set -e

RES=$1
CHROM=$2
RES_KB=$(($RES/1000))

mkdir -p hic_data

cd hic_data

if [ ! -e GSE63525_GM12878_combined_intrachromosomal_contact_matrices.tar.gz ]
	then
		curl ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE63nnn/GSE63525/suppl/GSE63525%5FGM12878%5Fcombined%5Fintrachromosomal%5Fcontact%5Fmatrices%2Etar%2Egz -o GSE65325_GM12878_combined_intrachromosomal_contact_matrices.tar.gz		
fi


RES_KB=$(($RES/1000))

if [ $RES_KB -lt 1000 ]
	then
		RES_STRING=$RES_KB"kb"
else
	RES_STRING=$(($RES_KB/1000))"mb"
fi

if [ $CHROM -eq 0 ]
	then
		for CHROM in 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X
		do
			DIR=$RES_STRING"_resolution_intrachromosomal"/chr$CHROM
			if [ ! -e GM12878_combined/$DIR ]
				then
					tar xzf GSE63525_GM12878_combined_intrachromosomal_contact_matrices.tar.gz GM12878_combined/$DIR
			fi

			if [ ! -e "GM12878_combined_"$CHROM"_"$RES_KB$RES_STRING.bed ]
				then
	  				python ../normalize.py GM12878_combined $RES $CHROM
			fi
		done

else
	DIR=$RES_STRING"_resolution_intrachromosomal"/chr$CHROM
	if [ ! -e GM12878_combined/$DIR ]
		then
			tar xzf GSE63525_GM12878_combined_intrachromosomal_contact_matrices.tar.gz GM12878_combined/$DIR
	fi

	if [ ! -e GM12878_combined_$CHROM"_"$RES_KB$RES_STRING.bed ]
		then
	  		python ../normalize.py GM12878_combined $RES $CHROM
	fi

fi

cd ..