From 921682f75ac22fac318163e6bf98e4f03ffe112a Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric.coissac@metabarcoding.org>
Date: Mon, 12 Oct 2015 07:26:18 -0300
Subject: [PATCH] enforce the annotation of full-length rrna genes only

Former-commit-id: 0669e643dea2391c8370246cd3182b6328c068dc
Former-commit-id: 7820b800405b2134f2f0c2e27c4ef1ec73e1dc0d
---
 detectors/rrna/bin/go_rrna.sh | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/detectors/rrna/bin/go_rrna.sh b/detectors/rrna/bin/go_rrna.sh
index 58aca33..832eccf 100755
--- a/detectors/rrna/bin/go_rrna.sh
+++ b/detectors/rrna/bin/go_rrna.sh
@@ -44,11 +44,12 @@ pushTmpDir ORG.rrna
 		               {loc=$5".."$6} \
 		     ($1 ~ /_RC$/) { \
 		                loc="complement("loc")"} \
-		               {match($1,"_..*S");\
+		     (full==1) {match($1,"_..*S");\
 		                rrna=substr($1,RSTART+1,RLENGTH-1);\
 		                print "FT   rRNA            " loc; \
 		                print "FT                   /gene=\"rrn"rrna"\""
-		                print "FT                   /product=\""rrna" ribosomal RNA\""\
+		                print "FT                   /product=\""rrna" ribosomal RNA\"";\
+		                full=0
 		                }'	
 
 popTmpDir