#!/usr/bin/env bash
DIR=$1
FASTAS1=$3
FASTAS2=$4
OUT=$2

echo "Computing index CSV..." > index.csv.temp

while [ "$(find . -size 0 | wc -l)" -ne 0 ]; do
        sleep 10s
done


EXT="mat"
EXTSCORE="scr.txt"
EXTGENERAL=".fa.fasta"



if [ $# != 4 ]; then
	echo "***ERROR*** Use: $0 <directory> <out> <fastas_directory_1> <fastas_directory_2>"
	exit -1
fi

rm $DIR/*.log

for i in $DIR/*.scr; do mv $i $i.txt; done

rm $OUT

for elem in $(ls -d $DIR/*.$EXT | awk -F "/" '{print $NF}' | awk -F ".$EXT" '{print $1}')
do
	IFS='-', read -a splits <<< "$elem"
	IFS='.', read -a getnum <<< "$elem"

	scorepath=$(basename $elem .mat).$EXTSCORE

	sed -i "/X.*/d" $DIR/$scorepath
	sed -i "s/\[1\]//g" $DIR/$scorepath

	score=$( head -1  $DIR/$scorepath)

	file1=${splits[0]}
	file2=$(basename ${splits[1]} .mat)

	ID1=$(head -1 $FASTAS1/$file1)
	ID2=$(head -1 $FASTAS2/$file2)

	
	#scorepath="$(basename $elem .mat).$EXTSCORE"
	#score="$(head -1 $DIR/$scorepath)"

	counter=0
	numX=0
	numY=0
	for i in "${getnum[@]}" 
	do
		counter=`expr $counter + 1`
		if [ "$numX" -eq 0 ] && [ "$i" == "chromosome" ]; then
			numX=$counter
			continue
		fi
		if [ "$numX" -ne 0 ] && [ "$i" == "chromosome" ]; then
			numY=$counter
		fi

	done


	echo "$(basename ${splits[0]} $EXTGENERAL),$(basename ${splits[1]} ${EXTGENERAL}.mat),$ID1,$ID2,$elem.$EXT.filt.png,${getnum[${numX}]},${getnum[${numY}]},$score" >> $OUT

done

sort -k5,5n -k6,6n -o $OUT $OUT 


sed -i '1iSpX, SpY, IDX, IDY, IMG, CHNumberX, CHNumberY, Score' $OUT

rm index.csv.temp