def test_pass_fail_variant_2():
"""
Tests the DP flag filter
:return:
"""
vcf_file = 'test/vcf/pass_fail_variant_2.vcf'
output_eff = 'test/vcf/pass_fail_variant_2.eff'
min_coverage = 5
cov_metric = 'DP'
reverse_split = False
flags = fv.vcf2eff(vcf_file, output_eff, min_coverage, cov_metric,
reverse_split)
assert flags['min_coverage'] == ['chrI:4295']
def test_pass_fail_variant_6():
"""
passes if we see an A/G variant on the reverse strand,
when the library is reverse stranded
:return:
"""
vcf_file = 'test/vcf/pass_fail_variant_6.vcf'
output_eff = 'test/vcf/pass_fail_variant_6.eff'
min_coverage = 5
cov_metric = 'DP'
reverse_split = True
flags = fv.vcf2eff(vcf_file, output_eff, min_coverage, cov_metric,
reverse_split)
assert flags['not_editing'] == ['chrI:3771']
def test_pass_fail_variant_3():
"""
passes if we see an A/G variant on the forward strand,
when the library is forward stranded
:return:
"""
vcf_file = 'vcf/pass_fail_variant_3.vcf'
output_eff = 'vcf/pass_fail_variant_3.eff'
min_coverage = 5
cov_metric = 'DP'
reverse_split = False
flags = fv.vcf2eff(vcf_file, output_eff, min_coverage, cov_metric,
reverse_split)
assert flags['not_editing'] == ['chrI:4295']