What does modkit extract calls do with reads that do not have a considered motif? #585
Description
I think I know the answer to this, but what does extract calls do for reads that do not have the motif of interest?
Eg if I run modkit extract calls --cpg what happens if I have reads with no CG motif? Does it skip over the read and not report it? Do I have to check the modkit log file to see how many were skipped because of this reason? Is the correct way then to not use --cpg (and also call dorado using 5mC instead of 5mCG) if I want to grab all reads in that table?