Metadata-Version: 2.1
Name: pybcf
Version: 1.0.2
Summary: Package for loading data from bcf files
Home-page: https://github.com/jeremymcrae/pybcf
Author: Jeremy McRae
Author-email: jmcrae@illumina.com
License: MIT
Classifier: Development Status :: 4 - Beta
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Description-Content-Type: text/markdown
License-File: LICENSE.txt
Requires-Dist: numpy
Provides-Extra: test
Requires-Dist: pysam ; extra == 'test'


### pybcf

This is a package for reading BCF files (binary call format). Similar to pysam/cyvcf2, but limited to reading from BCF files only, and oriented around getting genotype data into numpy arrays quickly.

'''py
from pybcf import BcfReader

bcf = BcfReader(bcf_path)

for var in bcf:
    # the usual attributes are available e.g.
    # var.chrom, var.pos, var.ref, var.alts, var.info['AF']
    
    # get genotypes as numpy array
    genotypes = var.samples['GT']  # as numpy array, missing=-1
'''

### Limitations
 - can't fetch variants from random regions yet
 - not extensively tested yet
 - extracting info fields is slow at the moment
