Nils Homer

@fleharty no urgency on my end, but just checking in on this.

@brentp I think you can take a look at pysam's use of `htslib` in their `setup.py` for some hints.

Probably the best way is via the `Writer.from_string` and `Writer.variant_from_string` methods.

Ditto, on vacation for a week or so but want to make a PR myself, but happy to work with yours @chrissype.

I’ll post one in the next week or so.

@brentp how about a param to `cyvcf2` to either 'stop', 'keep going', or 'throw an exception'? Similar to picard's strict, lenient, or silent.

I think this may be something very insidious going on here. The following works: ```python import cyvcf2 print(f"version: {cyvcf2.__version__}") fh = open("./bad_vcf.vcf") reader = cyvcf2.Reader(fh) for v in reader: print(v)...

Some quick googling found maybe a red herring, or maybe not: https://stackoverflow.com/a/8011863

@brentp where do you store the weakref? VCF? HtsFile?

@tavinathanson I have found using rclone to preserve timestamps works. Unfortunately, I have to pull the data locally still then run snakemake. See #1710.