Brent Pedersen

Hi Xavier, I agree this would be useful and it is suggested in another open issue. I just haven't had the time to implement. I'll try to get to it...

thanks for the clear report and diagnosis. I have pushed a fix. would you try the attached binary (gunzip, chmod +x and `./goleft_linux64 covstats ...` ) and verify it looks...

Hi, thanks for following up. You could try increasing the number of sampled reads, e.g.: ``` goleft covstats -n 10000000 ... ``` to see if it converges to match TBProfiler...

Hi, I tagged a release here: https://github.com/brentp/goleft/releases/tag/v0.2.6 let me know if you have any further suggestions. I see what you mean about increasing the number of sampled reads.

Hi, this could be done by not simply taking the max here: https://github.com/brentp/peddy/blob/master/peddy/pca.py#L82 I would accept a PR that reports the other probabilities. The interpretation would not be the same...

Hi Xabier, thanks for reporting. I pushed a fix for this. There are still many things that need to change throughout hts-nim to be fully compatible with ORC/ARC. I'll keep...

Thanks for the test files and diagnosing the exact location of the problem! I can't remember how `idx_set_meta` works either. :cry:

@graphenn , can you help with this? there are no arm files here: https://pypi.org/project/cyvcf2/0.30.27/#files but indeed there are here: https://pypi.org/project/cyvcf2/0.30.22/#files

Hi, You should be able to use cyvcf2 directly. But, if the handle you pass to `VCF` has a `fileno` method or is an integer, the it will be treated...

Hi Dave, Don't use `format` for GT. use `variant.genotype` for an object or `variant.genotypes` for an array.