adjust-mods --cpg bug #502
Description
Hi,
Could there be a small bug here? The documentation of adjust-mods indicates that --cpg is a short-hand for --motif CG 0, however it seems that --cpg is not correctly detected.
modkit adjust-mods IKE_1.bam CpG_only/IKE_1.bam --cpg
> Error! no edge-filter, ignore, motifs, or convert was provided, no work to do. Provide --edge-filter, --ignore, --filter-probs, --motif, or --convert option to use `modkit adjust-mods`
modkit adjust-mods IKE_1.bam CpG_only/IKE_1.bam --motif CG 0
> filtering base modification calls to patterns: CG
> 159 Adjusting modBAM, records processed