RefMapOpt.sh changes for SE

RefMapOpt.diff

diff --git a/RefMapOpt.sh.1 b/RefMapOpt.sh
index 47f8f02..ce0e168 100644
--- a/RefMapOpt.sh.1
+++ b/RefMapOpt.sh
@@ -11,9 +11,9 @@ if find ${PATH//:/ } -maxdepth 1 -name trimmomatic*jar 2> /dev/null| grep -q 'tr
     echo "The dependency trimmomatic is not installed or is not in your" '$PATH'"."
     NUMDEP=$((NUMDEP + 1))
 	fi
-	
-if find ${PATH//:/ } -maxdepth 1 -name TruSeq2-PE.fa 2> /dev/null | grep -q 'Tru' ; then
-	ADAPTERS=$(find ${PATH//:/ } -maxdepth 1 -name TruSeq2-PE.fa 2> /dev/null | head -1)
+
+if find ${PATH//:/ } -maxdepth 1 -name TruSeq2-SE.fa 2> /dev/null | grep -q 'Tru' ; then
+	ADAPTERS=$(find ${PATH//:/ } -maxdepth 1 -name TruSeq2-SE.fa 2> /dev/null | head -1)
 	else
     echo "The file listing adapters (included with trimmomatic) is not installed or is not in your" '$PATH'"."
     NUMDEP=$((NUMDEP + 1))
@@ -54,7 +54,7 @@ if [ ${NAMES[@]:(-1)}.F.fq.gz -nt ${NAMES[@]:(-1)}.uniq.seqs ];then
 		for i in "${NAMES[@]}";
         		do
         		zcat $i.R.fq.gz | head -2 | tail -1 >> lengths.txt
-        		done	
+        		done
         	MaxLen=$(mawk '{ print length() | "sort -rn" }' lengths.txt| head -1)
 		LENGTH=$(( $MaxLen / 3))
 		for i in "${NAMES[@]}"
@@ -63,8 +63,8 @@ if [ ${NAMES[@]:(-1)}.F.fq.gz -nt ${NAMES[@]:(-1)}.uniq.seqs ];then
 			done
 		cat namelist | parallel --no-notice -j $NUMProc "mawk '$AWK1' {}.assembled.fastq | mawk '$AWK2' | perl -e '$PERLT' > {}.uniq.seqs"
 	fi
-		
-	
+
+
 fi
 
 #Create a data file with the number of unique sequences and the number of occurrences
@@ -118,7 +118,7 @@ if [ "$ATYPE" == "PE" ]; then
 	mv ref.RC.fq ref.R.fq
 	LENGTH=$(mawk '!/>/' rainbow.fasta | mawk '(NR==1||length<shortest){shortest=length} END {print shortest}')
 	LENGTH=$(( $LENGTH * 5 / 4))
-	
+
 	pearRM -f ref.F.fq -r ref.R.fq -o overlap -p 0.001 -j $NUMProc -n $LENGTH &>kopt.log
 
 	rm ref.F.fq ref.R.fq
@@ -186,8 +186,8 @@ do
     	rm lengths.txt &> /dev/null
     		for k in "${RANDNAMES[@]}";
     		do
-    		zcat $k.R.fq.gz | head -2 | tail -1 >> lengths.txt
-    		done	
+    		zcat $k.F.fq.gz | head -2 | tail -1 >> lengths.txt
+    		done
     	MaxLen=$(mawk '{ print length() | "sort -rn" }' lengths.txt| head -1)
     	INSERT=$(($MaxLen * 2 ))
     	INSERTH=$(($INSERT + 100 ))
@@ -198,10 +198,11 @@ do
     	rm $i.$j.results 2>/dev/null
     		for k in "${RANDNAMES[@]}"
     		do
-    		bwa mem reference.fasta $k.R1.fq.gz $k.R2.fq.gz -L 20,5 -I $INSERT,$SD,$INSERTH,$INSERTL -t 32 -a -M -T 10 -A 1 -B 4 -O 6 -R "@RG\tID:$k\tSM:$k\tPL:Illumina" 2> bwa.$i.log | mawk '!/\t[2-9].[SH].*/' | mawk '!/[2-9].[SH]\t/' | samtools view -@32 -q 1 -SbT reference.fasta - > $k.bam
-    		samtools sort -@32 $k.bam $k 
+    		#bwa mem reference.fasta $k.R1.fq.gz $k.R2.fq.gz -L 20,5 -I $INSERT,$SD,$INSERTH,$INSERTL -t 32 -a -M -T 10 -A 1 -B 4 -O 6 -R "@RG\tID:$k\tSM:$k\tPL:Illumina" 2> bwa.$i.log | mawk '!/\t[2-9].[SH].*/' | mawk '!/[2-9].[SH]\t/' | samtools view -@32 -q 1 -SbT reference.fasta - > $k.bam
+            bwa mem reference.fasta $k.R1.fq.gz -L 20,5 -t 32 -a -M -T 10 -A 1 -B 4 -O 6 -R "@RG\tID:$k\tSM:$k\tPL:Illumina" 2> bwa.$i.log | mawk '!/\t[2-9].[SH].*/' | mawk '!/[2-9].[SH]\t/' | samtools view -@32 -q 1 -SbT reference.fasta - > $k.bam
+            samtools sort -@32 $k.bam $k
 		samtools index $k.bam
-    		MM=$(samtools flagstat $k.bam | grep -E 'mapped \(|properly' | cut -f1 -d '+' | tr -d '\n')
+    		MM=$(samtools flagstat $k.bam | grep -E 'mapped \(' | cut -f1 -d '+' | tr -d '\n')
     		CM=$(samtools idxstats $k.bam | mawk '$3 > 0' | wc -l)
     		CC=$(samtools idxstats $k.bam | mawk '{ sum += $3; n++ } END { if (n > 0) print sum / n; }')
 		DD=$(samtools idxstats $k.bam | mawk '$3 >0' | mawk '{ sum += $3; n++ } END { if (n > 0) print sum / n; }')
@@ -220,5 +221,5 @@ do
     	echo -e "$CCC\t$DDD\t$CON\t$AC\t$i\t$j\t$SUMM\t$SUMPM\t$AVEM\t$AVEP\t$BBM" >> mapping.results
 	fi
 	done
-    		
+
 done