--- a/chromeister/bin/index_chromeister.sh	Wed Dec 12 07:18:40 2018 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,80 +0,0 @@
-#!/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
-