def test_genotypes_snp_as_homozygous_when_supported_by_15_reads_out_of_16(
self):
self.calls_variants_with_sample_data(
"AAAAAAAAAAACGCACCCCCCATAAAAAAAATTTTTTTTTTT", # input
[
".....................C....................",
".....................C....................",
".....................C....................",
".....................C....................",
".....................C....................",
"..........................................",
".....................C....................",
".....................C....................",
".....................C....................",
".....................C....................",
".....................C....................",
".....................C....................",
".....................C....................",
".....................C....................",
".....................C....................",
".....................C...................."
],
[(21, "A", "C", {
"GT": GT("1/1"),
"GQ": [7],
"DP": [16],
"AD": [1, 15]
})])
def test_genotypes_one_base_deletion_as_homozygous_when_supported_by_5_reads_out_of_5(
self):
self.calls_variants_with_sample_data(
"AAAAAAAAAAACGCACCCCCCATAAAAAAAATTTTTTTTTTT", # input
[
".....................*....................",
".....................*....................",
".....................*....................",
".....................*....................",
".....................*...................."
],
[(20, "CA", "C", {
"GT": GT("1/1"),
"DP": [5],
"AD": [0, 5]
})])
def test_genotypes_snp_as_heterozygous_when_supported_by_4_reads_out_of_5(
self):
self.calls_variants_with_sample_data(
"AAAAAAAAAAACGCACCCCCCATAAAAAAAATTTTTTTTTTT", # input
[
"..........................................",
".....................C....................",
".....................C....................",
".....................C....................",
".....................C...................."
],
[(21, "A", "C", {
"GT": GT("1/0"),
"GQ": [27],
"DP": [5],
"AD": [1, 4]
})])