1.6.quality.filter

#!/bin/bash

source globals
DIR=$0.dir
mkdir -p $DIR

if [ ! -e $0.stats.log ]
then
        $USEARCH -fastq_stats 1.5.quality.filtering/cat.all.joined.bacteria.seqs.fastq -log $0.stats.log
fi

# look at stats file

echo based on stats.log using $TRUNCLEN and $MAXEE for trunclen and maxee respectively

for sample in $SAMPLES
do
	echo $sample
	paired_fq=1.join_paired_ends.dir/$sample.min_overlap_$J/fastqjoin.join.fastq

	$USEARCH -fastq_filter $paired_fq -fastq_maxee $MAXEE -fastq_trunclen $TRUNCLEN -fastqout $DIR/$sample.fastq

done