Mark DePristo c7f0ca8ac5 Optimization for LIBS: PerSampleReadStateManager now uses a simple LinkedList of AlignmentStateMachine ... -- Instead of storing a list of list of alignment starts, which is expensive to manipulate, we instead store a linear list of alignment starts. Not grouped as previously. This enables us to simplify iteration and update operations, making them much faster -- Critically, the downsampler still requires this list of list. We convert back and forth between these two representations as required, which is very rarely for normal data sets (WGS NA12878 on chr20 is 0.2%, 4x WGS is even less).		2013-01-14 16:30:16 -05:00
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config	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
src	Optimization for LIBS: PerSampleReadStateManager now uses a simple LinkedList of AlignmentStateMachine	2013-01-14 16:30:16 -05:00
test	Refactor PerSampleReadStates into a separate class	2013-01-14 16:30:16 -05:00