Radmeth performance improvements#282

Merged

andrewdavidsmith merged 12 commits intomasterfrom

radmeth-performance

Aug 11, 2025

Commits on Aug 10, 2025

src/radmeth/radmeth.cpp: moving some functions out of this source file and into the radmeth_model.chpp sources
andrewdavidsmith
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src/radmeth/radmeth_model.hpp: adding cumulative counts for the new algorithm to calculate the beta-binomial likelihood
andrewdavidsmith
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src/radmeth/radmeth_model.cpp: added functions to make groups and to get the mapping from sample to group; also put some functions here that were previously in radmeth.cpp because they belong with …
andrewdavidsmith
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src/radmeth/radmeth_optimize.cpp: implementing a new algorithm for computing the beta-binomial likelihood and gradients. This algorithm accumulates mass without the use of unstable gamma functions …
andrewdavidsmith
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src/radmeth/radmeth_model.hpp: shortening some names
andrewdavidsmith
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src/radmeth/radmeth_optimize.cpp: cleaning up some code and tweaking for more optimization
andrewdavidsmith
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src/radmeth/radmeth.cpp: no longer iterating over chunks because consecutive sites of extreme coverage can cause an imbalance in terms of work done by threads. Also using a decimal digit of precisi…
andrewdavidsmith
committed