From 8a1a1d57ba85c138e0a631bb0adc276ffcda1249 Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric.coissac@metabarcoding.org>
Date: Mon, 2 May 2016 12:25:05 +0200
Subject: [PATCH] remove the printing of an extra empty line at the beginning
 of the embl file

Former-commit-id: bba6581b86f21474d6e9b2acb3a9b4937984bbb8
Former-commit-id: 7570b9c21814614c45e57e253bdfae58c9ba3c2b
---
 org-annotate.sh | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/org-annotate.sh b/org-annotate.sh
index cdc579c..ef2f1ea 100755
--- a/org-annotate.sh
+++ b/org-annotate.sh
@@ -60,7 +60,7 @@ function usage {
 if ! options=$(getopt -o t:o:icrmh -l ncbi-taxid:,organism,no-ir-detection,chloroplast,nuclear-rdna,mitochondrion,help -- "$@")
 then
     # something went wrong, getopt will put out an error message for us
-    exit 1
+    usage $0 1
 fi
 
 eval set -- "$options"
@@ -82,11 +82,11 @@ do
     shift
 done
 
-echo $type
 #############################
 
 pushTmpDir ORG.organnot
 
+
 	if [[ ! "$1" =~ ^/ ]]; then
 		QUERY="${CALL_DIR}/$1"
 	else
@@ -96,10 +96,12 @@ pushTmpDir ORG.organnot
 
 	RESULTS=$(basename ${QUERY/.*/})
 	LOG="${CALL_DIR}/${RESULTS}.log"
+
 	
 	rm -f ${LOG}
 	openLogFile ${LOG}
 
+
 	case "$types" in 
 		chloro) 
 			loginfo "Annotating a plant chloroplast genome..."
@@ -156,9 +158,9 @@ pushTmpDir ORG.organnot
 			exit 1
 			;;
 		*) 
-			echo usage $0 1;;
+			usage $0 1;;
 	esac
-					
+						
 	if [[ "${organism}" == "no" ]]; then
 		organism="{organism}"
 	else