Brent Pedersen

cyvcf2 uses AD for `gt_*_depths` and expects diploid. your vcf looks like: ``` GT:AD:DP:ICNT:RGQ:SPL 0/0:25:23:26,0:60:0,61,255 ``` where there's only a single value for AD. the `gt_*_depths` and `gt_types` will only...

Thanks for looking into it. I'll use fromiter() or list() for now. Not sure I understand, but it segfaults not matter how small the carray: ``` ca = bcolz.carray(np.arange(1e1).astype(int)) np.array(bcolz.eval('ca...

@FrancescAlted I wonder if it's because of the odd (IMO) behavior of wheretrue() ``` Python import bcolz import numpy as np ca = bcolz.carray(np.arange(1e1).astype(int)) e = bcolz.eval('ca > 5').wheretrue() print...

I think the best way is to parse the string. The htslib API doesn't offer much to help here and I haven't implemented it in python as it's been simple...

I think copying pyvcf is fine for the API. I don't care about the `@lazy` this should be nearly immeasurable.

yeah, I somehow broke the install and I'm not sure how to fix it. you might be able to run `./configure` from the htslib/ directory and then re-do the setup.py...

indeed: https://github.com/brentp/cyvcf2/issues/96#issuecomment-422372156

Hi, these errors mean that you need libssl. You can also cd into the htslib directory and reconfigure.

while it shouldn't segfault, you don't have genotypes in your VCF, so `num_called` will never return something sensible. I'll add a guard for this scenario, but at best, it will...

ouch. it's been a long time since I looked at the `is_*` functions/properties. I'll see if I can et a fix for this case. Likely there are similar oversights in...