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Filter out duplicate intervals specified in the examples/genomicsdb_query command line #73

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Merged
nalinigans merged 1 commit into from
Jan 21, 2025
Merged

Filter out duplicate intervals specified in the examples/genomicsdb_query command line #73

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2 changes: 1 addition & 1 deletion examples/genomicsdb_common.py
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Original file line number Diff line number Diff line change
Expand Up @@ -74,7 +74,7 @@ def parse_vidmap_json(vidmap_file, intervals=None):
column_offset += contig_elem["length"]
if all_intervals:
intervals.append(contig_name)
return contigs_map, intervals
return contigs_map, set(intervals)


def parse_interval(interval: str):
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38 changes: 38 additions & 0 deletions examples/test.sh
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Expand Up @@ -72,6 +72,7 @@ die() {
# any other value if the command should return a failure
run_command() {
echo $EMPTY > $TEMP_DIR/output
rm -fr ${OUTPUT}*
declare -i EXPECT_NZ
declare -i GOT_NZ
EXPECT_NZ=0
Expand All @@ -93,6 +94,39 @@ run_command() {
fi
}

check_command_with_duplicates() {
# First argument should be the command
run_command "$1"
nFiles=$(ls -l ${OUTPUT}*.csv | wc -l)
# Second argument should be the number of files
if [[ nFiles -ne $2 ]]; then
die "Could not find the required number of files for '$cmd'"
fi
IFS=' ' read -r -a FILES <<< $3
for FILE in "${FILES[@]}"
do
if [[ ! -f ${OUTPUT}_${FILE}.csv ]]; then
echo "Could not find file=${OUTPUT}_${FILE}.csv"
exit 1
fi
nlines=$(wc -l < ${OUTPUT}_${FILE}.csv)
errmg="'${cmd}' does not return with the required number of lines for ${OUTPUT}_${FILE}.csv"
if [[ $FILE == "1" ]]; then
if [[ $1 == *"-s HG00141"* ]]; then
if [[ $nlines -ne 3 ]]; then
die $errmsg
fi
elif [[ $nlines -ne 5 ]]; then
die $errmsg
fi
else
if [[ $nlines -ne 2 ]]; then
die $errmsg
fi
fi
done
}

if [[ -z $WORKSPACE ]]; then
tar xzf $(dirname $0)/examples_ws.tgz -C $TEMP_DIR
WORKSPACE=$TEMP_DIR/ws
Expand Down Expand Up @@ -195,6 +229,10 @@ run_command "genomicsdb_query -w $WORKSPACE -i 1 --chunk-size=2 -o $OUTPUT"
run_command "genomicsdb_query -w $WORKSPACE -i 1 --chunk-size=2 -b -o $OUTPUT -d"
run_command "genomicsdb_query -w $WORKSPACE -i 1 --chunk-size=2 -b -o $OUTPUT"
run_command "genomicsdb_query -w $WORKSPACE -i 4 --chunk-size=4 -b -o $OUTPUT -d"
# Duplicates
check_command_with_duplicates "genomicsdb_query -w $WORKSPACE -i 1 -i 1 --chunk-size=2 -o $OUTPUT" 2 "1 1_1"
check_command_with_duplicates "genomicsdb_query -w $WORKSPACE -i 1 -i 1 --chunk-size=2 -s HG00141 -s HG00141 -o $OUTPUT" 1 "1"


OLDSTYLE_JSONS="-l $OLDSTYLE_DIR/loader.json -c $OLDSTYLE_DIR/callset_t0_1_2.json -v $OLDSTYLE_DIR/vid.json"
run_command "genomicsdb_cache -w $WORKSPACE $OLDSTYLE_JSONS $INTERVAL_ARGS"
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