From ee75859c118255085294e3cc981194b038ba8619 Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Thu, 28 Feb 2019 11:32:47 -0600
Subject: [PATCH] updates for bugs
---
alignment/hisat_genotype.sh | 5 ++---
variants/svcalling.sh | 2 +-
2 files changed, 3 insertions(+), 4 deletions(-)
diff --git a/alignment/hisat_genotype.sh b/alignment/hisat_genotype.sh
index 6e225eb..32d5d4d 100644
--- a/alignment/hisat_genotype.sh
+++ b/alignment/hisat_genotype.sh
@@ -11,10 +11,9 @@ usage() {
exit 1
}
OPTIND=1 # Reset OPTIND
-while getopts :r:x:y:p:uh opt
+while getopts :x:y:p:uh opt
do
case $opt in
- r) index_path=$OPTARG;;
x) fq1=$OPTARG;;
y) fq2=$OPTARG;;
u) umi='umi';;
@@ -26,7 +25,7 @@ done
shift $(($OPTIND -1))
# Check for mandatory options
-if [[ -z $pair_id ]] || [[ -z $index_path ]]; then
+if [[ -z $pair_id ]]; then
usage
fi
diff --git a/variants/svcalling.sh b/variants/svcalling.sh
index 17bc770..512fea2 100755
--- a/variants/svcalling.sh
+++ b/variants/svcalling.sh
@@ -11,7 +11,7 @@ usage() {
exit 1
}
OPTIND=1 # Reset OPTIND
-while getopts :r:p:b:i:e:n:a:h opt
+while getopts :r:p:b:i:n:a:h opt
do
case $opt in
r) index_path=$OPTARG;;
--
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