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5x throughput improvement#33

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geertvandeweyer wants to merge 11 commits intotkzeng:mainfrom
geertvandeweyer:main
Open

5x throughput improvement#33
geertvandeweyer wants to merge 11 commits intotkzeng:mainfrom
geertvandeweyer:main

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@geertvandeweyer
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@geertvandeweyer geertvandeweyer commented Feb 2, 2025

This PR rewrites the variant handling similar to my container for spliceAI, to optimize modern GPU usage.

I've reached over 5X speedup on a GeFore RTX 4090, boosting GPU usage from 50% to 100% consistently

Also :

  • pyvcf => pysam (see PR : 19)
  • make all alleles uppercase (issue 12)
  • added a dockerfile (based on cuda 12.4) (see : dockerhub)

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