Mauricio Carneiro ca11ab39e7 BitSets keys to lower BQSR's memory footprint ... 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)		2012-03-16 13:01:48 -04:00
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alignment	Reinitialize random seed in the bwa bindings from the fixed seed stored in the	2011-07-22 13:41:53 -04:00
commandline	Added ability to specify arguments in files via -args/--arg_file	2011-10-24 15:58:34 -04:00
gatk	BitSets keys to lower BQSR's memory footprint	2012-03-16 13:01:48 -04:00
jna	When using bam list mode in HSP deriving VCF name from bam list instead of requiring an additional parameter.	2011-12-16 18:09:25 -05:00
utils	BitSets keys to lower BQSR's memory footprint	2012-03-16 13:01:48 -04:00
BaseTest.java	CalibrateGenotypeLikelihoods now emits the position of the variant for debugging	2012-03-09 16:00:07 -05:00
MD5DB.java	Merged bug fix from Stable into Unstable	2011-10-13 18:02:06 -04:00
MedianUnitTest.java	Adding more unit tests and contracts to PairHMM util class. Updating HaplotypeCaller to use the new PairHMM util class. Now that the HMM result isn't dependent on the length of the haplotype there is no reason to ensure all haplotypes have the save length which simplifies the code considerably.	2012-03-05 08:28:42 -05:00
StingTextReporter.java	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
WalkerTest.java	Public-key authorization scheme to restrict use of NO_ET	2012-03-06 00:09:43 -05:00