From 3a28f5f86c894926c8291f28c93abef07ac275da Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Thu, 9 Aug 2018 13:41:48 -0500
Subject: [PATCH] update typo bamqc.sh
---
alignment/add_umi_sam.py | 2 ++
alignment/bamqc.sh | 3 +--
2 files changed, 3 insertions(+), 2 deletions(-)
diff --git a/alignment/add_umi_sam.py b/alignment/add_umi_sam.py
index c234af2..020e10a 100644
--- a/alignment/add_umi_sam.py
+++ b/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()
diff --git a/alignment/bamqc.sh b/alignment/bamqc.sh
index 82346c7..ad4ee6c 100644
--- a/alignment/bamqc.sh
+++ b/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
--
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