def test_add_variant_with_genotypes():
"""
Test to add a variant to a vcf
"""
parser = VCFParser(fileformat="VCFv4.1")
parser.metadata.add_info(info_id='MQ',
number='1',
entry_type='Float',
description="RMS Mapping Quality")
header_line = '#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\t'\
'father\tmother\tproband'
parser.metadata.parse_header_line(header_line)
parser.add_variant(chrom='1',
pos='11900',
rs_id='.',
ref='A',
alt='T',
qual='100',
filt='PASS',
info="MQ=1",
form="GT:GQ",
genotypes=["0/1:60", "0/1:60", "1/1:60"])
variant = parser.variants[0]
assert variant['POS'] == '11900'
assert variant['mother'] == '0/1:60'
def test_add_variant():
"""
Test to add a variant to a vcf
"""
parser = VCFParser(fileformat="VCFv4.1")
parser.metadata.add_info(info_id='MQ',
number='1',
entry_type='Float',
description="RMS Mapping Quality")
parser.add_variant(chrom='1',
pos='11900',
rs_id='.',
ref='A',
alt='T',
qual='100',
filt='PASS',
info="MQ=1")
variant = parser.variants[0]
assert variant['CHROM'] == '1'
assert variant['POS'] == '11900'
def test_add_variant():
"""
Test to add a variant to a vcf
"""
parser = VCFParser(fileformat="VCFv4.1")
parser.metadata.add_info(
info_id='MQ', number='1', entry_type='Float', description="RMS Mapping Quality")
parser.add_variant(chrom='1', pos='11900', rs_id='.', ref='A',
alt='T', qual='100', filt='PASS', info="MQ=1")
variant = parser.variants[0]
assert variant['CHROM'] == '1'
assert variant['POS'] == '11900'
def test_add_variant_with_genotypes():
"""
Test to add a variant to a vcf
"""
parser = VCFParser(fileformat="VCFv4.1")
parser.metadata.add_info(
info_id='MQ', number='1', entry_type='Float', description="RMS Mapping Quality")
header_line = '#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\t'\
'father\tmother\tproband'
parser.metadata.parse_header_line(header_line)
parser.add_variant(chrom='1', pos='11900', rs_id='.', ref='A',
alt='T', qual='100', filt='PASS', info="MQ=1",
form="GT:GQ", genotypes=["0/1:60", "0/1:60", "1/1:60"])
variant = parser.variants[0]
assert variant['POS'] == '11900'
assert variant['mother'] == '0/1:60'
