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…. Upgrade pybedtools. Added wave
…annotating with no flags."
…eated in create_consensus_panel.py
Implemented parallel processing of VEP annotation through configurable chunking: - Added `panel_sites_chunk_size` parameter (default: 0, no chunking) - When >0, splits sites file into chunks for parallel VEP annotation - Uses bash `split` command for efficient chunking with preserved headers - Modified SITESFROMPOSITIONS module: - Outputs multiple chunk files (*.sites4VEP.chunk*.tsv) instead of single file - Logs chunk configuration and number of chunks created - Chunk size configurable via `ext.chunk_size` in modules.config - Updated CREATE_PANELS workflow: - Flattens chunks with `.transpose()` for parallel processing - Each chunk gets unique ID for VEP tracking - Merges chunks using `collectFile` with header preservation - Added SORT_MERGED_PANEL module: - Sorts merged panels by chromosome and position (genomic order) - Prevents "out of order" errors in downstream BED operations - Applied to both compact and rich annotation outputs - Enhanced logging across chunking pipeline: - SITESFROMPOSITIONS: reports chunk_size and number of chunks created - POSTPROCESS_VEP_ANNOTATION: shows internal chunk_size and expected chunks - CUSTOM_ANNOTATION_PROCESSING: displays chr_chunk_size and processing info Configuration: - `panel_sites_chunk_size`: controls file chunking (0=disabled) - `panel_postprocessing_chunk_size`: internal memory management - `panel_custom_processing_chunk_size`: internal chromosome chunking Benefits: - Parallelizes VEP annotation for large panels - Reduces memory footprint per task - Maintains genomic sort order for downstream tools
- remove all optimization related updates (to be added later)
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