From 2d7006fd6c4733955d92d032144e3acc67c16669 Mon Sep 17 00:00:00 2001
From: alain viari <viari@aquifex.local>
Date: Sun, 8 Nov 2015 19:53:19 +0100
Subject: [PATCH] corrected Annotation reordering for CDS

Former-commit-id: c59ad42ebdd9772fbed5539388499840b57e3595
Former-commit-id: 5de4848d5d3b8e0d521120b7db92e145d9a6727f
---
 org-annotate.sh | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/org-annotate.sh b/org-annotate.sh
index e049753..5417d8c 100755
--- a/org-annotate.sh
+++ b/org-annotate.sh
@@ -55,17 +55,17 @@ pushTmpDir ORG.organnot
 	loginfo "Done."
 	
 	loginfo "Ordering annotations..."
-		awk '/^.....[^ ]/ { \
+		awk '/^.....(misc|repeat|rRNA|tRNA|gene)/ { \
 		        match($3,"[0-9][0-9]*"); \
 		        pos=substr($3,RSTART,RLENGTH)*1000 + 1; \
-		        print pos,$0} \
-		     /^..... / { \
-		        pos++; \
+		        print pos,$0;    \
+		        next} \
+		      { pos++; \
 		        print pos,$0}' "${RESULTS}.annot" | \
-		sort -nk1 | \
+		sort -nk1 |\
 		awk '{ \
 		        match($0,"^[0-9]* ");\
-		        line=substr($0,RLENGTH+1,100000);\
+		        line=substr($0,RLENGTH+1);\
 		        print line}' 
 	loginfo "Done."