ng_fix_run_sh (#66)

Fix examples/run.sh shell script

examples/run.sh

@@ -32,9 +32,9 @@ export VIDMAP_FILE=${VIDMAP_FILE:-$WORKSPACE/vidmap.json}
 export LOADER_FILE=${LOADER_FILE:-$WORKSPACE/loader.json}
 
 declare -a INTERVALS
-#INTERVALS=("1:1-1000000")
+INTERVALS=("1:1-1000000")
 #INTERVALS=("1:1-1000000" "1:1000001-2000000" "1:2000001-3137454")
-INTERVALS=("chr1:1-200000")
+#INTERVALS=("chr1:1-200000")
 #INTERVALS=("1:1-3137454")
 #INTERVALS=("1:1-40000000")
 #INTERVALS=("1:1-4000000" "1:8000001-16000000" "1:16000001-24000000" "1:24000001-32000000" "1:32000001-40000000" "2:3000" "3")
@@ -46,11 +46,11 @@ INTERVALS=("chr1:1-200000")
 
 #FILTER='resolve(GT, REF, ALT) &= "T/T"'
 
-OUTPUT_FILE=${OUTPUT_FILE=-my_output}
-OUTPUT_FILE_TYPE=${OUTPUT_FILE_TYPE=-json}
+export OUTPUT_FILE=${OUTPUT_FILE:-my_output}
+export OUTPUT_FILE_TYPE=${OUTPUT_FILE_TYPE:-json}
 
 export TILEDB_CACHE=1
-NTHREADS=${NTHREADS:=-8}
+NTHREADS=${NTHREADS:-8}
 
 ###########################################
 # Should not have to change anything below
@@ -100,7 +100,7 @@ fi
 run_query() {
   INTERVAL=$1
   OUTPUT_FILE=$2
-  echo genomicsdb_query -w $WORKSPACE -l $LOADER_FILE -c $CALLSET_FILE -v $VIDMAP_FILE -i $INTERVAL $SAMPLE_ARGS $FILTER_EXPR -o $OUTPUT_FILE
+  echo genomicsdb_query -w $WORKSPACE -l $LOADER_FILE -c $CALLSET_FILE -v $VIDMAP_FILE -i $INTERVAL $SAMPLE_ARGS $FILTER_EXPR -o $OUTPUT_FILE -t $OUTPUT_FILE_TYPE
   /usr/bin/time -l genomicsdb_query -w $WORKSPACE -l $LOADER_FILE -c $CALLSET_FILE -v $VIDMAP_FILE -i $INTERVAL $SAMPLE_ARGS $FILTER_EXPR -o $OUTPUT_FILE -t $OUTPUT_FILE_TYPE
 }