Rescue_small question and potential bug

[AroneyS]

It looks like rescue_small rescues small query sketches but not small reference sketches (see

skani/src/screen.rs

Line 159 in ec4e2e1

if query_sketch.marker_seeds.len() < 20 && rescue_small{

). This is a bug, right?

Also, do you have a rough estimate for the number of bp that corresponds to query_sketch.marker_seeds.len() < 20?

[bluenote-1577]

Hi @AroneyS,

Thanks for bringing this to my attention. Yes, the current screening algorithm is asymmetric between the queries and references for filtering, possibly giving different results when contigs are small. This appears to be a subtle bug.

This will take a bit of testing, so I'll leave this up and fix it in a bit.

[bluenote-1577]

The number of marker seeds is on average, genome size / m, where m is the -m parameter. So by default, approx 20kb genomes or contigs pass the filter