cyvcf2
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brentp
cython + htslib == fast VCF and BCF processing
Hi,@brentp I have installed cyvcf2,but there is en error like: cannot import name 'VCF' from 'cyvcf2' (unknown location) I need your help. thankyou very much~
Is there a way to know if the region supplied to the VCF reader is a valid region? ```python # reading vcf of chr19 reader = VCF("chr19.vcf") # try getting...
Missing values for Integer INFO/FORMAT fields are represented by the minimum int32 value (-2147483648, or `np.iinfo(np.int32).min`). It would be nice if a mask array could be retrieved that didn't rely...
For a variant `v` it's nice to be able to say `v.FORMAT` and to see the available fields names. Would it be difficult to do the same for `v.INFO`?
Hi, I'm getting strange genotype calls and then a crash with my GATK VCF. The zygosity call is strange, but the VCF passes validation. I've reduced it down to a...
Hi, Please understand that I do not have any experience with C or htslib. I would like to write missing values ('.') to FORMAT fields. I incidentally found that when...
Hi there, I'd like to be able to write new values to the filter field as part of writing out a new VCF. But I get the following issue: ```...
should be able to get `variant.errcode` as a property that returns variant.b.errcode. see #162
If the `PS` format field has type `Integer` but the _values_ are strings, then `cyvcf2` will skip the variant but not throw an exception. I would have expected, by default,...
Might be related to #46 as I manage to fix the assertion error by renaming the bcf.gz (and bcf.gz.csi) to bcf (and bcf.csi) Below is the relevant part of the...
