#!/bin/bash

File=$1
Primers=$2
Threads=$3

#for File in $(ls /data/ReadOnly-Data/*R1_001.fastq.gz); do

DirRoot=${File%%_R1_001.fastq.gz*}
Root=${DirRoot##*/}
echo $File
echo $DirRoot
echo $Root

fastp -i $DirRoot'_R1_001.fastq.gz' -I $DirRoot'_R2_001.fastq.gz' -o $Root'_R1_trim.fastq.gz' -O $Root'_R2_trim.fastq.gz' -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -l 25 -w $Threads -z 3 -U --umi_loc read1 --umi_len 14 --umi_prefix umi

mkdir $Root'_SplitFASTQ'
python3 FASTQ_R1_Split_from_primersBED_16Sep20.py $Root'_R1_trim.fastq.gz' $Root'_R2_trim.fastq.gz' $2 $Root'_SplitFASTQ'

cd $Root'_SplitFASTQ'
for i in [o,C]*fastq; do 
	j=${i%.*}; k=${j#*.} 
	cutadapt -j $Threads -a $k -m 50 --match-read-wildcards -n 5 -o $j'.trim.fastq' $i >> log.txt
done

cat [o,C]*.trim.fastq > $Root'_prepped_R1data.txt'
gzip $Root'_prepped_R1data.txt'

cd ../
mv $Root'_SplitFASTQ/'$Root'_prepped_R1data.txt.gz' ./
bowtie2 -p $Threads -x NC_045512.2.fasta -U $Root'_prepped_R1data.txt.gz' | samtools view -buSh - | samtools sort -@ 4 - -o $Root'_bwt2.bam'
samtools index $Root'_bwt2.bam'
pilon --threads $Threads --fix bases --genome NC_045512.2.fasta --mindepth 25 --unpaired $Root'_bwt2.bam' --vcf --changes --threads 4 --output $Root --outdir $Root'_pilon'
grep PASS $Root'_pilon/'$Root'.vcf' | awk '{OFS=""}{if($5 ~ /[A,T,G,C]/)print $4, $2, $5}' > $Root'.changes.txt'

python3 /data/RouthLab_Scripts/ViReMa_MAIN/ViReMa_0.22/ViReMa.py $Root'_pilon/'$Root'.fasta' $Root'_prepped_R1data.txt.gz' $Root'_ViReMa.sam' --Seed 30 --Output_Dir $Root'_ViReMa' --MicroInDel_Length 2 --Defuzz 0 --p $Threads --Chunk 10000000 -BED --X 3 --Host_Index /data/Indexes/bowtie/vero --Host_Seed 30 -Overwrite --Chunk 10000000
samtools view -buSh $Root'_ViReMa/'$Root'_ViReMa.sam' | samtools sort -@ $Threads - -o $Root'_ViReMa/'$Root'_ViReMa.bam'
samtools index $Root'_ViReMa/'$Root'_ViReMa.bam'

#done

