Quickly check chromosome sizes in hic file

hic_chrom_sizes

#!/usr/bin/env bash

# As hic files contain sparse matrices, the matrix size is usually smaller than the expected (especially at high resolutions)
# This needs straw to be installed, see here: https://github.com/aidenlab/straw

hic_file="SRR2184278-93.hic"
resolution=100000
chromosomes=($(seq 1 22) X Y)

if [ -f "$hic_file.chrom_size.tsv" ]; then
    rm "$hic_file.chrom_size.tsv"
    touch "$hic_file.chrom_size.tsv"
fi
for i in ${chromosomes[@]}; do
    size=$(straw observed KR $hic_file "$i" "$i" BP $resolution | tail -n 1 | cut -f 1)
    echo -e "$i\t$size" >> $hic_file.$resolution.chrom_size.tsv
done