Avoid potentially large stack allocation, clean up int usage

HKU-BAL / Clair3

Clair3 - Symphonizing pileup and full-alignment for high-performance long-read variant calling

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Avoid potentially large stack allocation, clean up int usage #282

Closed cjw85 closed 8 months ago

cjw85 commented 8 months ago

I'm starting to investigate various memory errors we have seen with clair3 code. This commit is a small one have getting acquianted with the bits full alignment feature code (the pileup one seems very familiar 🤔 🤣 ).

Avoids a stack allocation (fixes #265)
Cleans up integer use (I didn't think very long about all the casts, they look safe by inspection)

My compiler is a bit happier after these changes.

aquaskyline commented 8 months ago

Thanks for the PR. Sorry for the delay, we also have a working fix but will integrate it with yours. We shall release a new version with this and a few other fixes by this week.

aquaskyline commented 8 months ago

Merged into v1.0.6.