Zamin Iqbal
Zamin Iqbal
Actually this might be a RAM/speed tradeoff - if we lazy load gene/PRGs into RAM only when we see them?
(Hope i'm not misrepresenting you @Danderson123 , I can delete this or update it)
I have to say @Danderson123 , first mapping to an AMR-only PRG and only keeping those reads, and then mapping just those to the big PRG, would probably make a...
We had a long and v g discussion about this. we should have a call with @rmcolq
(fwiw John Lees and Johanna in the office next to us has been using robin hood hashing and got Dan into it too)
good spot! it used to be true that error rate was calculated for the first sample and then applied to all - is that bug gone or does it remain?
i think it's fine to map with a default rate and then re-estimate better. I dont think it's a great assumption to assume all samples given to compare have the...
makes sense - after the paper!
AARGH i thought this was fixed
Sorry it is currently too slow! Pandora is inherently parallelisable by sample when mapping, and then by gene when doing 'compare', and could then in principle run very fast on...