Quality of life suggestion for motif bed

[Ge0rges]

Hi @ArtRand

Just an unimpactful quality of life suggestion. It would be nice to have a --contig option on motif bed to restrict to the passed contig.

Just a small suggestion to go with --contig in motifs to streamline regions passed then to things like pileup.

[ArtRand]

Hello @Ge0rges,

I've been meaning to do this, thanks for the poke.

[Ge0rges]

@ArtRand, another suggestion would be to clarify the docs to state whether the positions printed are for the first nucleotide of the motif or the methylated nucleotide. I believe it's the methylated nucleotide from looking at the results correct? That would also make sense with being able to pass it on directly to pileup for example.