From a25ab81b38ec6fc31af89abc067c70f0bfc73864 Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric.coissac@metabarcoding.org>
Date: Thu, 18 Jan 2018 22:00:07 +0100
Subject: [PATCH] Add logs to print the sequence length and if the sequence is
 reverse complemented

Former-commit-id: ba55f354ea7a51119fe44bcb36aa5927194293e2
Former-commit-id: dd7715be54ac92c9625f0a2c30e572b7aee76dc7
---
 detectors/normalizerdna/bin/go_normalizerdna.sh | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/detectors/normalizerdna/bin/go_normalizerdna.sh b/detectors/normalizerdna/bin/go_normalizerdna.sh
index ab18d76..5fc49d4 100755
--- a/detectors/normalizerdna/bin/go_normalizerdna.sh
+++ b/detectors/normalizerdna/bin/go_normalizerdna.sh
@@ -23,7 +23,6 @@ source "${THIS_DIR}/../../../scripts/bash_init.sh"
 pushTmpDir ORG.its
 
 	loginfo "Normalizing nuclear rDNA cistron..."
-
 	RRNADB="${NUCRRNA_DATA_DIR}/plants/nuc_RRNA.hmm"
 	
 	if [[ ! "$1" =~ ^/ ]]; then
@@ -32,6 +31,7 @@ pushTmpDir ORG.its
 		QUERY="$1"
 	fi
 
+	loginfo "Sequence length $(seqlength ${QUERY})"
 
 	strand=( $(hmmsearch --max ${RRNADB} ${QUERY} | \
 				$AwkCmd '/Query: / { \
@@ -55,7 +55,8 @@ pushTmpDir ORG.its
 		if [[ "${strand[0]}" == "Forward" ]] ; then
 			cat ${QUERY}
 		else
-			fastarevcomp -f ${QUERY}
+			loginfo "Revert complement rDNA cluster cistron"
+			fastarevcomp  ${QUERY} 
 		fi
 	else
 		logerror "Cannot determine the Cistron orientation"