#!/bin/bash

set -euo pipefail

mynumber=0
for fq in *.fastq.gz;
do 
	newnumber=$(zcat $fq | wc -l);
	mynumber=$(($mynumber+$newnumber))
done

Cnumber=0
for u in Undetermined*;
do 
	Unumber=$(zcat $u | wc -l);
	Cnumber=$(($Cnumber+$Unumber))
done

allreads=$(($mynumber/4))
echo "all reads"
echo $allreads 
UndeReads=$(($Cnumber/4))
echo "undetermined reads"
echo $UndeReads
echo "percentage of PhiX (undetermined reads)"
echo $UndeReads/$allreads
echo $(($UndeReads*100/$allreads))%
