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)
* Turns DNA sequences (for context covariates) into bit sets for maximum compression
* Allows variable context size representation guaranteeing uniqueness.
* Works with long precision, so it is limited to a context size of 31 bases (can be extended with BigNumber precision if necessary).
* Unit Tests added
* Knuth-shuffle is a simple, yet effective array permutator (hope this is good english).
* added a simple randomSubset that returns a random subset without repeats of any given array with the same probability for every permutation.
* added unit tests to both functions
Guillermo del Angel
Ryan Poplin
Mauricio Carneiro
David Roazen