Brent Pedersen

extern structs

1

I am trying to use [this struct](https://github.com/smarco/WFA2-lib/blob/913447a95cf80dbb11d0c1c2cd8b652fe9a1b8bb/wavefront/wavefront_attributes.c#L37) which has default values. it's just [externed](https://github.com/smarco/WFA2-lib/blob/913447a95cf80dbb11d0c1c2cd8b652fe9a1b8bb/wavefront/wavefront_attributes.h#L154) in the header. I've manually set the defaults in nim because the futhark version of `wavefront_aligner_attr_default`...

segfault with pca without -d:danger or -d:release

5

I am getting a segfault with pca, but only when built without release and without danger. with gdb, I see: ``` Thread 16 "somalier" received signal SIGSEGV, Segmentation fault. [Switching...

c-api doesn't allow setting parameters when writing a new d4 file

2

for example, i'd like to turn on deflate and set the level.

zip ENH request add/extract single file [streams]

6

Thanks for the library. From what I can see, it supports only extracting all or adding all to a zip archive. I have potentially huge archives and want to be...

bigwig output

6

it will be useful to have bigwig output from mosdepth. this is my tentative plan; feedback by users would be appreciated. mosdepth will remain unchanged, except that when per-base output...

should take a vcf and a .ped and show transmission rates, rates of denovos for various cutoffs. a cutoff can be variant quality, genotype quality, depth, etc. should output in...

ContainsRange ?

4

I was trying to use `roaring.Bitmap` in place of an interval tree when I dont want to recover the interval, I just want to see if there's overlap. This works...

performance of avx512 bit ops and popcounts

4

as requested, I am opening an issue. [somalier](https://github.com/brentp/somalier) calculates relatedness between pairs of samples using bitwise operations and popcounts [here](https://github.com/brentp/somalier/blob/a6facc7a366e67f657a089ba1b0a7c723cef7fb0/src/somalierpkg/bitset.nim#L20-L31) where genotypes is effectively: ``` type genotypes* = tuple[hom_ref:seq[uint64], het:seq[uint64],...

better error messages

7

Nextflow is great!, But, it is sometimes quite difficult to debug nextflow errors due to uninformative error messages. Here is one example: ``` nextflow.enable.dsl=2 process wtf { input: val(a) val(b)...

check Y chromosome

2

might help resolve samples that are ambiguous from just looking at X.