From 5d3cdb74ccb5bc277af545fbf4170e36b2acf530 Mon Sep 17 00:00:00 2001
From: Ryan Williams <ryan.blake.williams@gmail.com>
Date: Tue, 22 Mar 2016 16:41:59 +0000
Subject: [PATCH] fix bash arg array processing in adam-submit

---
 bin/adam-submit | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/bin/adam-submit b/bin/adam-submit
index cd33c56163..2c9a156451 100755
--- a/bin/adam-submit
+++ b/bin/adam-submit
@@ -36,11 +36,11 @@ for ARG in "$@"; do
 done
 
 if [[ $DD == True ]]; then
-  SPARK_ARGS="${PRE_DD[@]}"
-  ADAM_ARGS="${POST_DD[@]}"
+  SPARK_ARGS=("${PRE_DD[@]}")
+  ADAM_ARGS=("${POST_DD[@]}")
 else
   SPARK_ARGS=()
-  ADAM_ARGS="${PRE_DD[@]}"
+  ADAM_ARGS=("${PRE_DD[@]}")
 fi
 
 # does the user have ADAM_OPTS set? if yes, then warn
@@ -99,6 +99,6 @@ echo "Using SPARK_SUBMIT=$SPARK_SUBMIT"
   --class $ADAM_MAIN \
   --conf spark.serializer=org.apache.spark.serializer.KryoSerializer \
   --conf spark.kryo.registrator=org.bdgenomics.adam.serialization.ADAMKryoRegistrator \
-  $SPARK_ARGS \
-  $ADAM_CLI_JAR \
-  $ADAM_ARGS
+  "${SPARK_ARGS[@]}" \
+  "$ADAM_CLI_JAR" \
+  "${ADAM_ARGS[@]}"