#!/bin/bash
raw_reads_dir=$1
output_dir=$2

#mkdir $output_dir
#mkdir trimmed_reads
#TRIM READS WITH ALIENTRIMMER
#for R1 in $(ls $raw_reads_dir/*R1.fastq);
#    do
#        R2=`echo $R1 | sed 's/R1/R2/g'`
#        oR1=`echo $R1 | sed 's/\.fastq/\.at\.fq/g'`
#        oR1=`echo $oR1 | sed 's/fastq\///g'`
#        oR2=`echo $R2 | sed 's/\.fastq/\.at\.fq/g'`
#        oR2=`echo $oR2 | sed 's/fastq\///g'`
#        java -jar soft/AlienTrimmer.jar -if $R1 -ir $R2 -q 20 -c databases/contaminants.fasta -of trimmed_reads/$oR1 -or trimmed_reads/$oR2
#    done


# MERGE READS AND OUTPUT FASTA
mkdir fasta
for R1 in $(ls trimmed_reads/*R1.at.fq);
    do
        R2=`echo $R1 | sed 's/R1/R2/g'`
        outname=`echo $R1 | sed 's/_R1\.at\.fq/\.fasta/g'`
        label=`echo $outname | sed 's/trimmed_reads\///g'`
        outname=`echo $outname | sed 's/trimmed_reads/fasta/g'`
        label=`echo $label | sed 's/\.fasta//g'`
        soft/vsearch --fastq_mergepairs $R1 --reverse $R2 --fastaout $outname --label_suffix ";sample=$label;"
    done

# MERGE ALL FASTAS TO 'amplicon.fasta'
cat fasta/*.fasta > fasta/amplicon.fasta