseudogene","unknown")
-		QQualifier("note","nonfunctional due to stop codon")
-	}
-	if (FrameShift==0)
+	if (FrameShift==0) {
+		if (match(Translat,/\*/)>0) {
+			QQualifier("pseudogene","unknown")
+			QQualifier("note","nonfunctional due to stop codon")
+		}
+		
 		QQualifier("translation", Translat)
+	}
+		
 	  
 	if (Nexon > 1) {
 		for (i = 1 ; i <= Nexon ; i++) {