Mauricio Carneiro f0c81b59b0 Implementation of the new BQSR plotting infrastructure ... * removed low quality bases from the recalibration report. * refactored the Datum (Recal and Accuracy) class structure * created a new plotting csv table for optimized performance with the R script * added a datum object that carries the accuracy information (AccuracyDatum) for plotting * added mean reported quality score to all covariates * added QualityScore as a covariate for plotting purposes * added unit test to the key manager to operate with one required covariate and multiple optional covariates * integrated the plotting into BQSR (automatically generates the pdf with the recalibration tearsheet)		2012-04-17 19:23:55 -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	Implementation of the new BQSR plotting infrastructure	2012-04-17 19:23:55 -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	AggregateMetrics:	2012-04-17 11:45:32 -04:00
BaseTest.java	Bug fix: BaseTest change shouldn't have been committed, first cleanup of SNP pool code (more to follow)	2012-04-03 18:55:52 -04:00
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	…
WalkerTest.java	New way to handle exceptions in multi-threaded GATK	2012-04-13 09:23:33 -04:00