Commit Graph

5 Commits (e86ce8f3d66f7cffc9e349e2b207d77ccab9f9c3)

Author SHA1 Message Date
Ryan Poplin 14a77b1e71 Getting rid of redundant methods in MathUtils. Adding unit tests for approximateLog10SumLog10 and normalizeFromLog10. Increasing the precision of the Jacobian approximation used by approximateLog10SumLog which changes the UG+HC integration tests ever so slightly. 2012-03-05 12:28:32 -05:00
Mauricio Carneiro d379c3763a DNA Sequence to BitSet and vice-versa conversion tools
* 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
2012-02-29 19:25:20 -05:00
Mauricio Carneiro 75783af6fc int <-> BitSet conversion utils for MathUtils
* added unit tests.
2012-02-21 14:10:36 -05:00
Mauricio Carneiro cd68cc239b Added knuth-shuffle (KS) and randomSubset using KS to MathUtils
* 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
2012-01-03 09:29:46 -05:00
David Roazen 3c9497788e Reorganized the codebase beneath top-level public and private directories,
removing the playground and oneoffprojects directories in the process. Updated
build.xml accordingly.
2011-06-28 06:55:19 -04:00