Brent Pedersen
Brent Pedersen
I pushed a fix for this exact case and made the is_indel handling more general. But yeah, likely other problems persist. Will fix as I see them. thanks for reporting.
done. thanks for the reminder
yes, the from_string methods are the way to go. htslib doesn't (or at least pre 1.10 didn't) provide much help here and I didn't add any helpers. There is some...
I think a pure python set-up would be fine. Happy to review a PR.
I can probably implement this like: ``` vcf.set_sample_name(int index, char *newname) ```
actually, I just looked into this. The reason no htslib wrapper does it (including cyvcf2) is because it's hard. It would involve splicing out characters from the header text, updating...
see: https://github.com/brentp/cyvcf2/tree/htslib-1.10
I'll have a look at this: https://jasonet.co/posts/scheduled-actions/ and/or gladly accept a PR
hmm. yeah. this needs to be addressed here: https://github.com/brentp/cyvcf2/blob/2dd88453ff4ec619311f860a2df4651f8b2ccf04/cyvcf2/cyvcf2.pyx#L572-L577 htslib returns -1 from bcf_read in this case, and prints a message. cyvcf2 currently just stops iteration.
So it looks like the way to handle this in cyvcf2 is to check the errcode which [gets set](https://github.com/samtools/htslib/blob/4162046b28a7d9d8a104ce28086d9467cc05c212/vcf.c#L2537) when there is a problem. It is set to one of...