3f923941d0c6025160491286c2d119170a6d9d59,cnvlib/vary.py,,read_vcf,#,10

Before Change

def read_vcf(vcf_fname, sample_id=None, min_depth=1, skip_hom=True,
             skip_reject=False, skip_somatic=True):
    Parse SNV coordinates from a VCF file into a DataFrame.
    with open(vcf_fname) as vcffile:
        vcf_reader = vcf.Reader(vcffile)
        rows = parse_records(vcf_reader, sample_id, min_depth, skip_hom,
                             skip_reject, skip_somatic)
        dframe = pd.DataFrame.from_records(rows, columns=[
            "chromosome", "start", "end",
            "ref", "alt", "zygosity", "depth", "alt_count"])
    dframe["alt_freq"] = dframe["alt_count"] / dframe["depth"]
    return dframe

After Change

    def read_vcf(cls, infile, sample_id=None, min_depth=1, skip_hom=True,
                 skip_reject=False, skip_somatic=True):
        Parse SNV coordinates from a VCF file into a VariantArray.
        if isinstance(infile, basestring):
            vcf_reader = vcf.Reader(filename=infile)
        else:
            vcf_reader = vcf.Reader(infile)

Instances