ca11ab39e7
Infrastructure: * Generic BitSet implementation with any precision (up to long) * Two's complement implementation of the bit set handles negative numbers (cycle covariate) * Memoized implementation of the BitSet utils for better performance. * All exponents are now calculated with bit shifts, fixing numerical precision issues with the double Math.pow. * Replace log/sqrt with bitwise logic to get rid of numerical issues BQSR: * All covariates output BitSets and have the functionality to decode them back into Object values. * Covariates are responsible for determining the size of the key they will use (number of bits). * Generalized KeyManager implementation combines any arbitrary number of covariates into one bitset key with event type * No more NestedHashMaps. Single key system now fits in one hash to reduce hash table objects overhead Tests: * Unit tests added to every method of BitSetUtils * Unit tests added to the generalized key system infrastructure of BQSRv2 (KeyManager) * Unit tests added to the cycle and context covariates (will add unit tests to all covariates) |
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| .. | ||
| datasources | ||
| executive | ||
| filters | ||
| iterators | ||
| refdata | ||
| report | ||
| samples | ||
| traversals | ||
| walkers | ||
| EngineFeaturesIntegrationTest.java | ||
| GenomeAnalysisEngineUnitTest.java | ||
| WalkerManagerUnitTest.java | ||