test_run

#!/bin/bash

function print_help()
{
    message=( \ 
        "Testing Script help\n\n" \
        " The testing script runs the full pipeline, testing both kernels by default.\n" \
        " \t\"help\" prints this brief manual\n" \
        " The first argument is the type of test that you want to run:\n" \
        " \t\"vcf\"     tests qLD-parse-VCF\n" \
        " \t\"mdf\"     tests qLD-parse-2MDF\n" \
        " \t\"compute\" tests qLD-compute\n" \
        " \t\"full\"    tests all components\n\n" \ 
        " The second argument is used only in tests that include \"compute\"\n" \
        " It is set to \"all\" by default:\n" \
        " \t\"blis\"     runs only using the blis kernel\n" \
        " \t\"gpu\"      runs only using the OpenCL kernel\n" \
        " \t\"fallback\" runs only using the fallback mode\n" \
        " \t\"all\"      runs all previous modes\n" \
        " An example of the default command if we used arguments:\n" \
        " ./test_run full all\n"
    )
    printf "${message[*]}"
    exit 0
}

run=${1:-full}
mode=${2:-all}
r2_lim=0.6
threads=1
vcf_dir="$(pwd)/test_dataset/vcf"
inp_dir="$(pwd)/test_dataset/input"
out_dir="$(pwd)/test_dataset/output"
vcf_file="$vcf_dir/test_covid.vcf.gz"
inp_file=$inp_dir/covid_19
mdf_file=$inp_dir/MDF_covid_19
out_file=$out_dir/blis/covid_19_report.txt
out_g_file=$out_dir/gpu/covid_19_report.txt
out_fb_file=$out_dir/fallback/covid_19_report.txt

[[ $run = "help" ]] && print_help
echo Testing qLD on COVID-19 dataset
echo -------------------------------
echo
sleep 1
if [[ $run = "full" || $run = "vcf" ]]
then 
    [ -d $inp_dir ] || mkdir -p $inp_dir
    [ -z "$(ls -A $inp_file 2> /dev/null)" ] || rm -rf $inp_file
    echo
    echo "Parsing VCF file with qLD-parse-VCF (needed only once per dataset)"
    echo "-----------------------------------------------------------------"
    ./bin/qLD-parse-VCF -input $vcf_file \
                        -output $inp_file \
                        -chrom 1 \
                        -size 1 
fi
if [[ $run = "full" || $run = "mdf" ]]
then
    [ -d $inp_dir ] || mkdir -p $inp_dir
    [ -z "$(ls -A $mdf_file 2> /dev/null)" ] || rm -rf $mdf_file
    echo
    echo "Creating MDF files with qLD-parse-2MDF (needed only once per dataset)"
    echo "---------------------------------------------------------------------"
    echo
    ./bin/qLD-parse-2MDF -input $inp_file -output $mdf_file 
fi
if [[ $run = "full" || $run = "compute" ]]
then
    echo
    echo Running Computations with the selected modes:
    echo ---------------------------------------------
    input="$inp_file"
    [ -d $mdf_file ] && { mdf="-mdf"; input="$mdf_file"; }
    [ -d $out_dir ] || mkdir -p $out_dir
    [ -z "$(ls -A $out_dir 2> /dev/null)" ] || rm -rf $out_dir/*
    if [[ $mode = "all" || $mode = "blis" ]]
    then
        [ -d $out_dir/blis ] || mkdir -p $out_dir/blis
        echo

        ./bin/qLD-compute \
            -input $input \
            -output $out_file \
            -r2limit $r2_lim \
            -ploidy haploid \
            $mdf \
            -blis \
        2>&1 | tee $out_dir/blis/log.txt
    
        mv input_report.txt thread_* $out_dir/blis 2>/dev/null; true;
    fi
    if [[ $mode = "all" || $mode = "gpu" ]]
    then
        [ -d $out_dir/gpu ] || mkdir -p $out_dir/gpu
        echo

        ./bin/qLD-compute \
            -input $input \
            -output $out_g_file \
            -r2limit $r2_lim \
            -ploidy haploid \
            $mdf \
            -gpu \
        2>&1 | tee $out_dir/gpu/log.txt

        mv input_report.txt thread_* $out_dir/gpu 2>/dev/null; true;
    fi
    if [[ $mode = "all" || $mode = "fallback" ]]
    then
        [ -d $out_dir/fallback ] || mkdir -p $out_dir/fallback
        echo
        ./bin/qLD-compute \
            -input $input \
            -output $out_fb_file \
            -r2limit $r2_lim \
            -ploidy haploid \
            $mdf \
        2>&1 | tee $out_dir/fallback/log.txt

        mv input_report.txt thread_* $out_dir/fallback 2>/dev/null; true;
    fi
fi

if [[ $run = "full" || $run = "heatmap" ]]
then
    echo
    echo "Creating heatmap for blis output:"
    echo "---------------------------------"
    echo
    python3 utilities/heatmap_viewer.py $out_file $out_dir/blis
fi

echo
echo Operation finished
exit 0