Brent Pedersen

Hi, I'd accept a PR to fix this, but am not able to keep up with python packaging issues lately

This is the latest build: https://github.com/brentp/fishers_exact_test/actions/runs/13974734435 I have it working except that the MacOS builds are not running

yes, see: https://github.com/samtools/htslib/blob/develop/htslib/faidx.h I can have a look at this in a couple weeks (unless @jmarshall beats me too it).

yes.

Hi @bredeson , can you pull the latest from github, re-build, and try again? You will need this version: ``` $ ./bin/bedtools --version bedtools v2.30.0-66-gb891a0b6 ```

Hi, it looks like your gemini is not executable: > /bin/sh: 1: gemini: Permission denied you can do `chmod +x /path/to/gemini` to make it so. You should be able to...

Hi, your gemini must be executable for gemini_load to work. If you run and show the full command and full output it will be easier to hep you.

hmm. that is odd. here is the code for raw header: https://github.com/brentp/cyvcf2/blob/541ab16a255a5287c331843d8180ed6b9ef10e00/cyvcf2/cyvcf2.pyx#L641-L650

is `__set__` somehow getting called? https://github.com/brentp/cyvcf2/blob/541ab16a255a5287c331843d8180ed6b9ef10e00/cyvcf2/cyvcf2.pyx#L1987-L1995

yeah, the contigs only get added when they are not found on a record. I think the solution is to document that in order to get the unaltered header, you...