Mauricio Carneiro e39a59594a BQSR triage and test routines ... * updated BQSR queue script for faster turnaround * implemented plot generation for scatter/gatherered runs * adjusted output file names to be cooperative with the queue script * added the recalibration report file to the argument table in the report * added ReadCovariates unit test -- guarantees that all the covariates are being generated for every base in the read * added RecalibrationReport unit test -- guarantees the integrity of the delta tables		2012-04-23 11:23:00 -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	BQSR triage and test routines	2012-04-23 11:23:00 -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	Fixing unit tests to register the user exception being thrown (instead of the NumberFormatException)	2012-04-23 10:06:51 -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	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
WalkerTest.java	New way to handle exceptions in multi-threaded GATK	2012-04-13 09:23:33 -04:00