def assertGVCF(self, gvcf, ref, gq, start, end, min_dp, chrom='chr1', gls=None, sample_name=None, gts=None):
    if chrom:
        self.assertEqual(gvcf.reference_name, chrom)
    call = variant_utils.only_call(gvcf)
    self.assertNotEmpty(gvcf.reference_name)
    self.assertEqual(gvcf.reference_bases, ref)
    self.assertEqual(gvcf.alternate_bases, ['<*>'])
    self.assertEqual(gvcf.start, start)
    self.assertEqual(gvcf.end, (end if end else (start + 1)))
    self.assertEqual(variantcall_utils.get_gq(call), gq)
    self.assertNotEmpty(call.genotype_likelihood)
    self.assertIn('MIN_DP', call.info)
    self.assertLen(call.info['MIN_DP'].values, 1)
    self.assertEqual(variantcall_utils.get_min_dp(call), min_dp)
    if (gls is not None):
        npt.assert_allclose(list(gvcf.calls[0].genotype_likelihood), gls)
    if sample_name:
        self.assertEqual(gvcf.calls[0].call_set_name, sample_name)
    if (gts is not None):
        self.assertEqual(list(gvcf.calls[0].genotype), gts)
def assertGVCF(self, gvcf, ref, gq, start, end, min_dp, chrom='chr1', gls=None, sample_name=None, gts=None):
    if chrom:
        self.assertEqual(gvcf.reference_name, chrom)
    call = variant_utils.only_call(gvcf)
    self.assertNotEmpty(gvcf.reference_name)
    self.assertEqual(gvcf.reference_bases, ref)
    self.assertEqual(gvcf.alternate_bases, ['<*>'])
    self.assertEqual(gvcf.start, start)
    self.assertEqual(gvcf.end, (end if end else (start + 1)))
    self.assertEqual(variantcall_utils.get_gq(call), gq)
    self.assertNotEmpty(call.genotype_likelihood)
    self.assertIn('MIN_DP', call.info)
    self.assertLen(call.info['MIN_DP'].values, 1)
    self.assertEqual(variantcall_utils.get_min_dp(call), min_dp)
    if (gls is not None):
        npt.assert_allclose(list(gvcf.calls[0].genotype_likelihood), gls)
    if sample_name:
        self.assertEqual(gvcf.calls[0].call_set_name, sample_name)
    if (gts is not None):
        self.assertEqual(list(gvcf.calls[0].genotype), gts)