Fix - Handle missing BED features per contig and internalize BED indexing logic #88
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Merge pull request #86 from pinellolab/v218
Refactored add_risk_score.py and remove_n_and_dots.py for modularity, readability, and error handling. Improved function documentation and chunked file processing. Updated annotation.py to handle missing contigs gracefully. Cleaned up post_analisi_indel.sh and submit_job_automated_new_multiple_vcfs.sh comments for clarity.
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This PR addresses an issue where CRISPRme’s annotation module failed when attempting to retrieve BED features from contigs/chromosomes without mapped entries. The fix ensures more robust handling of BED files and eliminates unnecessary external indexing requirements.