looselab / rftools Goto Github PK

Duplex read ids seem to be a combination of their parents read_ids, joined by a semi colon.
So we would compare both halves of the read_id in turn to the unblocked readids hashset.

If there is a match from either we would consider that read unblocked.

Would be nice if you could join up rftools with dorado with pipes. Something like:

dorado basecaller hac pod5s/ | rftools split-bam --bam-file - --unblocked-read-ids ...

Not sure how much work this would be, but might save some time/space? I anticipate that the BAM header might be a problem but might not?

Many tools exist to do this, but may as well do this all in one step.

Add a minimum length cut off to split_bam. Make it an Option<usize>, and add it to the filter step.

I wanna be able to install this bad boy. We should probably also do binaries at some point.

That's more of a stretch goal doe

Include how to build rust documentation

Use the same setup as in readfish stats