update typo bamqc.sh

alignment/add_umi_sam.py

@@ -18,6 +18,7 @@ def get_args():
     return args
 
 # set the tag names - take a look at SAM spec to pick an appropriate one
+
 args = get_args()
 infile = pysam.AlignmentFile(args.sam, "r")
 out = pysam.AlignmentFile(args.out, "wb", template=infile)
@@ -25,5 +26,6 @@ for read in infile.fetch():
       read.set_tag('RX', read.qname.split(":")[-1])
       out.write(read)
 
+    
 infile.close()
 out.close()

alignment/bamqc.sh

@@ -46,7 +46,6 @@ 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
     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
@@ -55,4 +54,4 @@ if [[ $nuctype == 'dna' ]]; then
     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
+fi