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example.sh
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example.sh
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DATA_DIR=./sample_data
export HTSLIB=dynamic
export LD_LIBRARY_PATH=`pwd`/hts/htslib:${LD_LIBRARY_PATH}
export DYLD_LIBRARY_PATH=`pwd`/hts/htslib:${DYLD_LIBRARY_PATH}
mkdir -p sample_data
function check_file() {
if [ ! -e ${DATA_DIR}/$1 ]
then
curl "http://home.chpc.utah.edu/~u0875014/$1" > ${DATA_DIR}/$1
fi
}
check_file hg002.cram
check_file hg002.cram.crai
check_file hg19.fa.gz
check_file hg19.fa.gz.fai
check_file hg19.fa.gz.gzi
if [ ! -e ${DATA_DIR}/hg002.d4 ]
then
cargo run --release -- create -r ${DATA_DIR}/hg19.fa.gz ${DATA_DIR}/hg002.cram ${DATA_DIR}/hg002.d4
fi
if [ ! -e ${DATA_DIR}/callset.bed ]
then
curl ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/AshkenazimTrio/analysis/NIST_SVs_Integration_v0.6/HG002_SVs_Tier1_v0.6.vcf.gz \
| zgrep 'SVTYPE=DEL' \
| awk '$7 == "PASS" {print}' \
| sed -n 's/^\(.*SVLEN=-\([0-9]*\);.*\)$/\2\t\1/gp' \
| awk '$1 > 200 { print $2"\t"$3"\t"($3+$1); }' \
> ${DATA_DIR}/callset.bed
fi
cargo run --release -- stat -r ${DATA_DIR}/callset.bed ${DATA_DIR}/hg002.d4