feature request paf filter

[colindaven]

Hi,

I couldn't find any utilities for filtering pafs and this tool seems to be the most capable and toolkit-like.

Maybe it would be an option to put in a filter to avoid users having to hack together one liners in awk, like I did here.

# this is nextflow so contains escaped $

   awk '{if ((P=\$11/\$2*100) >= $params.min_align_length) {print P"\t"\$_}}' $paf

Filters might include

• Mapping Quality if available ?
• NM number mismatches
• alignment length

It might be easy to do this in awk, but it is a bit hacky and error prone.

Other repos do not seem to offer a paf filter either AFAIK

https://github.com/AndreaGuarracino/paf2chain

https://github.com/AndreaGuarracino/pafgnostic

https://github.com/ekg/pafplot

etc

Thanks

[glennhickey]

I agree that these are useful features to add.

In the meantime, you can consider using gaffilter. It's a little specific to minigraph-cactus, but I think does some of what you want (and despite its name, works on PAF as well as GAF).

[colindaven]

Hi @glennhickey thanks, that is useful.

I wrote something similar for gaf filtering once and noticed it at least partially worked on PAF too.