Modkit pileup --modified-bases 5mC and 5hmC returning same results

[decibel-tom]

Hey all!

Long time user, first time poster. With the recent switch to modkit v0.6.0+ and the removal of the --ignore h flag, we've been having some trouble filtering to only include the 5mC results. We've noticed the recent change to include the --modified-bases but it seems like when we run this with 5mC and 5hmC we get the same results and I was wondering if I'm not understanding how this should be working?

My command looks like:
${bam_file} ${output_bed} --motif CG 0 --motif CHG 0 --motif CHH 0 --modified-bases 5mC --ref ${reference} --filter-threshold 0.66 -t ${threads}

and the output looks like:

However, when I run the same command as above, but with --modified-bases 5hmC it returns the following:

Both results contain both "h" and "m" rows, but I would expect the 5mC to not return any "h" rows.