Hi,
when I extract only one chromosome of bam and fasta files to run, GCI stills outputs all chromosomes. The other chromosomes are null but the desired chromosome also failed.

python /share/home/zhanglab/user/chenquanyu/scripts/GCI/GCI.py -r C022-CHA-S02_2-01.chrY.fa --nano C022-CHA-S02_2-01.chrY.bam -o C022-CHA-S02_2-01_ont -it png -p -ts 5 --force && touch C022-CHA-S02_2-01_ont.GCI.finish

Could you please add a parameter for specifically outputing one chromosome or one region?

Thanks