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Sort layers alphabetically for deterministic h5ad output #12

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Merged
ygao61 merged 1 commit into from
Feb 19, 2026
Merged

Sort layers alphabetically for deterministic h5ad output #12

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6 changes: 6 additions & 0 deletions src/qcatch/input_processing.py
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Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,7 @@
import logging
import os
import shutil
from collections import OrderedDict
from pathlib import Path

import numpy as np
Expand Down Expand Up @@ -469,6 +470,9 @@ def save_results(args, version, intermediate_result, valid_bcs):
args.input.mtx_data.obs_names.sort_values(), args.input.mtx_data.var_names.sort_values()
].copy()

# Sort layers alphabetically for deterministic h5ad output
args.input.mtx_data.layers = OrderedDict(sorted(args.input.mtx_data.layers.items()))

if args.input.is_h5ad and output_dir == args.input.dir:
# Inplace overwrite: same location as original
temp_file = os.path.join(output_dir, "quants.h5ad")
Expand All @@ -494,6 +498,8 @@ def save_results(args, version, intermediate_result, valid_bcs):
filter_mtx_data = filter_mtx_data[
filter_mtx_data.obs_names.sort_values(), filter_mtx_data.var_names.sort_values()
].copy()
# Sort layers alphabetically for deterministic h5ad output
filter_mtx_data.layers = OrderedDict(sorted(filter_mtx_data.layers.items()))
# Save the filtered anndata to a new file
filter_mtx_data_filename = os.path.join(output_dir, "filtered_quants.h5ad")
filter_mtx_data.write_h5ad(filter_mtx_data_filename, compression="gzip")
Expand Down