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fix(writer): guard per-gene thresholding against degenerate similarities #59

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fix(writer): guard per-gene thresholding against degenerate similarities #59

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12 changes: 11 additions & 1 deletion src/segger/data/writer.py
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Original file line number Diff line number Diff line change
Expand Up @@ -224,10 +224,20 @@ def assign_transcripts_to_cells(
logger.debug(f"Processing feature {i+1}/{n_groups} (feature {feature[0]} | transcripts {group.shape[0]/1e3:.1f}K)...")

# sample if too many
arr = group["segger_similarity"]
arr = group["segger_similarity"].drop_nulls()
if arr.shape[0] > n:
arr = arr.sample(n=n, seed=0)
arr = arr.to_numpy()
arr = arr[np.isfinite(arr)]

# Degenerate inputs crash threshold_yen / threshold_li: no finite
# values, or a single constant value (nothing to threshold).
if arr.size == 0:
failed_to_converge.append(feature[0])
continue
if arr.size == 1 or np.allclose(arr, arr[0]):
thresholds.append({tx_fields.feature: feature[0], "similarity_threshold": float(arr[0]), "converged": True})
continue

# threshold
try:
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