Does modkit sample-probs still have an option for only mapped regions?

[MafaldaSoares]

Hello modkit team,

I was trying to update modkit from version 0.5.0 to the current version 0.6.4. Before I used the argument --only-mapped to run modkit sample-probs based only on mapped regions. From what I can see this argument seems to not exist anymore. Is there any other option that I should be using in its place, or has the assumption changed and modkit sample-probs runs based only on mapped regions?

Thank you in advance,
Mafalda

[ArtRand]

Hello @MafaldaSoares,

Sorry about the delay. The easiest way to do this with the current release is to add --motif A 0 --motif C 0 --motif T 0 --motif G 0 to your command. Of course, if you know you don't have base modifications at certain primary sequence bases, you can omit those. These options will collect probabilities only at matched positions.

I've attached a build with --matched-only and --mapped-only flags in modkit modbam sample-probs. --matched-only is a shorthand for the --motif options above. --mapped-only simply discards unmapped reads, but does not require that the read's primary sequence base matches the reference base.

modkit_v0.6.4_2d0da7a.zip