add skip to qc steps when not necessary

alignment/bamqc.sh

@@ -13,7 +13,7 @@ usage() {
   exit 1
 }
 OPTIND=1 # Reset OPTIND
-while getopts :r:b:c:n:p:d:h opt
+while getopts :r:b:c:n:p:s:d:h opt
 do
     case $opt in
         r) index_path=$OPTARG;;
@@ -22,6 +22,7 @@ do
         n) nuctype=$OPTARG;;
         p) pair_id=$OPTARG;;
 	d) dedup=$OPTARG;;
+	s) skiplc=1;
         h) usage;;
     esac
 done
@@ -52,15 +53,18 @@ fi
 
 if [[ $nuctype == 'dna' ]]; then
     module load bedtools/2.26.0 picard/2.10.3
-    samtools view -@ $SLURM_CPUS_ON_NODE -b -L ${bed} -o ${pair_id}.ontarget.bam ${sbam}
-    samtools index -@ $SLURM_CPUS_ON_NODE ${pair_id}.ontarget.bam
-    samtools flagstat  ${pair_id}.ontarget.bam > ${pair_id}.ontarget.flagstat.txt
+    if [[ -z $skiplc ]]
+    then
+	samtools view -@ $SLURM_CPUS_ON_NODE -b -L ${bed} -o ${pair_id}.ontarget.bam ${sbam}
+	samtools index -@ $SLURM_CPUS_ON_NODE ${pair_id}.ontarget.bam
+	samtools flagstat  ${pair_id}.ontarget.bam > ${pair_id}.ontarget.flagstat.txt
+	java -Xmx64g -jar $PICARD/picard.jar CollectAlignmentSummaryMetrics R=${index_path}/genome.fa I=${pair_id}.ontarget.bam OUTPUT=${pair_id}.alignmentsummarymetrics.txt
+	java -Xmx64g -XX:ParallelGCThreads=$SLURM_CPUS_ON_NODE -jar $PICARD/picard.jar EstimateLibraryComplexity I=${sbam} OUTPUT=${pair_id}.libcomplex.txt    
+	samtools view  -@ $SLURM_CPUS_ON_NODE -b -q 1 ${sbam} | bedtools coverage -sorted -hist -g ${index_path}/genomefile.txt -b stdin -a ${bed} > ${pair_id}.mapqualcov.txt
+	samtools view  -@ $SLURM_CPUS_ON_NODE ${sbam} | awk '{sum+=$5} END { print "Mean MAPQ =",sum/NR}' > ${pair_id}.meanmap.txt
+    fi
     java -Xmx64g -jar $PICARD/picard.jar CollectInsertSizeMetrics INPUT=${sbam} HISTOGRAM_FILE=${pair_id}.hist.ps REFERENCE_SEQUENCE=${index_path}/genome.fa OUTPUT=${pair_id}.hist.txt
-    java -Xmx64g -jar $PICARD/picard.jar CollectAlignmentSummaryMetrics R=${index_path}/genome.fa I=${pair_id}.ontarget.bam OUTPUT=${pair_id}.alignmentsummarymetrics.txt
-    java -Xmx64g -jar $PICARD/picard.jar EstimateLibraryComplexity I=${sbam} OUTPUT=${pair_id}.libcomplex.txt
-    samtools view  -@ $SLURM_CPUS_ON_NODE -b -q 1 ${sbam} | bedtools coverage -sorted -hist -g ${index_path}/genomefile.txt -b stdin -a ${bed} > ${pair_id}.mapqualcov.txt
     bedtools coverage -sorted -g  ${index_path}/genomefile.txt -a ${bed} -b ${sbam} -hist > ${pair_id}.covhist.txt
     grep ^all ${pair_id}.covhist.txt >  ${pair_id}.genomecov.txt
-    samtools view  -@ $SLURM_CPUS_ON_NODE ${sbam} | awk '{sum+=$5} END { print "Mean MAPQ =",sum/NR}' > ${pair_id}.meanmap.txt
     perl $baseDir/calculate_depthcov.pl ${pair_id}.covhist.txt
 fi