Mauricio Carneiro 3bfca0ccfd BitSet implementation of the on-the-fly recalibration using the CSV format file. ... Infrastructure: * Added static interface to all different clipping algorithms of low quality tail clipping * Added reverse direction pileup element event lookup (indels) to the PileupElement and LocusIteratorByState * Complete refactor of the KeyManager. Much cleaner implementation that handles keys with no optional covariates (necessary for on-the-fly recalibration) * EventType is now an independent enum with added capabilities. All functionality is now centralized. BQSR and RecalibrateBases: * On-the-fly recalibration is now generic and uses the same bit set structure as BQSR for a reduced memory footprint * Refactored the object creation to take advantage of the compact key structure * Replaced nested hash maps with single hash maps indexed by bitsets * Eliminated low quality tails from the context covariate (using ReadClipper's write N's algorithm). * Excluded contexts with N's from the output file. * Fixed cycle covariate for discrete platforms (need to check flow cycle platforms now!) * Redfined error for indels to look at the previous base in negative strand reads (using new PE functionality) * Added the covariate ID (for optional covariates) to the output for disambiguation purposes * Refactored CovariateKeySet -- eventType functionality is now handled by the EventType enum. * Reduced memory usage of the BQSR script to 4 Tests: * Refactored BQSRKeyManagerUnitTest to handle the new implementation of the key manager * Added tests for keys without optional covariates * Added tests for on-the-fly recalibration (but more tests are necessary)		2012-03-16 13:02:15 -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	BitSet implementation of the on-the-fly recalibration using the CSV format file.	2012-03-16 13:02:15 -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	BitSet implementation of the on-the-fly recalibration using the CSV format file.	2012-03-16 13:02:15 -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