Add a patch for chloroplast annotation when no inverted repeats are

detected

Former-commit-id: 7e3ddd41cf0d0788223382fedbf45b183974233e
Former-commit-id: e5a8ceb825f78d243e37d22cd6b2e91f403c0ee8

detectors/ir/bin/go_ir.sh

@@ -29,8 +29,10 @@ pushTmpDir ORG.ir
 		loginfo " --> $genome_length bp"
 	loginfo "Done"
 	
-	IR=( $(lookForIR ${QUERY}) )
+	IRDetected=1
+	IR=( $(lookForIR ${QUERY}) ) || IRDetected=0
 
+	if (( IRDetected == 1 )) ; then 	
 		posIR1=${IR[4]}
 		posIR2=${IR[6]}
 		
@@ -57,7 +59,7 @@ pushTmpDir ORG.ir
 		echo "FT   repeat_region   ${posIR2}..${endIR2}"
 		echo "FT                   /rpt_type=INVERTED"
 		echo "FT                   /note=\"left inverted repeat A; IRA\""
-	
+	fi
 
 popTmpDir
 

detectors/normalize/bin/go_normalize.sh

@@ -41,7 +41,10 @@ pushTmpDir ORG.normalize
 		loginfo " --> $genome_length bp"
 	loginfo "Done"
 	
-	IR=( $(lookForIR ${QUERY}) )
+	IRDetected=1
+	IR=( $(lookForIR ${QUERY}) ) || IRDetected=0
+	
+	if (( IRDetected == 1 )) ; then
 	
 		posIR1=${IR[4]}
 		posIR2=${IR[6]}
@@ -162,7 +165,10 @@ pushTmpDir ORG.normalize
 		# Merges the four parts of the genome.
 		cat ${tmpLSC} ${tmpIR2} ${tmpSSC} ${tmpIR1} | joinfasta
 
-	
+	else
+		# No IR detected --> normalization has no effect
+		cat ${QUERY}
+	fi
 popTmpDir
 
 exit 0

detectors/normalize/lib/lookforIR.lib.sh

@@ -38,9 +38,16 @@ function lookForIR {
 	  
 	loginfo "Looking for long inverted repeats..."
 		repseek -c -p 0.001 -i ${QUERY} 2>> /dev/null > ${REPEATS}
-		loginfo " --> $(wc -l ${REPEATS} | awk '{print $1}') repeats identified"
+		nrepeat="$(wc -l ${REPEATS} | awk '{print $1}')"
 	loginfo "Done"
 
+	if (( nrepeat == 0 )) ; then
+		logwarning "No inverted repeat identified"
+		return 1
+	fi
+
+	loginfo " --> ${nrepeat} repeats identified"
+
 	loginfo "Marking and selecting the best inverted repeat..."
 		local IR=( $(${SELECTIR} ${MATCHES} ${REPEATS}) )
 	loginfo "Done"