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fix: handle indefinite Range bound of 0 in normalize #688

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fix: handle indefinite Range bound of 0 in normalize #688

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2 changes: 1 addition & 1 deletion src/ga4gh/vrs/normalize.py
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Original file line number Diff line number Diff line change
Expand Up @@ -58,7 +58,7 @@ def _get_allele_location_pos(
if not pos0_is_none and not pos1_is_none: # definite range
return None

val = pos.root[0] or pos.root[1]
val = pos.root[1] if pos0_is_none else pos.root[0]
pos_type = (
PosType.RANGE_LT_OR_EQUAL if pos0_is_none else PosType.RANGE_GT_OR_EQUAL
)
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17 changes: 17 additions & 0 deletions tests/test_vrs_normalize.py
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Original file line number Diff line number Diff line change
Expand Up @@ -966,6 +966,23 @@ def _bounds_allele(
"expected_start": [None, 4400],
"expected_end": [4501, None],
},
# a defined range bound of 0 must not be mistaken for the undefined one
{
"id": "indefinite-start-range-from-zero",
"start": [0, None],
"end": 1,
"sequence": "T",
"expected_start": [0, None],
"expected_end": 1,
},
{
"id": "indefinite-end-range-from-zero",
"start": [None, 0],
"end": [0, None],
"sequence": "A",
"expected_start": [None, 0],
"expected_end": [0, None],
},
]


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