From cf54e7dcb10966268b97a4f4aad346b2758f14bc Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric.coissac@metabarcoding.org>
Date: Fri, 18 Dec 2015 08:39:04 +0100
Subject: [PATCH] Close #15. Actually the bug in intron location was related to
 a misinterpretation of the aragorn output format. Now tRNA, and intron
 location are coherent with most of the locations extracted from genbank file
 with one or 2 base pairs of difference.

Former-commit-id: dac4fb731e0edaeaebde9edc5350fce38ad99601
Former-commit-id: f8a0590342aec2db1fe5deb4475b8a9380891a48
---
 detectors/trna/lib/aragorn_wrapper.awk | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/detectors/trna/lib/aragorn_wrapper.awk b/detectors/trna/lib/aragorn_wrapper.awk
index 90b9b2b..5a23512 100755
--- a/detectors/trna/lib/aragorn_wrapper.awk
+++ b/detectors/trna/lib/aragorn_wrapper.awk
@@ -112,7 +112,8 @@ function emblTRNA(geneid,trna,loc,anti,intron,seq) {
        intron=substr(intron,2,l-2);
        split(intron,intronpos,",");
 	   ib=intronpos[1];
-	   ie=intronpos[2];
+	   il=intronpos[2];
+	   ie=ib+il-1;
 	   match(loc,"[0-9][0-9]*");
 	   gb=substr(loc,RSTART,RLENGTH);
 	   if (complement==0) {