Add fgbio.sh better bash wrapper

1 files changed, 38 insertions, 2 deletions

diff --git a/fgbio.sh b/fgbio.sh
index adc1a4511783..99d753b531d2 100644
--- a/fgbio.sh
+++ b/fgbio.sh
@@ -1,2 +1,38 @@
-#!/bin/sh
-exec /usr/bin/java -jar '/usr/share/java/fgbio/fgbio.jar' "$@"
+#!/bin/bash
+set -eou pipefail
+export LC_ALL=en_US.UTF-8
+
+default_jvm_mem_opts="-Xms512m -Xmx1g"
+jvm_mem_opts=""
+jvm_prop_opts=""
+pass_args=""
+
+for arg in "$@"; do
+  case $arg in
+    '-D'*)
+      jvm_prop_opts="$jvm_prop_opts $arg"
+      ;;
+    '-XX'*)
+      jvm_prop_opts="$jvm_prop_opts $arg"
+      ;;
+     '-Xm'*)
+      jvm_mem_opts="$jvm_mem_opts $arg"
+      ;;
+     *)
+      pass_args="$pass_args $arg"
+      ;;
+  esac
+done
+
+if [ "$jvm_mem_opts" == "" ]; then
+  jvm_mem_opts="$default_jvm_mem_opts"
+fi
+
+pass_arr=($pass_args)
+if [[ ${pass_arr[0]:=} == org* ]]
+then
+  eval java $jvm_mem_opts $jvm_prop_opts -cp '/usr/share/java/fgbio/fgbio.jar' $pass_args
+else
+  eval java $jvm_mem_opts $jvm_prop_opts -jar '/usr/share/java/fgbio/fgbio.jar' $pass_args
+fi
+exit