def test_phasing_for_isolated_snp_on_one_sample_only(self):
sample_1 = "sample_1"
sample_2 = "sample_2"
chrom = "1"
svc_driver = SVCDriver(self)\
.with_ref_sequence(
"ACGCCCCTGCAAAAAAAAAAT", chrom=chrom
).with_read(
"........T............", n_fwd=10, n_rev=10, sample_name=sample_1
).with_read(
".....................", n_fwd=10, n_rev=10, sample_name=sample_2
)
svc_driver.with_output_phased_genotypes(True)
expect = svc_driver.call()
vcf_expect = expect.with_output_vcf()
vcf_expect.record_count(1)
record_expect = vcf_expect.has_record_for_variant(
Variant(chrom, 8, "G", "T"))
sample_1_expect = record_expect.with_sample(sample_1)
sample_1_expect.has_phased_genotype("1|1")
sample_1_expect.has_phase_set_id(str(8))
sample_1_expect.has_phase_set_quality(MAX_PHRED)
sample_2_expect = record_expect.with_sample(sample_2)
sample_2_expect.has_phased_genotype("0|0")
sample_2_expect.has_phase_set_id(str(8))
sample_2_expect.has_phase_set_quality(MAX_PHRED)
def test_phasing_for_isolated_heterozygous_variant(self):
sample_name = "a_sample"
chrom = "1"
svc_driver = SVCDriver(self)\
.with_ref_sequence(
"ACGCCCCTGCAAAAAAAAAAT", chrom=chrom) \
.with_read(
"........T............", n_fwd=10, n_rev=10, sample_name=sample_name) \
.with_read(
".....................", n_fwd=10, n_rev=10, sample_name=sample_name)
svc_driver.with_output_phased_genotypes(True)
expect = svc_driver.call()
vcf_expect = expect.with_output_vcf()
vcf_expect.record_count(1)
record_expect = vcf_expect.has_record_for_variants(
Variant(chrom, 8, "G", "T"))
sample_expect = record_expect.with_sample(sample_name)
sample_expect.has_phased_genotypes("0|1")
sample_expect.has_phase_set_id(str(8))
sample_expect.has_phase_set_quality(MAX_PHRED)
def test_phasing_for_two_snps_across_samples(self):
sample_1 = "sample_1"
sample_2 = "sample_2"
chrom = "1"
svc_driver = SVCDriver(self)\
.with_ref_sequence(
"ACGCCCCTGCAAAAAAAAAAT", chrom=chrom
).with_read(
"........T............", n_fwd=10, n_rev=10, sample_name=sample_1
).with_read(
".....................", n_fwd=10, n_rev=10, sample_name=sample_1
).with_read(
"........C............", n_fwd=10, n_rev=10, sample_name=sample_2
).with_read(
".....................", n_fwd=10, n_rev=10, sample_name=sample_2
)
svc_driver.with_output_phased_genotypes(True)
expect = svc_driver.call()\
.with_output_vcf() \
.record_count(2)
expect.has_record_for_variants(Variant(chrom, 8, "G", "T"),
Variant(chrom, 8, "G", "C"))
expected_phase_set_id = str(8)
expect \
.has_record_for_variants(Variant(chrom, 8, "G", "T"), Variant(chrom, 8, "G", "C")) \
.with_sample(sample_1)\
.has_phased_genotypes("0|1", "0|.") \
.has_phase_set_id(expected_phase_set_id) \
.has_phase_set_quality(MAX_PHRED)
expect \
.has_record_for_variants(Variant(chrom, 8, "G", "T"), Variant(chrom, 8, "G", "C")) \
.with_sample(sample_2)\
.has_phased_genotypes(".|0", "1|0") \
.has_phase_set_id(expected_phase_set_id) \
.has_phase_set_quality(MAX_PHRED)