Crashes when chromosomes have no CpG sites #307

Describe the bug
In amrfinder, seemingly hmr, and likely some others, when no CpG sites exist for a chromosome, the iteration over sites thinks the data is unsorted.

To Reproduce
dnmtools amrfinder -t 8 -c genomes/strPur2/strPur2.fa -S SRS1093758/SRX1294710/SRX1294710.amr.yaml -o SRS1093758/SRX1294710/SRX1294710.amr SRS1093758/SRX1294710/SRX1294710.states.gz

Expected behavior
Exception due to unsorted data that is expected to have entries for all chromosomes.