From 3746c07f5e253310b6a8223ea22ea39c16797eb2 Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Fri, 18 Sep 2020 13:33:54 -0500
Subject: [PATCH] update abra
---
alignment/abra2.sh | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/alignment/abra2.sh b/alignment/abra2.sh
index 228910d..173fdfa 100755
--- a/alignment/abra2.sh
+++ b/alignment/abra2.sh
@@ -17,7 +17,7 @@ do
r) index_path=$OPTARG;;
b) sbam=$OPTARG;;
p) pair_id=$OPTARG;;
- c) tbed==$OPTARG;;
+ c) tbed=$OPTARG;;
h) usage;;
esac
done
@@ -54,5 +54,5 @@ fi
which samtools
samtools index -@ $NPROC ${sbam}
mkdir tmpdir
-java -Xmx16G -jar ${abrajar} ${ioopt} --ref ${index_path}/genome.fa --threads $NRPOC $opt --tmpdir tmpdir --mbq 150 --mnf 5 --mer 0.05 > abra.log
+java -Xmx16G -jar ${abrajar} ${ioopt} --ref ${index_path}/genome.fa --threads $NPROC $opt --tmpdir tmpdir --mbq 150 --mnf 5 --mer 0.05 > abra.log
samtools index -@ $NPROC ${pair_id}.abra2.bam
--
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