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Fix exception in g_to_c mapping #765

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merged 2 commits into from
Mar 5, 2025
Merged

Fix exception in g_to_c mapping #765

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879f0d8
Fix exception in g_to_c mapping
b0d0nne11 Mar 4, 2025
4a7bbbf
Use fixtures from conftest.py
b0d0nne11 Mar 5, 2025
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1 change: 1 addition & 0 deletions src/hgvs/variantmapper.py
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Expand Up @@ -268,6 +268,7 @@ def g_to_c(self, var_g, tx_ac, alt_aln_method=hgvs.global_config.mapping.alt_aln
edit_c.type == "ins"
and pos_c.start.offset == 0
and pos_c.end.offset == 0
and pos_c.start.datum == pos_c.end.datum
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Great catch!

and pos_c.end - pos_c.start > 1
):
pos_c.start.base += 1
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5 changes: 5 additions & 0 deletions tests/conftest.py
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Expand Up @@ -29,6 +29,11 @@ def parser():
return hgvs.easy.parser


@pytest.fixture(scope="session")
def vm():
return hgvs.easy.vm


@pytest.fixture(scope="session")
def am37():
return hgvs.easy.am37
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10 changes: 10 additions & 0 deletions tests/issues/test_764.py
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@@ -0,0 +1,10 @@
def test_vm_g_to_c(parser, vm):
var_g = parser.parse("NC_000007.13:g.106545832_106545833insAG")
var_c = vm.g_to_c(var_g, "NM_002649.2")
assert str(var_c) == "NM_002649.2:c.3309_*1insAG"


def test_am37_g_to_c(parser, am37):
var_g = parser.parse("NC_000007.13:g.106545832_106545833insAG")
var_c = am37.g_to_c(var_g, "NM_002649.2")
assert str(var_c) == "NM_002649.2:c.3309_*1insAG"