jayhesselberth / cyvcf2

cython + htslib == fast VCF parsing

cyvcf2

cyvcf2 is a cython wrapper around htslib built for fast parsing of Variant Call Format (VCF) files. It is targetted toward our use-case in gemini but should also be of general utility.

On a file with 189 samples that takes cyvcf 21 seconds to parse and extract all sample information, it takes cyvcf2 1.4 seconds.

Attributes like variant.gt_ref_depths return a numpy array directly so they are immediately ready for downstream use. note that the array is backed by the underlying C data, so, once variant goes out of scope. The array will contain nonsense. To persist a copy, use: cpy = np.array(variant.gt_ref_depths) instead of just arr = variant.gt_ref_depths.

Example

from cyvcf2 import VCF

for variant in VCF('some.vcf.gz'):

	variant.gt_types # numpy array
	variant.gt_ref_depths, variant.gt_alt_depths # numpy arrays
	variant.gt_phases, variant.gt_quals # numpy arrays
	variant.gt_bases # numpy array
	variant.CHROM, variant.start, variant.end, variant.ID, \
				variant.REF, variant.ALT, variant.FILTER, variant.QUAL
	variant.INFO.get('DP') # int
	variant.INFO.get('FS') # float
	variant.INFO.get('AC') # float
    a = variant.gt_phred_ll_homref # numpy array
    b = variant.gt_phred_ll_het # numpy array
    c = variant.gt_phred_ll_homalt # numpy array

	str(variant)

Installation

pip install cyvcf2

Testing

Tests can be run with:

python setup.py test

See Also

Pysam also has a cython wrapper to htslib and one block of code here is taken directly from that library. But, the optimizations that we want for gemini are very specific so we have chosen to create a separate project.