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#!/bin/bash
mkdir -p /tmp/vcfs
cp /opt/tests/inputs/vcfs/t0.vcf.gz /tmp/vcfs/
cp /opt/tests/inputs/vcfs/t0.vcf.gz.tbi /tmp/vcfs/
cp /opt/tests/inputs/vcfs/t1.vcf.gz /tmp/vcfs/
cp /opt/tests/inputs/vcfs/t1.vcf.gz.tbi /tmp/vcfs/
cp /opt/tests/inputs/vcfs/t2.vcf.gz /tmp/vcfs/
cp /opt/tests/inputs/vcfs/t2.vcf.gz.tbi /tmp/vcfs/
vcf2genomicsdb_init -w /tmp/ws -S /tmp/vcfs -n 0
if [ ! -f /tmp/ws/loader.json ]; then
echo "vcf2genomicsdb_init failed"
exit 1
fi
vcf2genomicsdb /tmp/ws/loader.json
tdb_file_count=`find /tmp/ws/ -name "*tdb"|wc -l`
if (( tdb_file_count < 10 )); then
echo "vcf2genomicsdb failed, only found $tdb_file_count tdb files"
exit 1
fi
tee -a /tmp/ws/query.json > /dev/null <<EOT
{
"workspace" : "/tmp/ws",
"array" : "allcontigs\$1\$3101976562",
"query_column_ranges": [[[0,210306]]],
"query_row_ranges": [[[0, 2]]],
"query_attributes": ["GT","ALT","REF"],
"reference_genome": "/opt/tests/inputs/chr1_10MB.fasta.gz",
"callset_mapping_file": "/tmp/ws/callset.json",
"vid_mapping_file": "/tmp/ws/vidmap.json",
"produce_GT_field": true
}
EOT
variant_count=`gt_mpi_gather -j /tmp/ws/query.json --produce-Broad-GVCF| grep -v '#'| wc -l`
if (( variant_count != 4 )); then
echo "gt_mpi_gather failed, expected 4 variants, found $variant_count"
exit 1
fi
|
