Mauricio Carneiro 9f74969e3a BQSR with GATKReport implementation ... * restructured BQSR to report recalibrated tables. * implemented empirical quality calculation to the BQSR stage (instead of on-the-fly recalibration) * linked quality score quantization to the BQSR stage, outputting a quantization histogram * included the arguments used in BQSR to the GATK Report * included all three tables (RG, QUAL and COVARIATES) to the GATK Report with empirical qualities On-the-fly recalibration with GATK Report * loads all tables from the GATKReport using existing infrastructure (with minor updates) * implemented initialiazation of the covariates using BQSR's argument list * reduced memory usage significantly by loading only the empirical quality and estimated quality reported for each bit set key * applied quality quantization to the base recalibration * excluded low quality bases from on-the-fly recalibration for mismatches, insertions or deletions		2012-03-23 15:42:32 -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	Updated read group covariate to use sample.lane instead of the id	2012-03-23 15:24:07 -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	BQSR with GATKReport implementation	2012-03-23 15:42:32 -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	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