Michael Hall

Looking at https://github.com/google/googletest/issues/2224 and the PR it links to, I think upgrading out google test version from v1.10 to something like from v1.13 onwards *should* fix this? https://github.com/rmcolq/pandora/blob/32911655d1ccf8b8843f31fdad1f1da48a331de2/cmake/Hunter/config.cmake#L12

In the meantime, Wei Shen is awesome and there is (of course) a way to do this with seqkit https://github.com/shenwei356/seqkit/issues/403

Maybe, but it isn't blocking me (it only happened at a certain w and k value and I'm not using those w/k values currently)

I would argue this is also a make_prg issue. Shouldn't all three positions be a bubble as they have overlapping positions? > Common bases should not interfere on the likelihood...

I'm seeing these annoying duplications of positions a bit lately. And they're causing me to miss calls in drprg. A recent example I have. Here is an example of the...

The PRG string is technically representing this correctly, but my issue is I think the representation is somewhat flawed. With a minimum match length of 5, we should basically have...

Thanks for the detailed response. All of this makes sense. Deduplicating the alleles does seem like the better way to approach things I think. If you tested it out on...

Hmmm, so this has popped it's head up a number of times now in *pncA* and *rpoB* and *gid*. Any idea when there might be a binary available with your...

I've tested that out on two samples and I still get the same problem. Here is one of the examples that has a POS duplication at rpoB POS 1389 in...

I just noticed codon has glibc v 2.28 ``` $ ldd --version ldd (GNU libc) 2.28 Copyright (C) 2018 Free Software Foundation, Inc. This is free software; see the source...