@parameterized.parameters(([(0, 0, 'A')], [dict(start=1, end=2, ref='A', gq=1, min_dp=0)]), ([(0, 0, 'A'), (0, 0, 'C')], [dict(start=1, end=3, ref='A', gq=1, min_dp=0)]), ([(0, 0, 'C'), (0, 0, 'A')], [dict(start=1, end=3, ref='C', gq=1, min_dp=0)]), ([(0, 0, 'A'), (0, 0, 'C'), (0, 0, 'T')], [dict(start=1, end=4, ref='A', gq=1, min_dp=0)]), ([(0, 0, 'A'), (0, 100, 'C')], [dict(start=1, end=2, ref='A', gq=1, min_dp=0), dict(start=2, end=3, ref='C', gq=100, min_dp=100)]), ([(0, 100, 'A'), (0, 0, 'C')], [dict(start=1, end=2, ref='A', gq=100, min_dp=100), dict(start=2, end=3, ref='C', gq=1, min_dp=0)]), ([(0, 0, 'A'), (0, 20, 'C'), (0, 100, 'T')], [dict(start=1, end=2, ref='A', gq=1, min_dp=0), dict(start=2, end=3, ref='C', gq=59, min_dp=20), dict(start=3, end=4, ref='T', gq=100, min_dp=100)]))
def test_make_gvcfs(self, counts, expecteds):
    allele_counts = self.fake_allele_counter(1, counts).summary_counts()
    caller = PlaceholderVariantCaller(0.01, 100)
    gvcfs = list(caller.make_gvcfs(allele_counts))
    self.assertLen(gvcfs, len(expecteds))
    for (actual, expected) in zip(gvcfs, expecteds):
        self.assertGVCF(actual, **expected)
@parameterized.parameters(([(0, 0, 'A')], [dict(start=1, end=2, ref='A', gq=1, min_dp=0)]), ([(0, 0, 'A'), (0, 0, 'C')], [dict(start=1, end=3, ref='A', gq=1, min_dp=0)]), ([(0, 0, 'C'), (0, 0, 'A')], [dict(start=1, end=3, ref='C', gq=1, min_dp=0)]), ([(0, 0, 'A'), (0, 0, 'C'), (0, 0, 'T')], [dict(start=1, end=4, ref='A', gq=1, min_dp=0)]), ([(0, 0, 'A'), (0, 100, 'C')], [dict(start=1, end=2, ref='A', gq=1, min_dp=0), dict(start=2, end=3, ref='C', gq=100, min_dp=100)]), ([(0, 100, 'A'), (0, 0, 'C')], [dict(start=1, end=2, ref='A', gq=100, min_dp=100), dict(start=2, end=3, ref='C', gq=1, min_dp=0)]), ([(0, 0, 'A'), (0, 20, 'C'), (0, 100, 'T')], [dict(start=1, end=2, ref='A', gq=1, min_dp=0), dict(start=2, end=3, ref='C', gq=59, min_dp=20), dict(start=3, end=4, ref='T', gq=100, min_dp=100)]))
def test_make_gvcfs(self, counts, expecteds):
    allele_counts = self.fake_allele_counter(1, counts).summary_counts()
    caller = PlaceholderVariantCaller(0.01, 100)
    gvcfs = list(caller.make_gvcfs(allele_counts))
    self.assertLen(gvcfs, len(expecteds))
    for (actual, expected) in zip(gvcfs, expecteds):
        self.assertGVCF(actual, **expected)