Mauricio Carneiro 1b75663178 BQSR Gatherer implementation and integration tests ... * restructured the hash tables into one class (RecalibrationReport) that has all the functionality for the different tables and key managers * optmized empirical qual calculation when merging recalibration reports * centralized the quality score quantization functionalities * unified the creating/loading of all the key manager/hash table structures. * added unit tests for the gatherer (disabled because gatk report needs to be sorted for automated testing) * added integration tests for BQSR and on-the-fly recalibration		2012-03-27 13:50:22 -05:00
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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	BQSR Gatherer implementation and integration tests	2012-03-27 13:50:22 -05:00
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	BQSR Gatherer implementation and integration tests	2012-03-27 13:50:22 -05:00
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	Minor: cleaner way of turning off index-on-the-fly checking in case we want to turn it back on.	2012-03-18 00:53:29 -04:00