#!/bin/sh
#PBS -N HLA
#PBS -j oe
#PBS -l ncpus=12
#PBS -l nodes=1
#PBS -l mem=20G

#inputpath=$1
#sample=$2
source  /home/liuxiangqiong/miniconda3/bin/activate base
hlahd_dir=/cgdata/liuxiangqiong/software/hla/hlahd.1.3.0
target=/cgdata/liuxiangqiong/work62pancancer/Client/v0/script/refdata/NanOnco_Plus_Panel_v2.0_Covered_b37_cg.parY2X.sort.bed
export PATH=$hlahd_dir/bin:$PATH
outputdir=${inputpath}/7HLA-HD_unpair
cd ${outputdir}
samtools view -hb ${bam_dir}/${sample}_clean.bam 6:28477797-33448354 | samtools sort -n |samtools fastq - -1 ${inputpath}/${sample}_partial_t1.fq -2 ${inputpath}/${sample}_partial_t2.fq
samtools view -bh -f 4 ${bam_dir}/${sample}_clean.bam |samtools sort -n | samtools fastq - -1 ${inputpath}/${sample}_unmapped_1.fq -2 ${inputpath}/${sample}_unmapped_2.fq
cat ${inputpath}/${sample}_partial_t1.fq ${inputpath}/${sample}_unmapped_1.fq > ${inputpath}/${sample}_part_1.fq && rm ${inputpath}/${sample}_partial_t1.fq ${inputpath}/${sample}_unmapped_1.fq
cat ${inputpath}/${sample}_partial_t2.fq ${inputpath}/${sample}_unmapped_2.fq > ${inputpath}/${sample}_part_2.fq && rm ${inputpath}/${sample}_partial_t2.fq ${inputpath}/${sample}_unmapped_2.fq
hlahd.sh -t 10 -m 100 -f $hlahd_dir/freq_data/ ${inputpath}/${sample}_part_1.fq ${inputpath}/${sample}_part_2.fq $hlahd_dir/HLA_gene.split.txt $hlahd_dir/dictionary ${sample} ${outputdir}
cp ${outputdir}/${sample}/result/${sample}_final.result.txt ${outputdir}/${sample}.HLA.result.txt
rm -rf ${inputpath}/${sample}_part_1.fq
rm -rf ${inputpath}/${sample}_part_2.fq