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

#inputpath=$1
#sample=$2
source  /home/liuxiangqiong/miniconda3/bin/activate base
hg19=/cgdata/Database/GATK/b37/human_g1k_v37_decoy.fasta
target=/cgdata/liuxiangqiong/work62pancancer/Client/v0/script/refdata/NanOnco_Plus_Panel_v2.0_Covered_b37_cg.parY2X.sort.bed
#################################################################################1.trim#########################################################
runstart="`date '+%F%n%T'`"
echo ${sample} "start at" $runstart
echo "#--------------------------------------STEP1.clean the raw data--------------------------------------#"
starttime="`date '+%Y%m%d%H%M%S'`"
fastp -i ${inputpath}/${sample}_R1.fastq.gz -I ${inputpath}/${sample}_R2.fastq.gz  -o ${inputpath}/${sample}_clean_R1.fq.gz -O ${inputpath}/${sample}_clean_R2.fq.gz -c -l 50 -q 20 --umi --umi_loc read1 --umi_len 8 -j ${inputpath}/${sample}.fastp.json -h ${inputpath}/${sample}.fastp.html
#当打断片段太短，read被测穿了，同时去掉5端和3端的8bp
#fastp -i ${inputpath}/${sample}_R1.fastq.gz -I ${inputpath}/${sample}_R2.fastq.gz  -o ${inputpath}/${sample}_clean_R1.fq.gz -O ${inputpath}/${sample}_clean_R2.fq.gz -c -l 50 -q 20  -f 8 -F 8 -t 8 -T 8  -j ${inputpath}/${sample}.fastp.json -h ${inputpath}/${sample}.fastp.html

echo "#--------------------------------------STEP1.clean the raw data finished!---------------#"
#################################################################################2.mapping#########################################################
#2.1.speedseq align
echo "#--------------------------------------STEP2.align to refdata--------------------------------------#"
speedseq align -t 40  -o ${bam_dir}/${sample}_clean -R "@RG\tID:${sample}\tSM:${sample}\tLB:${sample}" ${hg19} ${inputpath}/${sample}_clean_R1.fq.gz ${inputpath}/${sample}_clean_R2.fq.gz
echo "#--------------------------------------STEP2.align to refdata finished!--------------------------------------#"
rm -rf ${bam_dir}/${sample}_clean.splitters.bam
rm -rf ${bam_dir}/${sample}_clean.splitters.bam.bai
rm -rf ${bam_dir}/${sample}_clean.discordants.bam
rm -rf ${bam_dir}/${sample}_clean.discordants.bam.bai
endtime="`date '+%Y%m%d%H%M%S'`"
echo "step1 run " $[$endtime-$starttime]"s">${inputpath}/${sample}_mapping.log
echo "${sample} mapping finish!" >>${inputpath}/${sample}_mapping.log

echo "#--------------------------------------STEP3.qualimap--------------------------------------#"
ourputdir=${inputpath}/9Ontarget
samtools flagstat ${bam_dir}/${sample}_clean.bam > ${ourputdir}/${sample}_clean.abra2.flagstat
#cd ${ourputdir}
#qualimap bamqc -bam  ${bam_dir}/${sample}_clean.bam  -c --java-mem-size=40G -gff ${target}
#去掉dup
qualimap bamqc -bam  ${bam_dir}/${sample}_clean.bam  -c -sd --java-mem-size=40G -gff ${target}