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Fix examples/run.sh shell script #66

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Merged
nalinigans merged 1 commit into from
Dec 16, 2024
Merged

Fix examples/run.sh shell script #66

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12 changes: 6 additions & 6 deletions examples/run.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -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")
Expand All @@ -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
Expand Down Expand Up @@ -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
}

Expand Down