Brent Pedersen

Hi Jinhua, slivar is agnostic to the organism. If you have a pedigree file for your pigs, then you can use it as explained in the documentation (which does use...

Hi, so you can use slivar expr first like this: ``` slivar expr \ --ped $your.ped \ --trio 'comphet_side:comphet_side(kid, mom, dad)' \ ... ``` and then run: ``` slivar compound-hets...

It should require only ~ 1GB of memory, perhaps 2. Do you see the same memory use if you remove --by and --thresholds ?

that sounds excessive! can you verify that mosdepth from the releases here has the same memory usage?

ok. just a quick point--does `whole_genome.mappable.binned_10bp.bed.gz` have, for example 24.9 million 10bp intervals for chromosome 1? That would be the reason. I do not optimize for bed files of this...

yes, `--by 10` should have lower memory requirement and it is consistent, it will always create 0..10, 10..20, etc. I am downloading your test-data on a slow connection so it...

phew! glad to hear it! I am surprised that the bed file is so bad. I am looking into it.

hmm. good sleuthing! this should not increase the memory so there should be a way we can improve this without a flag. I'll have a look this week.

so removing that section does not change the memory use for me! are you sure that's the issue?

for bed, it reads everything into memory and nim strings use 64 bits for length, 64 bits for capacity, and n-bytes for the actual data. what you describe for fragment...