Fix off-targets search processes join #90
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Refactored the script to launch reference and variant off-targets searches in parallel, tracking their process IDs and waiting for completion. Improved error handling and logging for job failures, and consolidated job completion waiting logic.
Simplifies and unifies the logic for selecting and creating genome index folders in the submit_job_automated_new_multiple_vcfs.sh script, prioritizing indexes with bMax+1 for alignments starting with gaps. Updates crisprme.py to consistently use bMax+1 for index naming and job submission, improving reliability and consistency in bulge parameter handling.
Updated pool_index_indels.py to accept bMax as a parameter and use it in output naming and crispritz.py arguments. Refactored submit_job_automated_new_multiple_vcfs.sh to improve directory handling, error checking, and folder creation for genome enrichment and indels indexing steps. Enhanced clarity and robustness of file and folder operations, and ensured consistent use of parameters between scripts.
Streamlines indels indexing by moving it to a dedicated step after genome indexing, updates directory naming conventions to use bMax, and improves error handling and logging. Cleans up variant enrichment logic, removes redundant code, and standardizes log messages for off-target and indels search steps.
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