Add parallel execution for extract_prescored.py#83
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yangyxt wants to merge 12 commits intokircherlab:masterfrom
Open
Add parallel execution for extract_prescored.py#83yangyxt wants to merge 12 commits intokircherlab:masterfrom
yangyxt wants to merge 12 commits intokircherlab:masterfrom
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I also refractor the esmSCore_inFrame and esmScore_frameshift script because I found them running over 30 hours to process a VCF file with 500k variants. The most time consuming part is using list appending (append a single item on a big list is incredibly slow in python), so I switch them to use numpy array instead. |
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This can at most lead to 24 parallel subprocesses to extract the prescored variants.
I did this because I run into a situation where this step has been running for over 41 hours to extract prescored records for a VCF file with near 300k variant records.