#!/bin/bash

set -e

test_dir="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null && pwd )"

cd ${test_dir}

mkdir -p example

cd example

if [ ! -f Homo_sapiens.GRCh37.75.dna.chromosome.22.fa ]

then

    if [ ! -f Homo_sapiens.GRCh37.75.dna.chromosome.22.fa.gz ]

    then

        docker run -v ${test_dir}:/mnt -u $UID --memory 30G  msahraeian/neusomatic:0.2.1 /bin/bash -c \

        "cd /mnt/example/ && wget ftp://ftp.ensembl.org/pub/release-75//fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.75.dna.chromosome.22.fa.gz"

    fi

    docker run -v ${test_dir}:/mnt -u $UID --memory 30G  msahraeian/neusomatic:0.2.1 /bin/bash -c \

    "cd /mnt/example/ && gunzip -f Homo_sapiens.GRCh37.75.dna.chromosome.22.fa.gz"

fi

if [ ! -f Homo_sapiens.GRCh37.75.dna.chromosome.22.fa.fai ]

then

    docker run -v ${test_dir}:/mnt -u $UID --memory 30G  msahraeian/neusomatic:0.2.1 /bin/bash -c \

    "samtools faidx /mnt/example/Homo_sapiens.GRCh37.75.dna.chromosome.22.fa"

fi

rm -rf work_standalone

#Stand-alone NeuSomatic test 

docker run -v ${test_dir}:/mnt -u $UID --memory 30G  msahraeian/neusomatic:0.2.1 /bin/bash -c \

"python /opt/neusomatic/neusomatic/python/preprocess.py \

    --mode call \

    --reference /mnt/example/Homo_sapiens.GRCh37.75.dna.chromosome.22.fa \

    --region_bed /mnt/region.bed \

    --tumor_bam /mnt/tumor.bam \

    --normal_bam /mnt/normal.bam \

    --work /mnt/example/work_standalone \

    --scan_maf 0.05 \

    --min_mapq 10 \

    --snp_min_af 0.05 \

    --snp_min_bq 20 \

    --snp_min_ao 10 \

    --ins_min_af 0.05 \

    --del_min_af 0.05 \

    --num_threads 1 \

    --scan_alignments_binary /opt/neusomatic/neusomatic/bin/scan_alignments"

docker run -v ${test_dir}:/mnt -u $UID --memory 30G --shm-size 8G msahraeian/neusomatic:0.2.1 /bin/bash -c \

"CUDA_VISIBLE_DEVICES= python /opt/neusomatic/neusomatic/python/call.py \

        --candidates_tsv /mnt/example/work_standalone/dataset/*/candidates*.tsv \

        --reference /mnt/example/Homo_sapiens.GRCh37.75.dna.chromosome.22.fa \

        --out /mnt/example/work_standalone \

        --checkpoint /opt/neusomatic/neusomatic/models/NeuSomatic_v0.1.0_standalone_Dream3_70purity.pth \

        --num_threads 1 \

        --batch_size 100"

docker run -v ${test_dir}:/mnt -u $UID --memory 30G  msahraeian/neusomatic:0.2.1 /bin/bash -c \

"python /opt/neusomatic/neusomatic/python/postprocess.py \

        --reference /mnt/example/Homo_sapiens.GRCh37.75.dna.chromosome.22.fa \

        --tumor_bam /mnt/tumor.bam \

        --pred_vcf /mnt/example/work_standalone/pred.vcf \

        --candidates_vcf /mnt/example/work_standalone/work_tumor/filtered_candidates.vcf \

        --output_vcf /mnt/example/work_standalone/NeuSomatic_standalone.vcf \

        --work /mnt/example/work_standalone "

rm -rf /mnt/example/work_ensemble

#Ensemble NeuSomatic test 

docker run -v ${test_dir}:/mnt -u $UID --memory 30G  msahraeian/neusomatic:0.2.1 /bin/bash -c \

"python /opt/neusomatic/neusomatic/python/preprocess.py \

    --mode call \

    --reference /mnt/example/Homo_sapiens.GRCh37.75.dna.chromosome.22.fa \

    --region_bed /mnt/region.bed \

    --tumor_bam /mnt/tumor.bam \

    --normal_bam /mnt/normal.bam \

    --work /mnt/example/work_ensemble \

    --scan_maf 0.05 \

    --min_mapq 10 \

    --snp_min_af 0.05 \

    --snp_min_bq 20 \

    --snp_min_ao 10 \

    --ins_min_af 0.05 \

    --del_min_af 0.05 \

    --num_threads 1 \

    --ensemble_tsv /mnt/ensemble.tsv \

    --scan_alignments_binary /opt/neusomatic/neusomatic/bin/scan_alignments"

docker run -v ${test_dir}:/mnt -u $UID --memory 30G --shm-size 8G msahraeian/neusomatic:0.2.1 /bin/bash -c \

"CUDA_VISIBLE_DEVICES= python /opt/neusomatic/neusomatic/python/call.py \

        --candidates_tsv /mnt/example/work_ensemble/dataset/*/candidates*.tsv \

        --reference /mnt/example/Homo_sapiens.GRCh37.75.dna.chromosome.22.fa \

        --out /mnt/example/work_ensemble \

        --checkpoint /opt/neusomatic/neusomatic/models/NeuSomatic_v0.1.0_ensemble_Dream3_70purity.pth \

        --num_threads 1 \

        --ensemble \

        --batch_size 100"

docker run -v ${test_dir}:/mnt -u $UID --memory 30G  msahraeian/neusomatic:0.2.1 /bin/bash -c \

"python /opt/neusomatic/neusomatic/python/postprocess.py \

        --reference /mnt/example/Homo_sapiens.GRCh37.75.dna.chromosome.22.fa \

        --tumor_bam /mnt/tumor.bam \

        --pred_vcf /mnt/example/work_ensemble/pred.vcf \

        --candidates_vcf /mnt/example/work_ensemble/work_tumor/filtered_candidates.vcf \

        --ensemble_tsv /mnt/ensemble.tsv \

        --output_vcf /mnt/example/work_ensemble/NeuSomatic_ensemble.vcf \

        --work /mnt/example/work_ensemble" 

cd ..

file1=${test_dir}/example/work_standalone/NeuSomatic_standalone.vcf

file2=${test_dir}/NeuSomatic_standalone.vcf

cmp --silent $file1 $file2 && echo "### NeuSomatic stand-alone: SUCCESS! ###" \

|| echo "### NeuSomatic stand-alone FAILED: Files ${file1} and ${file2} Are Different! ###"

file1=${test_dir}/example/work_ensemble/NeuSomatic_ensemble.vcf

file2=${test_dir}/NeuSomatic_ensemble.vcf

cmp --silent $file1 $file2 && echo "### NeuSomatic ensemble: SUCCESS! ###" \

|| echo "### NeuSomatic ensemble FAILED: Files ${file1} and ${file2} Are Different! ###"