From d7cba669e1de0545e8a6bcb71a042bde56bba7a8 Mon Sep 17 00:00:00 2001
From: Calvin Morrison <mutantturkey@gmail.com>
Date: Wed, 23 Apr 2014 15:19:32 -0400
Subject: better flag support

---
 SelectiveWholeGenomeAmplification | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

(limited to 'SelectiveWholeGenomeAmplification')

diff --git a/SelectiveWholeGenomeAmplification b/SelectiveWholeGenomeAmplification
index 5b33be1..104495f 100755
--- a/SelectiveWholeGenomeAmplification
+++ b/SelectiveWholeGenomeAmplification
@@ -49,7 +49,8 @@ check_mers() {
 	rmdir $tmp_directory/counts-lock
 }
 
-all=run
+all=1
+
 # Parse in our arguments
 if [[ -z "$foreground" ]] && [[ -z "$background" ]]; then 
 	if (( $# < 2 )); then  
@@ -64,7 +65,12 @@ else
 	start=1
 fi
 
-if (( $# > 2 )); then
+if [[ -n "$step_mers" ]] || [[ -n "$step_filters" ]] || [[ -n "$step_select" ]] || [[ -n "$step_score" ]]; then
+	echo "unset all"
+	unset all
+fi
+
+if (( $# != 0 )); then
 	unset all
 
 	for i in "${@:$start}"; do 
-- 
cgit v1.2.3