@parameterized.parameters(True, False)
def test_gvcfs_counts(self, include_gvcfs):
    counts = [(0, 0, 'A'), (10, 10, 'G'), (0, 0, 'G'), (0, 0, 'G'), (10, 10, 'T')]
    caller = PlaceholderVariantCaller(0.01, 100)
    allele_counter = self.fake_allele_counter(10, counts)
    allele_counters = {}
    allele_counters['sample_id'] = allele_counter
    (_, gvcfs) = caller.calls_and_gvcfs(allele_counters, include_gvcfs, 'sample_id')
    if include_gvcfs:
        self.assertLen(gvcfs, 4)
        flat_gls = np.log10(([(1.0 / 3)] * 3))
        self.assertGVCF(gvcfs[0], ref='A', start=10, end=11, gq=1, min_dp=0, gls=flat_gls)
        self.assertGVCF(gvcfs[1], ref='G', start=11, end=12, gq=0, min_dp=20, gls=np.array([(- 14.0230482368), (- 7.993606e-15), (- 14.0230482368)]), gts=[(- 1), (- 1)])
        self.assertGVCF(gvcfs[2], ref='G', start=12, end=14, gq=1, min_dp=0, gls=flat_gls)
    else:
        self.assertEmpty(gvcfs)
@parameterized.parameters(True, False)
def test_gvcfs_counts(self, include_gvcfs):
    counts = [(0, 0, 'A'), (10, 10, 'G'), (0, 0, 'G'), (0, 0, 'G'), (10, 10, 'T')]
    caller = PlaceholderVariantCaller(0.01, 100)
    allele_counter = self.fake_allele_counter(10, counts)
    allele_counters = {}
    allele_counters['sample_id'] = allele_counter
    (_, gvcfs) = caller.calls_and_gvcfs(allele_counters, include_gvcfs, 'sample_id')
    if include_gvcfs:
        self.assertLen(gvcfs, 4)
        flat_gls = np.log10(([(1.0 / 3)] * 3))
        self.assertGVCF(gvcfs[0], ref='A', start=10, end=11, gq=1, min_dp=0, gls=flat_gls)
        self.assertGVCF(gvcfs[1], ref='G', start=11, end=12, gq=0, min_dp=20, gls=np.array([(- 14.0230482368), (- 7.993606e-15), (- 14.0230482368)]), gts=[(- 1), (- 1)])
        self.assertGVCF(gvcfs[2], ref='G', start=12, end=14, gq=1, min_dp=0, gls=flat_gls)
    else:
        self.assertEmpty(gvcfs)