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Fix pvar/bim path search and update example map format #125

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Merged
ArniFreyrG merged 2 commits into from
Jan 29, 2026
Merged

Fix pvar/bim path search and update example map format #125

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7276e85
Fix pvar/bim path search and update example map format
Jan 25, 2026
e609f0d
fix wording
Jan 25, 2026
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7 changes: 3 additions & 4 deletions example/example_data.map
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Original file line number Diff line number Diff line change
@@ -1,4 +1,3 @@
1 1 0 0

1 2 19.5 15000000

pos chr cM
0 1 0
15000000 1 19.5
6 changes: 4 additions & 2 deletions src/threads_arg/utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -54,8 +54,10 @@ def read_map_file(map_file, expected_chromosome=None) -> Tuple[np.ndarray, np.nd


def _read_pgen_physical_positions(pgen_file):
pvar = pgen_file.replace("pgen", "pvar")
bim = pgen_file.replace("pgen", "bim")
if not pgen_file.endswith("pgen"):
raise ValueError(f"Cannot find .pvar or .bim files, {pgen_file} does not end with 'pgen'.")
pvar = pgen_file.rstrip("pgen") + "pvar"
bim = pgen_file.rstrip("pgen") + "bim"
physical_positions = None
if os.path.isfile(bim):
physical_positions = np.array(pd.read_table(bim, sep="\\s+", header=None, comment='#')[3]).astype(np.float64)
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