David Roazen 422e16c62e BaseRecalibration: don't cache instances of ReadCovariates across reads ... Caching and reusing ReadCovariates instances across reads sounds good in theory, but: -it doesn't work unless you zero out the internal arrays before each read -the internal arrays must be sized proportionally to the maximum POSSIBLE recalibrated read length (5000!!!), instead of the ACTUAL read lengths By contrast, creating a new instance per read is basically equivalent to doing an efficient low-level memset-style clear on a much smaller array (since we use the actual rather than the maximum read length to create it). So this should be faster than caching instances and calling clear() but slower than caching instances and not calling clear(). Credit to Ryan to proposing this approach.		2012-10-25 17:02:55 -04:00
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config	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
src	BaseRecalibration: don't cache instances of ReadCovariates across reads	2012-10-25 17:02:55 -04:00
test	Re-enable tests	2012-10-25 09:37:08 -04:00