Fix blacklist BED file parsing in cooler balance CLI (Fixes #196)

[ShigrafS]

PR Description:

Fixes: #209
Original Issues: #196

Overview

This PR fixes issue [#196](#196) by improving how blacklist BED files are parsed in the cooler balance CLI. Previously, single-line BED files, files with metadata headers (track=), and empty blacklist files were not handled correctly, leading to parsing errors and crashes.

The key fixes include:

• Switching blacklist parsing from custom logic to bioframe.read_table.
• Skipping track= headers in blacklist files.
• Handling empty blacklist files to prevent np.concatenate errors.
• Fixing an HDF5 writing scope error by correcting indentation.
• Explicitly setting dtype="float64" for HDF5 weights to handle NaN values.
• Adjusting test parameters to improve robustness.

Changes Made

✅ Replaced custom blacklist parsing with bioframe.read_table

• Previous method failed for single-line BED files due to csv.Sniffer assumptions.
• bioframe.read_table now ensures proper BED parsing.

✅ Added header skipping for track= metadata lines

• If the first line starts with track=, it is skipped before parsing.
• Prevents issues where the header was mistakenly interpreted as a chromosome entry.

✅ Handled empty blacklist files ("") gracefully

• Avoided np.concatenate errors by checking for empty results.
• Ensured that blacklist filtering works even if no regions are provided.

✅ Fixed indentation issue in HDF5 weight storage

• Ensured create_dataset operations remain within the with h5py.File(...) block.
• Prevented KeyError when writing to HDF5 files.

✅ Explicitly set dtype="float64" in HDF5 options

• Prevented ValueError: cannot convert float NaN to integer.
• Ensured robust handling of blacklist-masked bins.

✅ Adjusted test parameters for better stability

• Modified test_balancing_with_blacklist parameters (tol=0.1, max-iters=1000, nproc=1)
• Improved test reliability across different platforms.

Impact

• Fixes parsing for single-line BED files, ensuring correctness.
• Supports blacklist files with metadata headers (track=) without errors.
• Prevents crashes when the blacklist file is empty.
• Improves compatibility with bioframe for BED file handling.
• Ensures proper HDF5 weight storage, avoiding scope-related errors.
• Tests now pass reliably, improving maintainability.

Closes:

Fixes #196