threads=15
samples=(HG00512 HG00513 HG00514 HG00731 HG00732 HG00733 NA19238 NA19239 NA19240)
# samples=(NA19239)
src=/home/wangshuai/softwares//SpecLong/scripts/


reads_dir=/mnt/d/HLAPro_backup/Nanopore_optimize/data/reads_kir_hpc/
outdir=/mnt/d/HLAPro_backup/Nanopore_optimize/KIR_HGSCV2_hifi2
for sample in ${samples[@]}; do
    echo "Processing $sample"
    fq=$reads_dir/$sample.KIR.fastq.gz
    python3 $src/main.py -r $fq -n $sample -i KIR -j $threads -o $outdir --hete_p 0.2 #--align_method_1 minimap2 #--align_method_2 bwa #--align_method_1 minimap2
    # break
done



# reads_dir=/mnt/d/HLAPro_backup/Nanopore_optimize/data/hprc_hifi_kir/
# outdir=/mnt/d/HLAPro_backup/Nanopore_optimize/KIR_HPRC_hifi
# file_list_file=/mnt/d/HLAPro_backup/Nanopore_optimize/data/hprc_hifi_kir/hprc_hifi_kir.list
# while IFS= read -r file_path; do
#     # Extract the base name of the file
#     sample=$(basename "$file_path" ".KIR.fastq.gz")
#     # file_basename=$(basename "$file_path" ".hla.extract.fastq.gz")


#     echo $sample
#     # if [ "1" == "1" ]; then
#     if [ "$sample" == "HG00621" ]; then
#         echo "Processing $sample"
        
        
#         fq=$reads_dir/$sample.KIR.fastq.gz
#         # sample=HG02559_2
#         python3 $src/main.py -r $fq -n $sample -i KIR -j $threads -o $outdir --hete_p 0.2 #--align_method_1 minimap2 #--align_method_2 bwa #--align_method_1 minimap2
#         # break
        
#     fi

# done < "$file_list_file"