#!/bin/bash

function process_file(){
	file_name="$1"
	index=0
	i=0
        while read line ; do
                array[$index]="$line"
                index=$(($index+1))
	done < "$file_name"
	
	while [ $i -lt $index ]
	do	
		echo "processing file ${array[$i]}"
		while read line ; do
			if [ $line_index == 0 ]
			then
				if [[ "$line" == *1:Y:* ]]
				then
					out=""
				else
					out="$out$line"
				fi
				line_index=$((line_index+1))
			elif [ $line_index == 1 ]
			then
				if [ -z "$out" ]
				then
					out=""
				else
					ns="${line//[^N]}"
					perl float_compare.pl "${#line}" "${#ns}" "${max_rate}"
					r=$?
					if [ $r -eq 1 ]
					then								
						out="$out||$line"
						echo $out >> "$output_folder/file_$i";
						out=""
					else
						echo -e "$out||$line was removed\n"
						out=""
					fi
				fi
				line_index=$((line_index+1))
			elif [ $line_index == 2 ]
			then		
				line_index=$((line_index+1))

			elif [ $line_index == 3 ]
			then		
				line_index=0
			fi
		done < "${array[$i]}"
	done
}

input_folder=$1
output_folder=$2
max_rate=$3

echo -e "max_rate is $max_rate \n"

#check if the input and output folder are defined in command line
if [ -z "$input_folder" ]
then
	echo -e "Input folder is not defined \n"
	exit;	
elif [ -z "$output_folder" ]
then
	echo -e "Output folder is not defined \n"
	exit;
elif [ -z "$max_rate" ]
then
	echo -e "max rate is not defined \n"

else
	if [ -d "$output_folder" ]; then
	    	echo "output directory already exists. Exiting now!"
		exit;
	fi

	mkdir $output_folder
	#create two temp files - array1.txt and array2.txt. array1.txt contains all files from reading 1 in sorted order
	#array2.txt  contains all files from reading 2 in sorted order
	ls $input_folder*R1*.fastq | sort > array1.txt
	ls $input_folder*R2*.fastq | sort > array2.txt
	
	#put the fileNames from reading 1 in array - array1
	index1=0
	while read line ; do
		array1[$index1]="$line"
		index1=$(($index1+1))
	done < array1.txt

	#put the fileNames from reading 2 in array - array2
	index2=0
        while read line ; do
                array2[$index2]="$line"
                index2=$(($index2+1))
	done < array2.txt

	#  if array1 and array2 are not of equal size, then
	# some files are missing.
	if [ $index1 != $index2 ]
	then
		echo "some readings are missing\n";
		exit;
	fi

	# delete temp files as we dont' need them anymore. We already
	# have that information in array1 and array2
	i=0
	line_index=0
	out=""
	remove_entry=0
	
	# loop through each files in array1, filter them and put in a file
	process_file "array1.txt"
	process_file "array2.txt"
	rm -f array1.txt
	rm -f array2.txt


fi